COMPOUNDS AND METHODS FOR MODULATING HUNTINGTIN

Abstract
Provided are compounds, methods, and pharmaceutical compositions for reducing the amount or activity of HTT RNA in a cell or subject, and in certain instances reducing the amount of HTT protein in a cell or subject. Such compounds, methods, and pharmaceutical compositions are useful to prevent, treat, or ameliorate at least one symptom or hallmark of a repeat expansion disease. Such repeat expansion diseases include myotonic dystrophy, amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, polyglutamine disorders, Fragile X syndrome, and spinocerebellar ataxia. Such symptoms or hallmarks include brain atrophy, muscle atrophy, nerve degeneration, uncontrolled movement, seizure, tremor, anxiety, and depression.
Description
SEQUENCE LISTING

The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled BIOL0413WOSEQ_ST25.txt, created on Jan. 24, 2022, which is 1.204 MB in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.


FIELD

Provided herein are compounds, pharmaceutical compositions, and methods of use for reducing an amount of HTT RNA in a cell or a subject, and in certain instances reducing the amount of HTT protein in a cell or a subject. In certain embodiments, compounds, methods, and pharmaceutical compositions are useful for ameliorating at least one symptom or hallmark of a repeat expansion disease, e.g., Huntington's Disease. Such symptoms or hallmarks of Huntington's disease include, but are not limited to, brain atrophy, muscle atrophy, nerve degeneration, uncontrolled movement, seizure, tremor, anxiety, and depression.


BACKGROUND

Repeat expansion diseases are a group of diseases characterized by a pathological number of consecutive repeat units in a region of a gene, each repeat unit consisting of several linked nucleosides having the same nucleobase sequence as the other repeat units. In general, repeat expansion diseases are genetically inherited. In some cases, an individual is born with a pathological number of repeat units and is symptomatic from a young age. In other cases, an individual is born with a normal, or near normal, number of repeats. However, due to a genetic mutation and genetic instability, the number of repeats increases with cell division, time, and age. The expanded region of the gene ultimately has pathological effects, most often observed as neurological symptoms. Many repeat expansion diseases are classified as a spinocerebellar ataxia, a neurodegenerative disease, or a neuromuscular disease. Non-limiting examples of repeat expansion diseases are myotonic dystrophy (DM1 and DM2); Huntington's disease (HD) and many autosomal dominant spinocerebellar ataxias; some forms of amyotrophic lateral sclerosis and/or frontotemporal dementia; various polyglutamine disorders (including spinal and bulbar muscular atrophy); Fragile X syndrome; and Friedrich's ataxia.


HD is caused by the expansion of a cytosine-adenine-guanine (CAG) trinucleotide repeat region in IT15, the gene that encodes huntingtin protein (HTT protein). The resulting expanded CAG repeat region encodes an abnormally long polyglutamine (PolyQ) tract in HTT protein, resulting in the expression of a mutant HTT (mHTT) protein. As a result of excessive polyglutamine length, mHTT protein forms aggregates in the cytoplasm and nucleus of CNS neurons (Davies et al., Cell 1997, 90:537-548). Due to its genomic instability, the expanded CAG repeat region can further expand with age and during meiotic transmission to include additional CAG repeats. Individuals with 27 to 35 CAG repeats typically do not develop HD, but their children are at risk of developing HD. Individuals with 35 to 60 CAG repeats typically experience adult-onset HD. Individuals with greater than 60 CAG repeats generally develop juvenile HD, experiencing symptoms of HD before the age of 20 years. Individuals with a normal number of CAG repeats (<27) are not considered to be at risk of developing HD.


SUMMARY OF THE INVENTION

Provided herein are compounds, pharmaceutical compositions, and methods of use for reducing the amount of HTT RNA, and in certain embodiments reducing the amount or activity of HTT protein in a cell or a subject. In certain embodiments, the HTT RNA is mHTT RNA. In certain embodiments, the HTT protein is mHTT protein. In certain embodiments, the subject has or is at risk of having a neurodegenerative disease. In certain embodiments, the neurodegenerative disease is a repeat expansion disease. In certain embodiments, the repeat expansion disease is myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, various polyglutamine disorders, Fragile X syndrome, or a spinocerebellar ataxia (SCA1, SCA2, SCA3, SCA6, SCA7, SCA8, SCA10, SCA17, or Friedrich's ataxia). In certain embodiments, compounds useful for reducing the amount of HTT RNA and/or HTT protein are oligomeric compounds. In certain embodiments, oligomeric compounds comprise modified oligonucleotides.


Also provided herein are methods useful for ameliorating a symptom or hallmark of a neurodegenerative disease. In certain embodiments, the neurodegenerative disease is a repeat expansion disease. In certain embodiments, the repeat expansion disease is myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, various polyglutamine disorders, Fragile X syndrome, or a spinocerebellar ataxia (SCA1, SCA2, SCA3, SCA6, SCA7, SCA8, SCA0, SCA17, or Friedrich's ataxia). In certain embodiments, the symptom or hallmark is brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, disordered muscle movement, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, suicidal behavior, or a combination thereof.







DETAILED DESCRIPTION OF THE INVENTION

It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive. Herein, the use of the singular includes the plural unless specifically stated otherwise. As used herein, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including” as well as other forms, such as “includes” and “included”, is not limiting. Also, terms such as “element” or “component” encompass both elements and components comprising one unit and elements and components that comprise more than one subunit, unless specifically stated otherwise.


The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated-by-reference for the portions of the document discussed herein, as well as in their entirety.


Definitions

Unless specific definitions are provided, the nomenclature used in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Where permitted, all patents, applications, published applications and other publications and other data referred to throughout the disclosure are incorporated by reference herein in their entirety.


Unless otherwise indicated, the following terms have the following meanings:


As used herein, “2′-deoxynucleoside” means a nucleoside comprising a 2′-H(H) deoxyribosyl sugar moiety. In certain embodiments, a 2′-deoxynucleoside is a 2′-β-D-deoxynucleoside and comprises a 2′-β-D-deoxyribosyl sugar moiety, which has the β-D configuration as found in naturally occurring deoxyribonucleic acids (DNA). In certain embodiments, a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (uracil).


As used herein, “2′-MOE” or “2′-MOE sugar moiety” or “2′-O-methoxyethylribose modified sugar” means a 2′-OCH2CH2OCH3 group in place of the 2′-OH group of a ribosyl sugar moiety. “MOE” means methoxyethyl. Unless otherwise indicated, a 2′-MOE has the β-D stereochemical configuration.


As used herein, “2′-MOE nucleoside” means a nucleoside comprising a 2′-MOE sugar moiety.


As used herein, “2′-OMe” or “2′-O-methyl sugar moiety” means a 2′-OCH3 group in place of the 2′—OH group of a ribosyl sugar moiety. Unless otherwise indicated, a 2′-OMe has the β-D stereochemical configuration.


As used herein, “2′-OMe nucleoside” means a nucleoside comprising a 2′-OMe sugar moiety.


As used herein, “2′-substituted nucleoside” means a nucleoside comprising a 2′-substituted furanosyl sugar moiety. As used herein, “2′-substituted” in reference to a sugar moiety means a sugar moiety comprising at least one 2′-substituent group other than H or OH.


As used herein, “5-methylcytosine” means a cytosine modified with a methyl group attached to the 5 position. A 5-methylcytosine is a modified nucleobase.


As used herein, “abasic sugar moiety” means a sugar moiety of a nucleoside that is not attached to a nucleobase. Such abasic sugar moieties are sometimes referred to in the art as “abasic nucleosides.”


As used herein, “administration” or “administering” means providing a pharmaceutical agent or composition to a subject.


As used herein, “ameliorate” in reference to a treatment means improvement in at least one symptom or hallmark relative to the same symptom or hallmark in the absence of the treatment. In certain embodiments, amelioration is the reduction in the severity or frequency of a symptom or hallmark, or the delayed onset of or slowing of progression in the severity or frequency of a symptom or hallmark. In certain embodiments, the symptom or hallmark is brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, or suicidal behavior. The progression or severity of indicators may be determined by subjective or objective measures, which are known to those skilled in the art.


As used herein, “antisense activity” means any detectable and/or measurable change attributable to the hybridization of an antisense compound to its target nucleic acid. In certain embodiments, antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid compared to target nucleic acid levels or target protein levels in the absence of the antisense compound.


As used herein, “antisense agent” means an antisense compound and optionally one or more additional features, such as a sense compound.


As used herein, “antisense compound” means an oligomeric compound capable of achieving at least one antisense activity. In certain embodiments, an antisense compound further comprises one or more additional features, such as a conjugate group.


As used herein, “sense compound” means a sense oligonucleotide and optionally one or more additional features, such as a conjugate group. As used herein, “bicyclic nucleoside” or “BNA” means a nucleoside comprising a bicyclic sugar moiety.


As used herein, “bicyclic sugar” or “bicyclic sugar moiety” means a modified sugar moiety comprising two rings, wherein the second ring is formed via a bridge connecting two of the atoms in the first ring thereby forming a bicyclic structure. In certain embodiments, the first ring of the bicyclic sugar moiety is a furanosyl sugar moiety. In certain embodiments, the furanosyl sugar moiety is a ribosyl sugar moiety. In certain embodiments, the bicyclic sugar moiety does not comprise a furanosyl sugar moiety.


As used herein, “CAG repeat” means one of multiple contiguous trinucleotide units, wherein each trinucleotide unit consists of three contiguous nucleosides having a nucleobase sequence from 5′ to 3′ of cytosine (C), adenine (A), and guanine (G).


As used herein, “cerebrospinal fluid” or “CSF” means the fluid filling the space around the brain and spinal cord. “Artificial cerebrospinal fluid” or “aCSF” means a prepared or manufactured fluid that has certain properties of cerebrospinal fluid. aCSF is a buffered solution that closely matches the electrolyte concentrations of CSF.


As used herein, “cleavable moiety” means a bond or group of atoms that is cleaved under physiological conditions, for example, inside a cell, a subject, or a human.


As used herein, “cell-targeting moiety” means a conjugate moiety that interacts with a cell or a portion thereof. In certain embodiments, the cell-targeting moiety binds a receptor on a surface of a cell.


As used herein, “chirally enriched population” means a plurality of molecules of identical molecular formula, wherein the number or percentage of molecules within the population that contain a particular stereochemical configuration at a particular chiral center is greater than the number or percentage of molecules expected to contain the same particular stereochemical configuration at the same particular chiral center within the population if the particular chiral center were stereorandom. Chirally enriched populations of molecules having multiple chiral centers within each molecule may contain one or more stereorandom chiral centers. In certain embodiments, the molecules are modified oligonucleotides. In certain embodiments, the molecules are compounds comprising modified oligonucleotides.


As used herein, “chirally controlled” in reference to an internucleoside linkage means chirality at that linkage is enriched for a particular stereochemical configuration.


As used herein, “complementary” in reference to an oligonucleotide means that at least 70% of the nucleobases of the oligonucleotide or one or more portions thereof and the nucleobases of a target nucleic acid or one or more portions thereof are capable of hydrogen bonding with one another when the nucleobase sequence of the oligonucleotide and the other nucleic acid are aligned in opposing directions. As used herein, “complementary nucleobases” means nucleobases that are capable of forming hydrogen bonds with one another. Complementary nucleobase pairs include adenine (A) and thymine (T), adenine (A) and uracil (U), cytosine (C) and guanine (G), 5-methylcytosine (mC) and guanine (G). Certain modified nucleobases that pair with natural nucleobases or with other modified nucleobases are known in the art. For example, inosine can pair with adenosine, cytosine, or uracil. Complementary oligonucleotides and/or target nucleic acids need not have nucleobase complementarity at each nucleoside. Rather, some mismatches are tolerated. As used herein, “fully complementary” or “100% complementary” in reference to an oligonucleotide, or a portion thereof, means that the oligonucleotide, or portion thereof, is complementary to another oligonucleotide or target nucleic acid at each nucleobase of the shorter of the two oligonucleotides, or at each nucleoside if the oligonucleotides are the same length.


As used herein, “conjugate group” means a group of atoms that is directly attached to an oligonucleotide. Conjugate groups include a conjugate moiety and a conjugate linker that attaches the conjugate moiety to the oligonucleotide. In certain embodiments, the conjugate moiety comprises a cell-targeting moiety.


As used herein, “conjugate linker” means a single bond or a group of atoms comprising at least one bond that connects a conjugate moiety to an oligonucleotide.


As used herein, “conjugate moiety” means a group of atoms that is attached to an oligonucleotide via a conjugate linker.


As used herein, “constrained ethyl” or “cEt” or “cEt modified sugar moiety” means a β-D ribosyl bicyclic sugar moiety wherein the second ring of the bicyclic sugar is formed via a bridge connecting the 4′-carbon and the 2′-carbon of the β-D ribosyl sugar moiety, wherein the bridge has the formula 4′-CH(CH3)—O-2′, and wherein the methyl group of the bridge is in the S configuration.


As used herein, “cEt nucleoside” means a nucleoside comprising a cEt modified sugar moiety.


As used herein, “contiguous” in the context of an oligonucleotide refers to nucleosides, nucleobases, sugar moieties, or internucleoside linkages that are immediately adjacent to each other. For example, “contiguous nucleobases” means nucleobases that are immediately adjacent to each other in a sequence.


As used herein, “deoxy region” means a region of 5-12 contiguous nucleotides, wherein at least 70% of the nucleosides are 2′-β-D-deoxynucleosides. In certain embodiments, each nucleoside is selected from a 2′-β-D-deoxynucleoside, a bicyclic nucleoside, and a 2′-substituted nucleoside. In certain embodiments, a deoxy region supports RNase H activity. In certain embodiments, a deoxy region is the gap or internal region of a gapmer.


As used herein, “diluent” means an ingredient in a composition that lacks pharmacological activity, but is pharmaceutically necessary or desirable. For example, the diluent in an injected composition can be a liquid, e.g. aCSF, PBS, or saline solution.


As used herein, “gapmer” means an oligonucleotide having a central region comprising a plurality of nucleosides that support RNase H1 cleavage positioned between a 5′-region and a 3′-region. Herein, the nucleosides of the 5′-region and 3′-region each comprise a 2′-modified furanosyl sugar moiety, and the 3′- and 5′-most nucleosides of the central region each comprise a sugar moiety independently selected from a 2′-deoxyfuranosyl sugar moiety or a sugar surrogate. The positions of the central region refer to the order of the nucleosides of the central region and are counted starting from the 5′-end of the central region. Thus, the 5′-most nucleoside of the central region is at position 1 of the central region. The “central region” may be referred to as a “gap”, and the “5′-region” and “3′-region” may be referred to as “wings” or “wing segments.” In certain embodiments, the central region is a deoxy region. Unless otherwise indicated, a gapmer may comprise one or more modified internucleoside linkages and/or modified nucleobases and such modifications do not necessarily follow the gapmer pattern of the sugar modifications.


As used herein, the term “MOE gapmer” indicates a gapmer having a gap comprising 2′-β-D-deoxynucleosides and wings comprising 2′-MOE nucleosides.


As used herein, the term “mixed wing gapmer” indicates a gapmer having wings comprising modified nucleosides comprising at least two different sugar modifications.


As used herein, “hotspot region” is a range of nucleobases on a target nucleic acid that is amenable to oligomeric agent or oligomeric compound-mediated reduction of the amount or activity of the target nucleic acid.


As used herein, “HTT RNA” is the RNA expression product of the human gene, IT15. “mHTT RNA” is the RNA expression product of the human gene, IT15, that contains 27 or more contiguous CAG repeats.


As used herein, “HTT protein” is the protein expression product of HTT RNA. “mHTT protein” is the protein expression product of mHTT.


As used herein, “hybridization” means the annealing of oligonucleotides and/or nucleic acids. While not limited to a particular mechanism, the most common mechanism of hybridization involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases. In certain embodiments, complementary nucleic acid molecules include, but are not limited to, an antisense compound and a nucleic acid target. In certain embodiments, complementary nucleic acid molecules include, but are not limited to, an oligonucleotide and a nucleic acid target.


As used herein, “IT15 gene” refers to a genomic sequence encoding an HTT RNA. In general, a human has two IT15 genes which may have the same or different nucleobase sequences.


As used herein, “identifying a subject at risk for developing a repeat expansion disease” means identifying a subject having been diagnosed with a repeat expansion disease or identifying a subject that has a risk factor for developing a repeat expansion disease.


As used herein, “internucleoside linkage” means the covalent linkage between contiguous nucleosides in an oligonucleotide. As used herein, “modified internucleoside linkage” means any internucleoside linkage other than a phosphodiester internucleoside linkage. “Phosphorothioate internucleoside linkage” or “PS internucleoside linkage” is a modified internucleoside linkage in which one of the non-bridging oxygen atoms of a phosphodiester internucleoside linkage is replaced with a sulfur atom.


As used herein, “inverted nucleoside” means a nucleotide having a 3′ to 3′ and/or 5′ to 5′ internucleoside linkage, as shown herein.


As used herein, “inverted sugar moiety” means the sugar moiety of an inverted nucleoside or an abasic sugar moiety having a 3′ to 3′ and/or 5′ to 5′ internucleoside linkage.


As used herein, “linked nucleosides” are nucleosides that are connected in a contiguous sequence (i.e., no additional nucleosides are presented between those that are linked).


As used herein, “linker-nucleoside” means a nucleoside that links, either directly or indirectly, an oligonucleotide to a conjugate moiety. Linker-nucleosides are located within the conjugate linker of an oligomeric compound. Linker-nucleosides are not considered part of the oligonucleotide portion of an oligomeric compound even if they are contiguous with the oligonucleotide.


As used herein, “mismatch” or “non-complementary” means a nucleobase of a first nucleic acid sequence that is not complementary with the corresponding nucleobase of a second nucleic acid sequence when the first and second nucleic acid sequences are aligned in opposing directions.


As used herein, “motif” means the pattern of unmodified and/or modified sugar moieties, nucleobases, and/or internucleoside linkages, in an oligonucleotide.


As used herein, “non-bicyclic modified sugar moiety” means a modified sugar moiety that comprises a modification, such as a substituent, that does not form a bridge between two atoms of the sugar to form a second ring.


As used herein, “nucleobase” means an unmodified nucleobase or a modified nucleobase. As used herein an “unmodified nucleobase” is adenine (A), thymine (T), cytosine (C), uracil (U), or guanine (G). As used herein, a “modified nucleobase” is a group of atoms other than unmodified A, T, C, U, or G capable of pairing with at least one unmodified nucleobase. A “5-methylcytosine” is a modified nucleobase. A universal base is a modified nucleobase that can pair with any one of the five unmodified nucleobases.


As used herein, “nucleobase sequence” means the order of contiguous nucleobases in a target nucleic acid or oligonucleotide independent of any sugar or internucleoside linkage modification.


As used herein, “nucleoside” means a compound, or a fragment of a compound, comprising a nucleobase and a sugar moiety. The nucleobase and sugar moiety are each, independently, unmodified or modified.


As used herein, “modified nucleoside” means a nucleoside comprising a modified nucleobase and/or a modified sugar moiety. Modified nucleosides include abasic nucleosides, which lack a nucleobase. “Linked nucleosides” are nucleosides that are connected in a contiguous sequence (i.e., no additional nucleosides are presented between those that are linked).


As used herein, “oligomeric agent” means an oligomeric compound and optionally one or more additional features, such as a second oligomeric compound. An oligomeric agent may be a single-stranded oligomeric compound or may be an oligomeric duplex formed by two complementary oligomeric compounds.


As used herein, “oligomeric compound” means an oligonucleotide and optionally one or more additional features, such as a conjugate group or terminal group. An oligomeric compound may be paired with a second oligomeric compound that is complementary to the first oligomeric compound or may be unpaired. A “singled-stranded oligomeric compound” is an unpaired oligomeric compound.


The term “oligomeric duplex” means a duplex formed by two oligomeric compounds having complementary nucleobase sequences. Each oligomeric compound of an oligomeric duplex may be referred to as a “duplexed oligomeric compound.”


As used herein, “oligonucleotide” means a strand of linked nucleosides connected via internucleoside linkages, wherein each nucleoside and internucleoside linkage may be modified or unmodified. Unless otherwise indicated, oligonucleotides consist of 8-50 linked nucleosides. As used herein, “modified oligonucleotide” means an oligonucleotide, wherein at least one nucleoside or internucleoside linkage is modified. As used herein, “unmodified oligonucleotide” means an oligonucleotide that does not comprise any nucleoside modifications or internucleoside modifications. An oligonucleotide may be paired with a second oligonucleotide that is complementary to the oligonucleotide or it may be unpaired. A “single-stranded oligonucleotide” is an unpaired oligonucleotide. A “double-stranded oligonucleotide” is an oligonucleotide that is paired with a second oligonucleotide.


As used herein, “pharmaceutically acceptable carrier or diluent” means any substance suitable for use in administering to a subject. Certain such carriers enable pharmaceutical compositions to be formulated as, for example, tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspension and lozenges for the oral ingestion by an animal. In certain embodiments, a pharmaceutically acceptable carrier or diluent is sterile water, sterile saline, sterile buffer solution, or sterile artificial cerebrospinal fluid. In certain embodiments, a pharmaceutically acceptable carrier or diluent is phosphate buffered saline. In certain embodiments, a pharmaceutically acceptable carrier or diluent is artificial cerebrospinal fluid.


As used herein, “pharmaceutically acceptable salts” means physiologically and pharmaceutically acceptable salts of compounds. Pharmaceutically acceptable salts retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto. As used herein, “potassium salt” means a salt of a modified oligonucleotide, wherein the cation of the salt is potassium.


As used herein, “sodium salt” means a salt of a modified oligonucleotide, wherein the cation of the salt is sodium.


As used herein, “pharmaceutical composition” means a mixture of substances suitable for administering to a subject. For example, a pharmaceutical composition may comprise an oligomeric compound and a sterile aqueous solution. In certain embodiments, a pharmaceutical composition shows activity in free uptake assay in certain cell lines.


As used herein, “prevent” or “preventing” refers to delaying or forestalling the onset or development of a neurodegenerative disease, or a symptom or hallmark thereof, for a period of time or indefinitely.


As used herein, “prodrug” means a therapeutic agent in a first form outside the body that is converted to a second form within a subject or cells thereof. Typically, conversion of a prodrug within the subject is facilitated by the action of an enzymes (e.g., endogenous or viral enzyme) or chemicals present in cells or tissues and/or by physiologic conditions. In certain embodiments, the first form of the prodrug is less active than the second form.


As used herein, “reducing the amount or activity,” or “inhibiting the amount or activity,” in connection with a gene transcript (RNA) refers to a reduction or blockade of the transcriptional expression or activity relative to the transcriptional expression or activity in an untreated or control sample and does not necessarily indicate a total elimination of transcriptional expression or activity.


As used herein, “reducing the amount or activity,” or “inhibiting the amount or activity,” in connection with a protein refers to a reduction or blockade of the protein's expression or activity relative to the protein expression or activity in an untreated or control sample and does not necessarily indicate a total elimination of protein expression or activity.


As used herein, “repeat expansion disease” means a disease associated with an increased number of contiguous repeat units in a region of a gene of a subject, each repeat unit consisting of 3-10 linked nucleosides having the same nucleobase sequence as the other repeat units, relative to a control subject without the disease. In certain embodiments, the subject experiences a symptom or hallmark of the repeat expansion disease.


As used herein, “repeat region” means a region of a gene comprising three or more contiguous repeat units, each repeat unit consisting of 3-10 linked nucleosides having the same nucleobase sequence as the other repeat units. Non-limiting examples of repeat units are CTG, CUG, CAG, CUG, GGGGCC, CAG, GAA, CAA and ATTCT.


As used herein, “RNA” means an RNA transcript and includes pre-mRNA and mature mRNA unless otherwise specified.


As used herein, “RNAi agent” means an antisense agent that acts, at least in part, through RISC or Ago2 to modulate a target nucleic acid and/or protein encoded by a target nucleic acid. RNAi agents include, but are not limited to double-stranded siRNA, single-stranded RNA (ssRNAi), and microRNA, including microRNA mimics. RNAi agents may comprise conjugate groups and/or terminal groups. In certain embodiments, an RNAi agent modulates the amount, activity, and/or splicing of a target nucleic acid. The term RNAi agent excludes antisense agents that act through RNase H.


As used herein, “RNase H agent” means an antisense agent that acts through RNase H to modulate a target nucleic acid and/or protein encoded by a target nucleic acid. In certain embodiments, RNase H agents are single-stranded. In certain embodiments, RNase H agents are double-stranded. RNase H agents may comprise conjugate groups and/or terminal groups. In certain embodiments, an RNase H agent modulates the amount and/or activity of a target nucleic acid. The term RNase H agent excludes antisense agents that act principally through RISC/Ago2.


As used herein, “single-stranded” means a nucleic acid (including but not limited to an oligonucleotide) that is unpaired and is not part of a duplex. Single-stranded compounds are capable of hybridizing with complementary nucleic acids to form duplexes, at which point they are no longer single-stranded.


As used herein, “stabilized phosphate group” means a 5′-phosphate analog that is metabolically more stable than a 5′-phosphate as naturally occurs on DNA or RNA.


As used herein, “standard in vitro assay” means the assay described in Examples 1, 2, and 3, and reasonable variations thereof.


As used herein, “standard in vivo assay” means the assay described in Example 9 and reasonable variations thereof.


As used herein, “stereorandom chiral center” in the context of a population of molecules of identical molecular formula means a chiral center having a random stereochemical configuration. For example, in a population of molecules comprising a stereorandom chiral center, the number of molecules having the (S) configuration of the stereorandom chiral center may be but is not necessarily the same as the number of molecules having the (R) configuration of the stereorandom chiral center. The stereochemical configuration of a chiral center is considered random when it is the result of a synthetic method that is not designed to control the stereochemical configuration. In certain embodiments, a stereorandom chiral center is a stereorandom phosphorothioate internucleoside linkage.


As used herein, “subject” means a human or non-human animal. In certain embodiments, the subject is a human subject. A “subject in need thereof,” is a subject who would benefit from administration of a modified oligonucleotide disclosed herein. In certain embodiments, the subject in need thereof has HD.


As used herein, “sugar moiety” means an unmodified sugar moiety or a modified sugar moiety. As used herein, “unmodified sugar moiety” means a 2′-OH(H) β-D-ribosyl sugar moiety, as found in RNA (an “unmodified RNA sugar moiety”), or a 2′-H(H) β-D-deoxyribosyl sugar moiety, as found in DNA (an “unmodified DNA sugar moiety”). Unmodified sugar moieties have one hydrogen at each of the 1′, 3′, and 4′ positions, an oxygen at the 3′ position, and two hydrogens at the 5′ position. As used herein, “modified sugar moiety” or “modified sugar” means a modified furanosyl sugar moiety or a sugar surrogate.


As used herein, “sugar surrogate” means a modified sugar moiety having other than a furanosyl moiety that can link a nucleobase to another group, such as an internucleoside linkage, conjugate group, or terminal group in an oligonucleotide. Modified nucleosides comprising sugar surrogates can be incorporated into one or more positions within an oligonucleotide and such oligonucleotides are capable of hybridizing to complementary oligomeric compounds or target nucleic acids.


As used herein, “symptom or hallmark” means any physical feature or test result that indicates the existence or extent of a disease or disorder. In certain embodiments, a symptom is apparent to a subject or to a medical professional examining or testing said subject. In certain embodiments, a hallmark is apparent upon invasive diagnostic testing, including, but not limited to, post-mortem tests.


As used herein, “target nucleic acid” and “target RNA” mean a nucleic acid that an antisense compound is designed to affect. Target RNA means an RNA transcript and includes pre-mRNA and mRNA unless otherwise specified.


As used herein, “target region” means a portion of a target nucleic acid to which an oligomeric compound is designed to hybridize.


As used herein, “terminal group” means a chemical group or group of atoms that is covalently linked to a terminus of an oligonucleotide.


As used herein, “treating” means improving a subject's disease or condition by administering an oligomeric agent or oligomeric compound described herein. In certain embodiments, treating a subject improves a symptom relative to the same symptom in the absence of the treatment. In certain embodiments, treatment reduces in the severity or frequency of a symptom, or delays the onset of a symptom, slows the progression of a symptom, or slows the severity or frequency of a symptom.


As used herein, “therapeutically effective amount” means an amount of a pharmaceutical agent that provides a therapeutic benefit to a subject. For example, a therapeutically effective amount improves a symptom or hallmark of a disease.


CERTAIN EMBODIMENTS

The present disclosure provides the following non-limiting numbered embodiments:


Embodiment 1. An oligomeric compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides, wherein the nucleobase sequence of the modified oligonucleotide is at least 80% complementary to an equal length portion of an HTT RNA, and wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar moiety and a modified internucleoside linkage.


Embodiment 2. An oligomeric compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of SEQ ID NOs: 26-3707.


Embodiment 3. An oligomeric compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising:

    • a) at least 12, at least 13, at least 14, at least 15, at least 16, or 17 contiguous nucleobases of any of SEQ ID NOs: 26-857 or 3552-3590;
    • b) at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of any of SEQ ID NOs: 858-3551 or 3591-3682; or
    • c) at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, or 18 contiguous nucleobases of any of SEQ ID NOs: 3683-3707.


Embodiment 4. An oligomeric compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases complementary to:

    • an equal length portion of nucleobases 56443-56500 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 62833-62860 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 69788-69824 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 9984-10008 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 106863-106924 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 115297-115337 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 117868-117902 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 119644-119670 of SEQ ID NO: 2;
    • an equal length portion of nucleobases 126780-126829 of SEQ ID NO: 2; or
    • an equal length portion of nucleobases 130388-130418 of SEQ ID NO: 2;
    • wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar moiety and a modified internucleoside linkage.


Embodiment 5. An oligomeric compound comprising a modified oligonucleotide consisting of 12 to 30 linked nucleosides and having a nucleobase sequence comprising at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, or 20 contiguous nucleobases of a sequence selected from:

    • SEQ ID NOs: 1184, 1274, 1331, 1455, 1481, 1562, and 1684;
    • SEQ ID NOs: 3029, 3104, 3557, 3562, 3569, 3586, 3610, 3620, 3622, 3623, 3627, 3634, 3664, 3687, 3692, and 3697;
    • SEQ ID NOs: 2750, 2814, 2887, 2991, and 3090;
    • SEQ ID NOs: 2581, 2640, 2736, 2857, and 2917;
    • SEQ ID NOs: 1105, 1232, 1249, 3330, 3342, 3344, 3362, 3382, 3411, 3419, 3439, 3456, 3475, 3488, 3491, 3511, 3531, 3550, and 3551;
    • SEQ ID NOs: 2208, 2310, 2335, 2471, 3553, 3559, 3563, 3565, 3570, 3580, 3581, 3583, 3585, 3589, 3593, 3594, 3597, 3600, 3601, 3604, 3614, 3616, 3630, 3631, 3637, 3648, 3650, 3652, 3653, 3660, 3661, 3662, 3684, and 3689;
    • SEQ ID NOs: 2644, 2770, 2786, 2916, 3574, 3576, 3578, 3587, 3665, 3666, 3667, 3668, 3669, 3670, 3671, 3672, 3673, 3674, 3675, 3676, 3686, 3694, and 3698;
    • SEQ ID NOs: 919, 940, 3677, 3678, 3679, 3680, 3681, 3682, 3705, 3706, and 3707;
    • SEQ ID NOs: 1576, 1652, 1771, 1813, 1933, 1987, 2078, 3552, 3555, 3558, 3560, 3572, 3573, 3575, 3579, 3584, 3598, 3608, 3611, 3613, 3619, 3628, 3635, 3644, 3646, 3649, 3663, 3683, 3688, 3690, 3700, 3701, 3702, 3703, and 3704; and
    • SEQ ID NOs: 1343, 1406, 1539, 3335, 3401, 3472, 3477, 3519, and 3591;


wherein the modified oligonucleotide comprises at least one modification selected from a modified sugar moiety and a modified internucleoside linkage.


Embodiment 6. The oligomeric compound of any of embodiments 1-5, wherein the modified oligonucleotide has a nucleobase sequence that is at least 85%, at least 90%, at least 95%, or 100% complementary to the nucleobase sequence of any one of SEQ ID NOS: 1-5 when measured across the entire nucleobase sequence of the modified oligonucleotide.


Embodiment 7. The oligomeric compound of any of embodiments 1-6, wherein the modified oligonucleotide consists of 10 to 25, 10 to 30, 12 to 20, 12 to 25, 12 to 30, 13 to 20, 13 to 25, 13 to 30, 14 to 20, 14 to 25, 14 to 30, 15 to 20, 15 to 25, 15 to 30, 16 to 18, 16 to 20, 16 to 25, 16 to 30, 17 to 20, 17 to 25, 17 to 30, 18 to 20, 18 to 25, 18 to 30, 19 to 20, 19 to 25, 19 to 30, 20 to 25, 20 to 30, 21 to 25, 21 to 30, 22 to 25, 22 to 30, 23 to 25, or 23 to 30 linked nucleosides.


Embodiment 8. The oligomeric compound of any of embodiments 1-7, wherein the modified oligonucleotide comprises at least one modified nucleoside.


Embodiment 9. The oligomeric compound of embodiment 8, wherein the modified oligonucleotide comprises at least one modified nucleoside comprising a modified sugar moiety.


Embodiment 10. The oligomeric compound of embodiment 9, wherein the modified oligonucleotide comprises at least one modified nucleoside comprising a bicyclic sugar moiety.


Embodiment 11. The oligomeric compound of embodiment 10, wherein the bicyclic sugar moiety has a 2′-4′ bridge selected from —O—CH2—; and —O—CH(CH3)—.


Embodiment 12. The oligomeric compound of any of embodiments 8-11, wherein the modified oligonucleotide comprises at least one modified nucleoside comprising a non-bicyclic modified sugar moiety.


Embodiment 13. The oligomeric compound of embodiment 12, wherein the non-bicyclic modified sugar moiety is a 2′-MOE modified sugar moiety or a 2′-cEt modified sugar moiety.


Embodiment 14. The oligomeric compound of any of embodiments 8-13, wherein the modified oligonucleotide comprises at least one modified nucleoside comprising a sugar surrogate.


Embodiment 15. The oligomeric compound of embodiment 14, wherein the sugar surrogate is any of morpholino, modified morpholino, PNA, THP, and F-HNA.


Embodiment 16. The oligomeric compound of any of embodiments 1-15, wherein the modified oligonucleotide is a gapmer.


Embodiment 17. The oligomeric compound of any of embodiments 1-16, wherein the modified oligonucleotide has a sugar motif comprising:

    • a 5′-region consisting of 1-6 linked 5′-region nucleosides;
    • a central region consisting of 6-10 linked central region nucleosides; and
    • a 3′-region consisting of 1-6 linked 3′-region nucleosides,
    • wherein each of the 5′-region nucleosides and each of the 3′-region nucleosides comprises a modified sugar moiety and each of the central region nucleosides comprises a 2′-β-D-deoxyribosyl sugar moiety.


Embodiment 18. The oligomeric compound of embodiment 17, wherein

    • the 5′-region consists of 5 linked 5′-region nucleosides;
    • the central region consists of 10 linked central region nucleosides; and
    • the 3′-region consists of 5 linked 3′-region nucleosides, and
    • wherein each of the 5′-region nucleosides and each of the 3′-region nucleosides comprises a 2′-MOE sugar moiety and each of the central region nucleosides comprises a 2′-β-D-deoxyribosyl sugar moiety.


Embodiment 19. The oligomeric compound of embodiment 17, wherein

    • the 5′-region consists of 6 linked 5′-region nucleosides;
    • the central region consists of 10 linked central region nucleosides; and
    • the 3′-region consists of 4 linked 3′-region nucleosides, and
    • wherein each of the 5′-region nucleosides and each of the 3′-region nucleosides comprises a 2′-MOE sugar moiety and each of the central region nucleosides comprises a 2′-β-D-deoxyribosyl sugar moiety.


Embodiment 20. The oligomeric compound of embodiment 17, wherein

    • the 5′-region consists of 5 linked 5′-region nucleosides;
    • the central region consists of 8 linked central region nucleosides; and
    • the 3′-region consists of 5 linked 3′-region nucleosides, and
    • wherein each of the 5′-region nucleosides and each of the 3′-region nucleosides comprises a 2′-MOE sugar moiety and each of the central region nucleosides comprises a 2′-β-D-deoxyribosyl sugar moiety.


Embodiment 21. The oligomeric compound of embodiment 17, wherein

    • the 5′-region consists of 4 linked 5′-region nucleosides;
    • the central region consists of 8 linked central region nucleosides; and
    • the 3′-region consists of 5 linked 3′-region nucleosides, and
    • wherein each of the 5′-region nucleosides and each of the 3′-region nucleosides comprises a modified sugar moiety selected from a 2′-MOE sugar moiety and a 2′-cEt sugar moiety and each of the central region nucleosides comprises a 2′-β-D-deoxyribosyl sugar moiety.


Embodiment 22. The oligomeric compound of any of embodiments 1-21, wherein the modified oligonucleotide comprises at least one modified internucleoside linkage.


Embodiment 23. The oligomeric compound of embodiment 22, wherein each internucleoside linkage of the modified oligonucleotide is a modified internucleoside linkage.


Embodiment 24. The oligomeric compound of embodiment 22 or embodiment 23, wherein each internucleoside linkage is a phosphorothioate internucleoside linkage.


Embodiment 25. The oligomeric compound of embodiment 22, wherein the modified oligonucleotide comprises at least one phosphodiester internucleoside linkage.


Embodiment 26. The oligomeric compound of any of embodiments 22, 23, or 25, wherein each internucleoside linkage is independently selected from a phosphodiester internucleoside linkage and a phosphorothioate internucleoside linkage.


Embodiment 27. The oligomeric compound of any of embodiments 22, 23, or 25-26, wherein at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, or 19 internucleoside linkages of the modified oligonucleotide are phosphorothioate internucleoside linkages.


Embodiment 28. The oligomeric compound of any of embodiments 1-23 or 25-27, wherein the internucleoside linkage motif of the modified oligonucleotide is selected from: 5′-soosssssssssooss-3′, 5′-sooosssssssssssooss-3′, 5′-sooosssssssssssooos-3′, 5′-sossssssssssssssoss-3′, 5′-ssoosssssssssssooss-3′, 5′-sooosssssssssooss-3′, 5′-sossssssssssssoss-3′, and 5′-sooooossssssssssoss-3′, wherein each “s” represents a phosphorothioate internucleoside linkage and each “o” represents a phosphodiester internucleoside linkage.


Embodiment 29. The oligomeric compound of any of embodiments 1-28, wherein the modified oligonucleotide comprises a modified nucleobase.


Embodiment 30. The oligomeric compound of embodiment 29, wherein the modified nucleobase is a 5-methylcytosine.


Embodiment 31. The oligomeric compound of any of embodiments 1-30, wherein the modified oligonucleotide comprises a deoxy region.


Embodiment 32. The oligomeric compound of embodiment 31, wherein each nucleoside of the deoxy region is a 2′-β-D-deoxynucleoside.


Embodiment 33. The oligomeric compound of embodiment 31 or embodiment 32, wherein the deoxy region consists of 6, 7, 8, 9, 10, or 6-10 linked nucleosides.


Embodiment 34. The oligomeric compound of any of embodiments 31-33, wherein each nucleoside immediately adjacent to the deoxy region comprises a modified sugar moiety.


Embodiment 35. The oligomeric compound of any of embodiments 31-34, wherein the deoxy region is flanked on the 5′-side by a 5′-region consisting of 1-6 linked 5′-region nucleosides and on the 3′-side by a 3′-region consisting of 1-6 linked 3′-region nucleosides; wherein at least one nucleoside of the 5′-region comprises a modified sugar moiety; and at least one nucleoside of the 3′-region comprises a modified sugar moiety.


Embodiment 36. The oligomeric compound of embodiment 35, wherein each nucleoside of the 5′-region comprises a modified sugar moiety.


Embodiment 37. The oligomeric compound of embodiment 35 or embodiment 36, wherein each nucleoside of the 3′-region comprises a modified sugar moiety.


Embodiment 38. The oligomeric compound of any of embodiments 1-37, wherein the modified oligonucleotide consists of 12-30, 12-22, 12-20,14-18, 14-20, 15-17, 15-25, 16-20, 18-22, or 18-20 linked nucleosides.


Embodiment 39. The oligomeric compound of any of embodiments 1-38, wherein the modified oligonucleotide consists of 17 linked nucleosides.


Embodiment 40. The oligomeric compound of any of embodiments 1-38, wherein the modified oligonucleotide consists of 18 linked nucleosides.


Embodiment 41. The oligomeric compound of any of embodiments 1-38, wherein the modified oligonucleotide consists of 20 linked nucleosides.


Embodiment 42. The oligomeric compound of any of embodiments 1-41, wherein the modified oligonucleotide is a pharmaceutically acceptable salt.


Embodiment 43. The oligomeric compound of embodiment 42, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.


Embodiment 44. The oligomeric compound of any of embodiments 1-43, consisting of the modified oligonucleotide.


Embodiment 45. The oligomeric compound of any of embodiments 1-44, wherein the oligomeric compound comprises a conjugate group.


Embodiment 46. The oligomeric compound of embodiment 45, wherein the conjugate group comprises a conjugate moiety and a conjugate linker.


Embodiment 47. The oligomeric compound of embodiment 46, wherein the conjugate linker consists of a single bond.


Embodiment 48. The oligomeric compound of embodiment 46, wherein the conjugate linker is cleavable.


Embodiment 49. The oligomeric compound of embodiment 46, wherein the conjugate linker comprises 1-3 linker-nucleosides.


Embodiment 50. The oligomeric compound of embodiment 46, wherein the oligomeric compound does not comprise a linker-nucleoside.


Embodiment 51. The oligomeric compound of any of embodiments 45-50, wherein the conjugate group is attached to the modified oligonucleotide at the 5′-end of the modified oligonucleotide.


Embodiment 52. The oligomeric compound of any of embodiments 45-50, wherein the conjugate group is attached to the modified oligonucleotide at the 3′-end of the modified oligonucleotide.


Embodiment 53. The oligomeric compound of any of embodiments 1-52, comprising a terminal group.


Embodiment 54. The oligomeric compound of embodiment 53, wherein the terminal group is an abasic sugar moiety.


Embodiment 55. The oligomeric compound of any of embodiments 1-54, wherein the modified oligonucleotide is a single-stranded modified oligonucleotide.


Embodiment 56. The oligomeric compound of any of embodiments 1-55, wherein the oligomeric compound is an RNase H agent comprising the oligomeric compound.


Embodiment 57. An oligomeric compound comprising a modified oligonucleotide according to the following chemical notation:









(SEQ ID NO: 3619)



mCes AeomCeo Aeo GeomCeo Tds Tds Tds Tds Ads Tds Tds TdsmCds  







mCds Aeo Tes AesmCe,








wherein
    • A=an adenine,
    • mC=a 5-methylcytosine,
    • G=a guanine,
    • T=a thymine,
    • e=a 2′-O-methoxyethylribose modified sugar,
    • d=a 2′-deoxyribose sugar moiety,
    • s=a phosphorothioate internucleoside linkage, and
    • o=a phosphodiester internucleoside linkage.


Embodiment 58. An oligomeric compound comprising a modified oligonucleotide according to the following chemical notation:









(SEQ ID NO: 1502)


GesmCeo Teo Teo Tes Gds Ads Tds Tds Tds Tds Tds AdsmCdsmCds





Aeo Geo Tes Tes Ae,







wherein
    • A=an adenine,
    • mC=a 5-methylcytosine,
    • G=a guanine,
    • T=a thymine,
    • e=a 2′-O-methoxyethylribose modified sugar,
    • d=a 2′-deoxyribose sugar moiety,
    • s=a phosphorothioate internucleoside linkage, and
    • o=a phosphodiester internucleoside linkage.


Embodiment 59. An oligomeric compound comprising a modified oligonucleotide according to the following chemical notation:









(SEQ ID NO: 3646)


AesmCeo Aeo GeomCeo Teo Tds Tds Tds Ads Tds Tds TdsmCdsmCds





Ads Teo AesmCes Ae,







wherein
    • A=an adenine,
    • mC=a 5-methylcytosine,
    • G=a guanine,
    • T=a thymine,
    • e=a 2′-O-methoxyethylribose modified sugar,
    • d=a 2′-deoxyribose sugar moiety,
    • s=a phosphorothioate internucleoside linkage, and
    • o=a phosphodiester internucleoside linkage.


Embodiment 60. The oligomeric compound of any of embodiments 57-59, wherein the modified oligonucleotide is a pharmaceutically acceptable salt.


Embodiment 61. The oligomeric compound of embodiment 60, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.


Embodiment 62. The oligomeric compound of any of embodiments 57-61, wherein the oligomeric compound is a singled-stranded oligomeric compound.


Embodiment 63. A modified oligonucleotide according to the following chemical structure:




embedded image


or a pharmaceutically acceptable salt thereof.


Embodiment 64. The modified oligonucleotide of embodiment 63, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.


Embodiment 65. A modified oligonucleotide according to the following chemical structure:




embedded image


Embodiment 66. A modified oligonucleotide according to the following chemical structure:




embedded image


or a pharmaceutically acceptable salt thereof.


Embodiment 67. The modified oligonucleotide of embodiment 66, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.


Embodiment 68. A modified oligonucleotide according to the following chemical structure:




embedded image


Embodiment 69. A modified oligonucleotide according to the following chemical structure:




embedded image


or a pharmaceutically acceptable salt thereof.


Embodiment 70. The modified oligonucleotide of embodiment 69, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.


Embodiment 71. A modified oligonucleotide according to the following chemical structure:




embedded image


Embodiment 72. A chirally enriched population of oligomeric compounds of any of embodiments 1-62 or modified oligonucleotides of any of embodiments 63-71, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having a particular stereochemical configuration.


Embodiment 73. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having the (Sp) configuration.


Embodiment 74. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides comprising at least one particular phosphorothioate internucleoside linkage having the (Rp) configuration.


Embodiment 75. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides having a particular, independently selected stereochemical configuration at each phosphorothioate internucleoside linkage.


Embodiment 76. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides having the (Sp) configuration at each phosphorothioate internucleoside linkage.


Embodiment 77. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides having the (Rp) configuration at each phosphorothioate internucleoside linkage.


Embodiment 78. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides having the (Rp) configuration at one particular phosphorothioate internucleoside linkage and the (Sp) configuration at each of the remaining phosphorothioate internucleoside linkages.


Embodiment 79. The chirally enriched population of embodiment 72, wherein the population is enriched for modified oligonucleotides having at least 3 contiguous phosphorothioate internucleoside linkages in the Sp, Sp, and Rp configurations, in the 5′ to 3′ direction.


Embodiment 80. A population of oligomeric compounds of any of embodiments 1-62 or modified oligonucleotides of any of embodiments 63-71, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.


Embodiment 81. An oligomeric duplex, comprising a first oligomeric compound and a second oligomeric compound comprising a second modified oligonucleotide, wherein the first oligomeric compound is an oligomeric compound of any of embodiments 1-62.


Embodiment 82. The oligomeric duplex of embodiment 81, wherein the second modified oligonucleotide consists of 12 to 30 linked nucleosides, and wherein the nucleobase sequence of the second modified oligonucleotide comprises a complementary region of at least 8 nucleobases that is at least 90% complementary to an equal length portion of the first modified oligonucleotide.


Embodiment 83. The oligomeric duplex of embodiment 81 or embodiment 82, wherein the modified oligonucleotide of the first oligomeric compound comprises a 5′-stabilized phosphate group.


Embodiment 84. The oligomeric duplex of embodiment 83, wherein the stabilized phosphate group comprises a cyclopropyl phosphonate or a vinyl phosphonate.


Embodiment 85. The oligomeric duplex of any of embodiments 81-84, wherein at least one nucleoside of the second modified oligonucleotide comprises a modified sugar moiety.


Embodiment 86. The oligomeric duplex of embodiment 85, wherein the modified sugar moiety of the second modified oligonucleotide comprises a bicyclic sugar moiety.


Embodiment 87. The oligomeric duplex of embodiment 86, wherein the bicyclic sugar moiety of the second modified oligonucleotide comprises a 2′-4′ bridge selected from —O—CH2—; and —O—CH(CH3)—.


Embodiment 88. The oligomeric duplex of embodiment 85, wherein the modified sugar moiety of the second modified oligonucleotide comprises a non-bicyclic modified sugar moiety.


Embodiment 89. The oligomeric duplex of embodiment 88, wherein the non-bicyclic modified sugar moiety of the second modified oligonucleotide is a 2′-MOE sugar moiety, a 2′-cEt sugar moiety, a 2′-F sugar moiety, or a 2′-OMe sugar moiety.


Embodiment 90. The oligomeric duplex of any of embodiments 81-89, wherein at least one internucleoside linkage of the second modified oligonucleotide is a modified internucleoside linkage.


Embodiment 91. The oligomeric duplex of embodiment 90, wherein at least one modified internucleoside linkage of the second modified oligonucleotide is a phosphorothioate internucleoside linkage.


Embodiment 92. The oligomeric duplex of any of embodiments 81-91, wherein at least one internucleoside linkage of the second modified oligonucleotide is a phosphodiester internucleoside linkage.


Embodiment 93. The oligomeric duplex of any of embodiments 81-92, wherein each internucleoside linkage of the second modified oligonucleotide is independently selected from a phosphodiester or a phosphorothioate internucleoside linkage.


Embodiment 94. The oligomeric duplex of any of embodiments 81-93, wherein the second modified oligonucleotide comprises at least one modified nucleobase.


Embodiment 95. The oligomeric duplex of embodiment 94, wherein the at least one modified nucleobase of the second modified oligonucleotide is 5-methylcytosine.


Embodiment 96. The oligomeric duplex of any of embodiments 81-95, wherein the second modified oligonucleotide comprises a conjugate group.


Embodiment 97. The oligomeric duplex of embodiment 96, wherein the conjugate group comprises a conjugate linker and a conjugate moiety.


Embodiment 98. The oligomeric duplex of embodiment 96 or embodiment 97, wherein the conjugate group is attached to the 5′-end of the second modified oligonucleotide.


Embodiment 99. The oligomeric duplex of embodiment 96 or embodiment 97, wherein the conjugate group is attached to the 3′-end of the second modified oligonucleotide.


Embodiment 100. The oligomeric duplex of any of embodiments 96-99, wherein the conjugate group comprises a lipid.


Embodiment 101. The oligomeric duplex of any of embodiments 81-100, wherein the second modified oligonucleotide comprises a terminal group.


Embodiment 102. The oligomeric duplex of embodiment 101, wherein the terminal group is an abasic sugar moiety.


Embodiment 103. The oligomeric duplex of any of embodiments 81-102, wherein the second modified oligonucleotide consists of 12 to 20, 12 to 25, 12 to 30, 13 to 20, 13 to 25, 13 to 30, 14 to 20, 14 to 25, 14 to 30, 15 to 20, 15 to 25, 15 to 30, 16 to 18, 16 to 20, 16 to 25, 16 to 30, 17 to 20, 17 to 25, 17 to 30, 18 to 20, 18 to 22, 18 to 25, 18 to 30, 19 to 20, 19 to 25, 19 to 30, 20 to 25, 20 to 30, 21 to 25, 21 to 30, 22 to 25, 22 to 30, 23 to 25, or 23 to 30 linked nucleosides.


Embodiment 104. An antisense agent comprising an antisense compound, wherein the antisense compound is an oligomeric compound of any of embodiments 1-62.


Embodiment 105. An antisense agent comprising an antisense compound, wherein the antisense compound is an oligomeric duplex of any of embodiments 81-103.


Embodiment 106. The antisense agent of embodiment 104 or embodiment 105, wherein the antisense agent is:

    • a) an RNase H agent capable of reducing the amount of HTT nucleic acid through the activation of RNase H; or
    • b) an RNAi agent capable of reducing the amount of HTT nucleic acid through the activation of RISC/Ago2.


Embodiment 107. A pharmaceutical composition comprising an oligomeric compound of any of embodiments 1-62, a modified oligonucleotide of any of embodiments 63-71, a population of any of embodiments 72-79, an oligomeric duplex of any of embodiments 81-103, or an antisense agent of any of embodiments 104-106; and a pharmaceutically acceptable carrier or diluent.


Embodiment 108. The pharmaceutical composition of embodiment 107, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).


Embodiment 109. The pharmaceutical composition of embodiment 108, wherein the pharmaceutical composition consists essentially of the oligomeric compound of any of embodiments 1-62, the modified oligonucleotide of any of embodiments 63-71, the population of any of embodiments 72-79, the oligomeric duplex of any of embodiments 81-103, or the antisense agent of any of embodiments 104-106, and PBS.


Embodiment 110. The pharmaceutical composition of embodiment 108, wherein the pharmaceutical composition consists essentially of the oligomeric compound of any of embodiments 1-62, the modified oligonucleotide of any of embodiments 63-71, the population of any of embodiments 72-79, the oligomeric duplex of any of embodiments 81-103, or the antisense agent of any of embodiments 104-106, and aCSF.


Embodiment 111. A method comprising administering to a subject an oligomeric compound of any of embodiments 1-62, a modified oligonucleotide of any of embodiments 63-71, a population of any of embodiments 72-79, an oligomeric duplex of any of embodiments 81-103, an antisense agent of any of embodiments 104-106, or a pharmaceutical composition of any of embodiments 107-110.


Embodiment 112. A method of ameliorating or preventing a repeat expansion disease, comprising administering to a subject in need thereof a therapeutically effective amount of an oligomeric compound of any of embodiments 1-62, a modified oligonucleotide of any of embodiments 63-71, a population of any of embodiments 72-79, an oligomeric duplex of any of embodiments 81-103, an antisense agent of any of embodiments 104-106, or a pharmaceutical composition of any of embodiments 107-110.


Embodiment 113. The method of embodiment 112, wherein the repeat expansion disease is selected from myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, a polyglutamine disorder, Fragile X syndrome, and a spinocerebellar ataxia.


Embodiment 114. The method of embodiment 112, wherein the repeat expansion disease is Huntington's disease.


Embodiment 115. The method of embodiment 112, wherein the repeat expansion disease is a spinocerebellar ataxia.


Embodiment 116. The method of any of embodiments 112-115, wherein at least one symptom or hallmark of the repeat expansion disease is ameliorated.


Embodiment 117. The method of embodiment 116, wherein the symptom or hallmark is selected from brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, suicidal behavior, and a combination thereof.


Embodiment 118. The method of any of embodiments 116-117, wherein administering the oligomeric compound of any of embodiments 1-62, the modified oligonucleotide of any of embodiments 63-71, the population of any of embodiments 72-79, the oligomeric duplex of any of embodiments 81-103, the antisense agent of any of embodiments 104-106, or the pharmaceutical composition of any of embodiments 107-110 reduces or delays the onset or progression of brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, or suicidal behavior.


Embodiment 119. The method of any of embodiments 111-118, comprising identifying the subject as having the repeat expansion disease or at risk for having the repeat expansion disease.


Embodiment 120. The method of any of embodiments 111-119, wherein the oligomeric compound of any of embodiments 1-62, the modified oligonucleotide of any of embodiments 63-71, the population of any of embodiments 72-79, the oligomeric duplex of any of embodiments 81-103, the antisense agent of any of embodiments 104-106, or the pharmaceutical composition of any of embodiments 107-110 is administered to the central nervous system or systemically.


Embodiment 121. The method of any of embodiments 111-119, wherein the oligomeric compound of any of embodiments 1-62, the modified oligonucleotide of any of embodiments 63-71, the population of any of embodiments 72-79, the oligomeric duplex of any of embodiments 81-103, the antisense agent of any of embodiments 104-106, or the pharmaceutical composition of any of embodiments 107-110 is administered intrathecally.


Embodiment 122. The method of any of embodiments 111-121, wherein the subject is a human.


Embodiment 123. A method of reducing expression of HTT in a cell comprising contacting the cell with an oligomeric compound of any of embodiments 1-62, a modified oligonucleotide of any of embodiments 63-71, a population of any of embodiments 72-79, an oligomeric duplex of any of embodiments 81-103, an antisense agent of any of embodiments 104-106, or a pharmaceutical composition of any of embodiments 107-110.


Embodiment 124. The method of embodiment 123, wherein the cell is from a brain tissue, optionally from the cortex, substantia nigra, striatum, midbrain, brainstem, or spinal cord.


Embodiment 125. The method of embodiment 123 or embodiment 124, wherein the cell is a human cell.


Embodiment 126. Use of an oligomeric compound of any of embodiments 1-62, a modified oligonucleotide of any of embodiments 63-71, a population of any of embodiments 72-79, an oligomeric duplex of any of embodiments 81-103, an antisense agent of any of embodiments 104-106, or a pharmaceutical composition of any of embodiments 107-110 for ameliorating or preventing a repeat expansion disease.


Embodiment 127. Use of an oligomeric compound of any of embodiments 1-62, a modified oligonucleotide of any of embodiments 63-71, a population of any of embodiments 72-79, an oligomeric duplex of any of embodiments 81-103, an antisense agent of any of embodiments 104-106, or a pharmaceutical composition of any of embodiments 107-110 in the manufacture of a medicament for ameliorating or preventing a repeat expansion disease.


Embodiment 128. The use of embodiment 126 or embodiment 127, wherein the repeat expansion disease is Huntington's disease.


I. Certain Oligonucleotides

In certain embodiments, provided herein are oligomeric compounds comprising oligonucleotides, which consist of linked nucleosides. Oligonucleotides may be unmodified oligonucleotides (RNA or DNA) or may be modified oligonucleotides. Modified oligonucleotides comprise at least one modification relative to unmodified RNA or DNA. That is, modified oligonucleotides comprise at least one modified nucleoside (comprising a modified sugar moiety and/or a modified nucleobase) and/or at least one modified internucleoside linkage. Certain modified nucleosides and modified internucleoside linkages suitable for use in modified oligonucleotides are described below.


A. Certain Modified Nucleosides

Modified nucleosides comprise a modified sugar moiety or a modified nucleobase or both a modified sugar moiety and a modified nucleobase. In certain embodiments, modified nucleosides comprising the following modified sugar moieties and/or the following modified nucleobases may be incorporated into modified oligonucleotides.


1. Certain Sugar Moieties

In certain embodiments, modified sugar moieties are non-bicyclic modified sugar moieties. In certain embodiments, modified sugar moieties are bicyclic or tricyclic sugar moieties. In certain embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of other types of modified sugar moieties.


In certain embodiments, modified sugar moieties are non-bicyclic modified furanosyl sugar moieties comprising one or more acyclic substituent, including, but not limited, to substituents at the 2′, 3′, 4′, and/or 5′ positions. In certain embodiments, the furanosyl sugar moiety is a ribosyl sugar moiety. In certain embodiments, one or more acyclic substituent of non-bicyclic modified sugar moieties is branched.


In certain embodiments, non-bicyclic modified sugar moieties comprise a substituent group at the 2′-position. Examples of substituent groups suitable for the 2′-position of modified sugar moieties include but are not limited to: —F, —OCH3 (“OMe” or “O-methyl”), and —O(CH2)2OCH3 (“MOE”). In certain embodiments, 2′-substituent groups are selected from among: halo, allyl, amino, azido, SH, CN, OCN, CF3, OCF3, O—C1-C10 alkoxy, O—C1-C10 substituted alkoxy, O—C1-C10 alkyl, O—C1-C10 substituted alkyl, S-alkyl, N(Rm)-alkyl, O-alkenyl, S-alkenyl, N(Rm)-alkenyl, O-alkynyl, S-alkynyl, N(Rm)-alkynyl, O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH2)2SCH3, O(CH2)2ON(Rm)(Rn) or OCH2C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group, or substituted or unsubstituted C1-C10 alkyl, —O(CH2)2ON(CH3)2(“DMAOE”), 2′-O(CH2)2O(CH2)2N(CH3)2 (“DMAEOE”), and the 2′-substituent groups described in Cook et al., U.S. Pat. No. 6,531,584; Cook et al., U.S. 5,859,221; and Cook et al., U.S. Pat. No. 6,005,087. Certain embodiments of these 2′-substituent groups can be further substituted with one or more substituent groups independently selected from among: hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO2), thiol, thioalkoxy, thioalkyl, halogen, alkyl, aryl, alkenyl and alkynyl.


In certain embodiments, a 2′-substituted non-bicyclic modified nucleoside comprises a sugar moiety comprising a non-bridging 2′-substituent group selected from: F, NH2, N3, OCF3, OCH3, O(CH2)3NH2, CH2CH═CH2, OCH2CH═CH2, OCH2CH2OCH3, O(CH2)2SCH3, O(CH2)2ON(Rm)(Rn), O(CH2)2O(CH2)2N(CH3)2, and N-substituted acetamide (OCH2C(═O)—N(Rm)(Rn)), where each Rm and Rn is, independently, H, an amino protecting group, or substituted or unsubstituted C1-C10 alkyl.


In certain embodiments, a 2′-substituted nucleoside non-bicyclic modified nucleoside comprises a sugar moiety comprising a non-bridging 2′-substituent group selected from: F, OCF3, OCH3, OCH2CH2OCH3, O(CH2)2SCH3, O(CH2)2ON(CH3)2, O(CH2)2O(CH2)2N(CH3)2, and OCH2C(═O)—N(H)CH3 (“NMA”).


In certain embodiments, a 2′-substituted non-bicyclic modified nucleoside comprises a sugar moiety comprising a non-bridging 2′-substituent group selected from: F, OCH3, and OCH2CH2OCH3.


In certain embodiments, modified furanosyl sugar moieties and nucleosides incorporating such modified furanosyl sugar moieties are further defined by isomeric configuration. For example, a 2′-deoxyfuranosyl sugar moiety may be in seven isomeric configurations other than the naturally occurring β-D-deoxyribosyl configuration. Such modified sugar moieties are described in, e.g., WO 2019/157531, incorporated by reference herein. A 2′-modified sugar moiety has an additional stereocenter at the 2′-position relative to a 2′-deoxyfuranosyl sugar moiety; therefore, such sugar moieties have a total of sixteen possible isomeric configurations. 2′-modified sugar moieties described herein are in the β-D-ribosyl isomeric configuration unless otherwise specified.


In certain embodiments, non-bicyclic modified sugar moieties comprise a substituent group at the 4′-position. Examples of substituent groups suitable for the 4′-position of modified sugar moieties include but are not limited to alkoxy (e.g., methoxy), alkyl, and those described in Manoharan et al., WO 2015/106128.


In certain embodiments, non-bicyclic modified sugar moieties comprise a substituent group at the 3′-position. Examples of substituent groups suitable for the 3′-position of modified sugar moieties include but are not limited to alkoxy (e.g., methoxy), alkyl (e.g., methyl, ethyl).


In certain embodiments, non-bicyclic modified sugar moieties comprise a substituent group at the 5′-position. Examples of substituent groups suitable for the 5′-position of modified sugar moieties include but are not limited to vinyl, alkoxy (e.g., methoxy), alkyl (e.g., methyl (R or S), ethyl).


In certain embodiments, non-bicyclic modified sugar moieties comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties and the modified sugar moieties and modified nucleosides described in Migawa et al., WO 2008/101157 and Rajeev et al., US2013/0203836).


In naturally occurring nucleic acids, sugars are linked to one another 3′ to 5′. In certain embodiments, oligonucleotides include one or more nucleoside or sugar moiety linked at an alternative position, for example at the 2′ position or inverted 5′ to 3′. For example, where the linkage is at the 2′ position, the 2′-substituent groups may instead be at the 3′-position.


Certain modified sugar moieties comprise a substituent that bridges two atoms of the furanosyl ring to form a second ring, resulting in a bicyclic sugar moiety. In certain such embodiments, the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms. Examples of such 4′ to 2′ bridging sugar substituents include but are not limited to: 4′-CH2-2′, 4′-(CH2)2-2′, 4′-(CH2)3-2′, 4′-CH2—O-2′ (“LNA”), 4′-CH2—S-2′, 4′-(CH2)2—O-2′ (“ENA”), 4′-CH(CH3)—O-2′ (referred to as “constrained ethyl” or “cEt”), 4′-CH2—O—CH2-2′, 4′-CH2—N(R)-2′, 4′-CH(CH2OCH3)—O-2′ (“constrained MOE” or “cMOE”) and analogs thereof (see, e.g., Seth et al., U.S. Pat. No. 7,399,845, Bhat et al., U.S. Pat. No. 7,569,686, Swayze et al., U.S. Pat. No. 7,741,457, and Swayze et al., U.S. Pat. No. 8,022,193), 4′-C(CH3)(CH3)—O-2′ and analogs thereof (see, e.g., Seth et al., U.S. Pat. No. 8,278,283), 4′-CH2—N(OCH3)-2′ and analogs thereof (see, e.g., Prakash et al., U.S. Pat. No. 8,278,425), 4′-CH2—O—N(CH3)-2′ (see, e.g., Allerson et al., U.S. Pat. No. 7,696,345 and Allerson et al., U.S. Pat. No. 8,124,745), 4′-CH2—C(H)(CH3)-2′ (see, e.g., Zhou, et al., J. Org. Chem., 2009, 74, 118-134), 4′-CH2—C(═CH2)-2′ and analogs thereof (see e.g., Seth et al., U.S. Pat. No. 8,278,426), 4′-C(RaRb)—N(R)—O-2′, 4′-C(RaRb)—O—N(R)-2′, 4′-CH2—O—N(R)-2′, and 4′-CH2—N(R)—O-2′, wherein each R, Ra, and Rb is, independently, H, a protecting group, or C1-C12 alkyl (see, e.g. Imanishi et al., U.S. Pat. No. 7,427,672).


In certain embodiments, such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from: —[C(Ra)(Rb)]n—, —[C(Ra)(Rb)]n—O—, —C(Ra)═C(Rb)—, —C(Ra)═N—, —C(═NRa)—, —C(═O)—, —C(═S)—, —O—, —Si(Ra)2—, —S(═O)x—, and —N(Ra)—;

    • wherein:
    • x is 0, 1, or 2;
    • n is 1, 2, 3, or 4;
    • each Ra and Rb is, independently, H, a protecting group, hydroxyl, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C5-C7 alicyclic radical, substituted C5-C7 alicyclic radical, halogen, OJ1, NJ1J2, SJ1, N3, COOJ1, acyl (C(═O)—H), substituted acyl, CN, sulfonyl (S(═O)2-J1), or sulfoxyl (S(═O)-J1); and
    • each J1 and J2 is, independently, H, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, acyl (C(═O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, C1-C12 aminoalkyl, substituted C1-C12 aminoalkyl, or a protecting group.


Additional bicyclic sugar moieties are known in the art, see, for example: Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443, Albaek et al., J. Org. Chem., 2006, 71, 7731-7740, Singh et al., Chem. Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54, 3607-3630; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8, 2219-2222; Singh et al., J. Org. Chem., 1998, 63, 10035-10039; Srivastava et al., J. Am. Chem. Soc., 2007, 129, 8362-8379; Wengel et al., U.S. Pat. No. 7,053,207; Imanishi et al., U.S. Pat. No. 6,268,490; Imanishi et al. U.S. Pat. No. 6,770,748; Imanishi et al., U.S. RE44,779; Wengel et al., U.S. Pat. No. 6,794,499; Wengel et al., U.S. Pat. No. 6,670,461; Wengel et al., U.S. Pat. No. 7,034,133; Wengel et al., U.S. Pat. No. 8,080,644; Wengel et al., U.S. Pat. No. 8,034,909; Wengel et al., U.S. Pat. No. 8,153,365; Wengel et al., U.S. Pat. No. 7,572,582; and Ramasamy et al., U.S. Pat. No. 6,525,191; Torsten et al., WO 2004/106356; Wengel et al., WO 1999/014226; Seth et al., WO 2007/134181; Seth et al., U.S. Pat. No. 7,547,684; Seth et al., U.S. Pat. No. 7,666,854; Seth et al., U.S. Pat. No. 8,088,746; Seth et al., U.S. Pat. No. 7,750,131; Seth et al., U.S. Pat. No. 8,030,467; Seth et al., U.S. Pat. No. 8,268,980; Seth et al., U.S. Pat. No. 8,546,556; Seth et al., U.S. Pat. No. 8,530,640; Migawa et al., U.S. Pat. No. 9,012,421; Seth et al., U.S. Pat. No. 8,501,805; and U.S. Patent Publication Nos. Allerson et al., US2008/0039618 and Migawa et al., US2015/0191727.


In certain embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, an LNA nucleoside (described herein) may be in the α-L configuration or in the β-D configuration.




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α-L-methyleneoxy (4′-CH2—O—2′) or α-L-LNA bicyclic nucleosides have been incorporated into oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372). Herein, general descriptions of bicyclic nucleosides include both isomeric configurations. When the positions of specific bicyclic nucleosides (e.g., LNA or cEt) are identified in exemplified embodiments herein, they are in the β-D configuration, unless otherwise specified.


In certain embodiments, modified sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars).


In certain embodiments, modified sugar moieties are sugar surrogates. In certain such embodiments, the oxygen atom of the sugar moiety is replaced, e.g., with a sulfur, carbon or nitrogen atom. In certain such embodiments, such modified sugar moieties also comprise bridging and/or non-bridging substituents as described herein. For example, certain sugar surrogates comprise a 4′-sulfur atom and a substitution at the 2′-position (see, e.g., Bhat et al., U.S. Pat. No. 7,875,733 and Bhat et al., U.S. Pat. No. 7,939,677) and/or the 5′ position.


In certain embodiments, sugar surrogates comprise rings having other than 5 atoms. For example, in certain embodiments, a sugar surrogate comprises a six-membered tetrahydropyran (“THP”). Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include but are not limited to hexitol nucleic acid (“HNA”), anitol nucleic acid (“ANA”), manitol nucleic acid (“MNA”) (see, e.g., Leumann, CJ. Bioorg. & Med. Chem. 2002, 10, 841-854), fluoro HNA:




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(“F-HNA”, see e.g. Swayze et al., U.S. Pat. No. 8,088,904; Swayze et al., U.S. Pat. No. 8,440,803; Swayze et al., U.S. Pat. No. 8,796,437; and Swayze et al., U.S. Pat. No. 9,005,906; F-HNA can also be referred to as a F-THP or 3′-fluoro tetrahydropyran), and nucleosides comprising additional modified THP compounds having the formula:




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wherein, independently, for each of said modified THP nucleoside:

    • Bx is a nucleobase moiety;
    • T3 and T4 are each, independently, an internucleoside linking group linking the modified THP nucleoside to the remainder of an oligonucleotide or one of T3 and T4 is an internucleoside linking group linking the modified THP nucleoside to the remainder of an oligonucleotide and the other of T3 and T4 is H, a hydroxyl protecting group, a linked conjugate group, or a 5′ or 3′-terminal group; q1, q2, q3, q4, q5, q6 and q7 are each, independently, H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl, or substituted C2-C6 alkynyl; and
    • each of R1 and R2 is independently selected from among: hydrogen, halogen, substituted or unsubstituted alkoxy, NJ1J2, SJ1, N3, OC(═X)J1, OC(═X)NJ1J2, NJ3C(═X)NJ1J2, and CN, wherein X is O, S or NJ1, and each J1, J2, and J3 is, independently, H or C1-C6 alkyl.


In certain embodiments, modified THP nucleosides are provided wherein q1, q2, q3, q4, q5, q6 and q7 are each H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is other than H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is methyl. In certain embodiments, modified THP nucleosides are provided wherein one of R1 and R2 is F. In certain embodiments, R1 is F and R2 is H, in certain embodiments, R1 is methoxy and R2 is H, and in certain embodiments, R1 is methoxyethoxy and R2 is H.


In certain embodiments, sugar surrogates comprise rings having more than 5 atoms and more than one heteroatom. For example, nucleosides comprising morpholino sugar moieties and their use in oligonucleotides have been reported (see, e.g., Braasch et al., Biochemistry, 2002, 41, 4503-4510 and Summerton et al., U.S. Pat. No. 5,698,685; Summerton et al., U.S. Pat. No. 5,166,315; Summerton et al., U.S. Pat. No. 5,185,444; and Summerton et al., U.S. Pat. No. 5,034,506). As used here, the term “morpholino” means a sugar surrogate having the following structure:




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In certain embodiments, morpholinos may be modified, for example by adding or altering various substituent groups from the above morpholino structure. Such sugar surrogates are referred to herein as “modified morpholinos.”


In certain embodiments, sugar surrogates comprise acyclic moieties. Examples of nucleosides and oligonucleotides comprising such acyclic sugar surrogates include but are not limited to: peptide nucleic acid (“PNA”), acyclic butyl nucleic acid (see, e.g., Kumar et al., Org. Biomol. Chem., 2013, 11, 5853-5865), and nucleosides and oligonucleotides described in Manoharan et al., WO2011/133876. In certain embodiments, sugar surrogates comprise acyclic moieties. Examples of nucleosides and oligonucleotides comprising such acyclic sugar surrogates include, but are not limited to: peptide nucleic acid (“PNA”), acyclic butyl nucleic acid (see, e.g., Kumar et al., Org. Biomol. Chem., 2013, 11, 5853-5865), and nucleosides and oligonucleotides described in Manoharan et al., US2013/130378. Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262. Additional PNA compounds suitable for use in the oligonucleotides of the invention are described in, for example, in Nielsen et al., Science, 1991, 254, 1497-1500.


In certain embodiments, sugar surrogates are the “unlocked” sugar structure of UNA (unlocked nucleic acid) nucleosides. UNA is an unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked sugar surrogate. Representative U.S. publications that teach the preparation of UNA include, but are not limited to, U.S. Pat. No. 8,314,227; and US Patent Publication Nos. 2013/0096289; 2013/0011922; and 2011/0313020, the entire contents of each of which are hereby incorporated herein by reference.


In certain embodiments, sugar surrogates are the glycerol as found in GNA (glycol nucleic acid) nucleosides as depicted below:


(S)-GNA



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where Bx represents any nucleobase.


Many other bicyclic and tricyclic sugar and sugar surrogate ring systems are known in the art that can be used in modified nucleosides.


2. Certain Modified Nucleobases

In certain embodiments, modified oligonucleotides comprise one or more nucleosides comprising an unmodified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more nucleosides comprising a modified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more nucleosides that does not comprise a nucleobase, referred to as an abasic nucleoside. In certain embodiments, modified oligonucleotides comprise one or more inosine nucleosides (i.e., nucleosides comprising a hypoxanthine nucleobase).


In certain embodiments, modified nucleobases are selected from: 5-substituted pyrimidines, 6-azapyrimidines, alkyl or alkynyl substituted pyrimidines, alkyl substituted purines, and N-2, N-6 and O-6 substituted purines. In certain embodiments, modified nucleobases are selected from: 2-aminopropyladenine, 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-N-methylguanine, 6-N-methyladenine, 2-propyladenine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-propynyl (—C═C—CH3) uracil, 5-propynylcytosine, 6-azouracil, 6-azocytosine, 6-azothymine, 5-ribosyluracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl, 8-aza and other 8-substituted purines, 5-halo, particularly 5-bromo, 5-trifluoromethyl, 5-halouracil, and 5-halocytosine, 7-methylguanine, 7-methyladenine, 2-F-adenine, 2-aminoadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, 3-deazaadenine, 6-N-benzoyladenine, 2-N-isobutyrylguanine, 4-N-benzoylcytosine, 4-N-benzoyluracil, 5-methyl 4-N-benzoylcytosine, 5-methyl 4-N-benzoyluracil, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases. Further modified nucleobases include tricyclic pyrimidines, such as 1,3-diazaphenoxazine-2-one, 1,3-diazaphenothiazine-2-one and 9-(2-aminoethoxy)-1,3-diazaphenoxazine-2-one (G-clamp). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in Merigan et al., U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288; and those disclosed in Chapters 6 and 15, Antisense Drug Technology, Crooke S. T., Ed., CRC Press, 2008, 163-166 and 442-443.


Publications that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include without limitation, Manoharan et al., US2003/0158403; Manoharan et al., US2003/0175906; Dinh et al., U.S. Pat. No. 4,845,205; Spielvogel et al., U.S. Pat. No. 5,130,302; Rogers et al., U.S. Pat. No. 5,134,066; Bischofberger et al., U.S. Pat. No. 5,175,273; Urdea et al., U.S. Pat. No. 5,367,066; Benner et al., U.S. Pat. No. 5,432,272; Matteucci et al., U.S. Pat. No. 5,434,257; Gmeiner et al., U.S. Pat. No. 5,457,187; Cook et al., U.S. Pat. No. 5,459,255; Froehler et al., U.S. Pat. No. 5,484,908; Matteucci et al., U.S. Pat. No. 5,502,177; Hawkins et al., U.S. Pat. No. 5,525,711; Haralambidis et al., U.S. Pat. No. 5,552,540; Cook et al., U.S. Pat. No. 5,587,469; Froehler et al., U.S. Pat. No. 5,594,121; Switzer et al., U.S. Pat. No. 5,596,091; Cook et al., U.S. Pat. No. 5,614,617; Froehler et al., U.S. Pat. No. 5,645,985; Cook et al., U.S. Pat. No. 5,681,941; Cook et al., U.S. Pat. No. 5,811,534; Cook et al., U.S. Pat. No. 5,750,692; Cook et al., U.S. Pat. No. 5,948,903; Cook et al., U.S. Pat. No. 5,587,470; Cook et al., U.S. Pat. No. 5,457,191; Matteucci et al., U.S. Pat. No. 5,763,588; Froehler et al., U.S. Pat. No. 5,830,653; Cook et al., U.S. Pat. No. 5,808,027; Cook et al., 6,166,199; and Matteucci et al., U.S. Pat. No. 6,005,096.


3. Certain Modified Internucleoside Linkages

The naturally occurring internucleoside linkage of RNA and DNA is a 3′ to 5′ phosphodiester linkage. In certain embodiments, nucleosides of modified oligonucleotides may be linked together using any internucleoside linkage. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus-containing internucleoside linkages include but are not limited to phosphates, which contain a phosphodiester bond (“P═O”) (also referred to as unmodified or naturally occurring linkages), phosphotriesters, methylphosphonates, phosphoramidates, and phosphorothioates (“P═S”), and phosphorodithioates (“HS—P═S”). Representative non-phosphorus containing internucleoside linking groups include but are not limited to methylenemethylimino (—CH2—N(CH3)—O—CH2—), thiodiester, thionocarbamate (—O—C(═O)(NH)—S—); siloxane (—O—SiH2—O—); and N,N′-dimethylhydrazine (—CH2—N(CH3)—N(CH3)—). Modified internucleoside linkages, compared to naturally occurring phosphate linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide. In certain embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.


In certain embodiments, a modified internucleoside linkage is any of those described in WO/2021/030778, incorporated by reference herein. In certain embodiments, a modified internucleoside linkage comprises the formula:




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wherein independently for each internucleoside linking group of the modified oligonucleotide:

    • X is selected from O or S;
    • R1 is selected from H, C1-C6 alkyl, and substituted C1-C6 alkyl; and
    • T is selected from SO2R2, C(═O)R3, and P(═O)R4R5, wherein:
    • R2 is selected from an aryl, a substituted aryl, a heterocycle, a substituted heterocycle, an aromatic heterocycle, a substituted aromatic heterocycle, a diazole, a substituted diazole, a C1-C6 alkoxy, C1-C6 alkyl, C1-C6 alkenyl, C1-C6 alkynyl, substituted C1-C6 alkyl, substituted C1-C6 alkenyl substituted C1-C6 alkynyl, and a conjugate group;
    • R3 is selected from an aryl, a substituted aryl, CH3, N(CH3)2, OCH3 and a conjugate group;
    • R4 is selected from OCH3, OH, C1-C6 alkyl, substituted C1-C6 alkyl and a conjugate group; and
    • R5 is selected from OCH3, OH, C1-C6 alkyl, and substituted C1-C6 alkyl.


In certain embodiments, a modified internucleoside linkage comprises a mesyl phosphoramidate linking group having a formula:




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In certain embodiments, a mesyl phosphoramidate internucleoside linkage may comprise a chiral center. In certain embodiments, modified oligonucleotides comprising (Rp) and/or (Sp) mesyl phosphoramidates comprise one or more of the following formulas, respectively, wherein “B” indicates a nucleobase:




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Representative internucleoside linkages having a chiral center include but are not limited to alkylphosphonates and phosphorothioates. Modified oligonucleotides comprising internucleoside linkages having a chiral center can be prepared as populations of modified oligonucleotides comprising stereorandom internucleoside linkages, or as populations of modified oligonucleotides comprising phosphorothioate linkages in particular stereochemical configurations. In certain embodiments, populations of modified oligonucleotides comprise phosphorothioate internucleoside linkages wherein all of the phosphorothioate internucleoside linkages are stereorandom. Such modified oligonucleotides can be generated using synthetic methods that result in random selection of the stereochemical configuration of each phosphorothioate linkage. Nonetheless, as is well understood by those of skill in the art, each individual phosphorothioate of each individual oligonucleotide molecule has a defined stereoconfiguration. In certain embodiments, populations of modified oligonucleotides are enriched for modified oligonucleotides comprising one or more particular phosphorothioate internucleoside linkages in a particular, independently selected stereochemical configuration. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 65% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 70% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 80% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 90% of the molecules in the population. In certain embodiments, the particular configuration of the particular phosphorothioate linkage is present in at least 99% of the molecules in the population. Such chirally enriched populations of modified oligonucleotides can be generated using synthetic methods known in the art, e.g., methods described in Oka et al., JACS 125, 8307 (2003), Wan et al. Nuc. Acid. Res. 42, 13456 (2014), and WO 2017/015555. In certain embodiments, a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one indicated phosphorothioate in the (Sp) configuration. In certain embodiments, a population of modified oligonucleotides is enriched for modified oligonucleotides having at least one phosphorothioate in the (Rp) configuration. In certain embodiments, modified oligonucleotides comprising (Rp) and/or (Sp) phosphorothioates comprise one or more of the following formulas, respectively, wherein “B” indicates a nucleobase:




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Unless otherwise indicated, chiral internucleoside linkages of modified oligonucleotides described herein can be stereorandom or in a particular stereochemical configuration.


Neutral internucleoside linkages include, without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH2—N(CH3)—O—5′), amide-3 (3′-CH2—C(═O)—N(H)-5′), amide-4 (3′-CH2—N(H)—C(═O)-5′), formacetal (3′-O—CH2—O-5′), methoxypropyl, and thioformacetal (3′-S—CH2—O—5′). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH2 component parts.


In certain embodiments, modified oligonucleotides comprise one or more inverted nucleoside, as shown below:




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wherein each Bx independently represents any nucleobase.


In certain embodiments, an inverted nucleoside is terminal (i.e., the last nucleoside on one end of an oligonucleotide) and so only one internucleoside linkage depicted above will be present. In certain such embodiments, additional features (such as a conjugate group) may be attached to the inverted nucleoside. Such terminal inverted nucleosides can be attached to either or both ends of an oligonucleotide.


In certain embodiments, such groups lack a nucleobase and are referred to herein as inverted sugar moieties. In certain embodiments, an inverted sugar moiety is terminal (i.e., attached to the last nucleoside on one end of an oligonucleotide) and so only one internucleoside linkage above will be present. In certain such embodiments, additional features (such as a conjugate group) may be attached to the inverted sugar moiety. Such terminal inverted sugar moieties can be attached to either or both ends of an oligonucleotide.


In certain embodiments, nucleic acids can be linked 2′ to 5′ rather than the standard 3′ to 5′ linkage. Such a linkage is illustrated below.




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wherein each Bx represents any nucleobase.


B. Certain Motifs

In certain embodiments, modified oligonucleotides comprise one or more modified nucleosides comprising a modified sugar moiety. In certain embodiments, modified oligonucleotides comprise one or more modified nucleosides comprising a modified nucleobase. In certain embodiments, modified oligonucleotides comprise one or more modified internucleoside linkage. In such embodiments, the modified, unmodified, and differently modified sugar moieties, nucleobases, and/or internucleoside linkages of a modified oligonucleotide define a pattern or motif. In certain embodiments, the patterns of sugar moieties, nucleobases, and internucleoside linkages are each independent of one another. Thus, a modified oligonucleotide may be described by its sugar motif, nucleobase motif and/or internucleoside linkage motif (as used herein, nucleobase motif describes the modifications to the nucleobases independent of the sequence of nucleobases).


1. Certain Sugar Motifs

In certain embodiments, oligonucleotides comprise one or more type of modified sugar and/or unmodified sugar moiety arranged along the oligonucleotide or region thereof in a defined pattern or sugar motif. In certain instances, such sugar motifs include but are not limited to any of the sugar modifications discussed herein.


In certain embodiments, modified oligonucleotides comprise or consist of a region having a gapmer motif, which is defined by two external regions or “wings” and a central or internal region or “gap.” The three regions of a gapmer motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap. Specifically, at least the sugar moieties of the nucleosides of each wing that are closest to the gap (the 3′-most nucleoside of the 5′-wing and the 5′-most nucleoside of the 3′-wing) differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap (i.e., the wing/gap junction). In certain embodiments, the sugar moieties within the gap are the same as one another. In certain embodiments, the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap. In certain embodiments, the sugar motifs of the two wings are the same as one another (symmetric gapmer). In certain embodiments, the sugar motif of the 5′-wing differs from the sugar motif of the 3′-wing (asymmetric gapmer).


In certain embodiments, the wings of a gapmer comprise 1-6 nucleosides. In certain embodiments, each nucleoside of each wing of a gapmer is a modified nucleoside. In certain embodiments, at least one nucleoside of each wing of a gapmer is a modified nucleoside. In certain embodiments, at least two nucleosides of each wing of a gapmer are modified nucleosides. In certain embodiments, at least three nucleosides of each wing of a gapmer are modified nucleosides. In certain embodiments, at least four nucleosides of each wing of a gapmer are modified nucleosides. In certain embodiments, at least five nucleosides of each wing of a gapmer comprises a modified sugar moiety.


In certain embodiments, the gap of a gapmer comprises 7-12 nucleosides. In certain embodiments, each nucleoside of the gap of a gapmer comprises a 2′-β-D-deoxyribosyl sugar moiety. In certain embodiments, at least one nucleoside of the gap of a gapmer comprises a modified sugar moiety.


In certain embodiments, the gapmer is a deoxy gapmer. In certain embodiments, the nucleosides on the gap side of each wing/gap junction comprise 2′-β-D-deoxyribosyl sugar moieties and the nucleosides on the wing sides of each wing/gap junction comprise modified sugar moieties. In certain embodiments, each nucleoside of the gap comprise 2′-β-D-deoxyribosyl sugar moieties. In certain embodiments, each nucleoside of each wing of a gapmer comprises a modified sugar moiety. In certain embodiments, at least one nucleoside of the gap of a gapmer comprises a modified sugar moiety. In certain embodiments, at least one nucleoside of the gap of a gapmer comprises a 2′-OMe or a 2′-cEt sugar moiety.


In certain embodiments, modified oligonucleotides comprise or consist of a region having a fully modified sugar motif. In such embodiments, each nucleoside of the fully modified region of the modified oligonucleotide comprises a modified sugar moiety. In certain embodiments, each nucleoside of the entire modified oligonucleotide comprises a modified sugar moiety. In certain embodiments, modified oligonucleotides comprise or consist of a region having a fully modified sugar motif, wherein each nucleoside within the fully modified region comprises the same modified sugar moiety, referred to herein as a uniformly modified sugar motif. In certain embodiments, a fully modified oligonucleotide is a uniformly modified oligonucleotide. In certain embodiments, each nucleoside of a uniformly modified comprises the same 2′-modification.


Herein, the lengths (number of nucleosides) of the three regions of a gapmer may be provided using the notation [# of nucleosides in the 5′-wing]−[# of nucleosides in the gap]−[# of nucleosides in the 3′-wing]. Thus, a 5-10-5 gapmer consists of 5 linked nucleosides in each wing and 10 linked nucleosides in the gap. Where such nomenclature is followed by a specific modification, that modification is the modification in each sugar moiety of each wing and the gap nucleosides comprise unmodified deoxynucleosides sugars. Thus, a 5-10-5 MOE gapmer consists of 5 linked MOE modified nucleosides in the 5′-wing, 10 linked deoxynucleosides in the gap, and 5 linked MOE nucleosides in the 3′-wing.


In certain embodiments, modified oligonucleotides are 5-10-5 MOE gapmers. In certain embodiments, modified oligonucleotides are 3-10-3 BNA gapmers. In certain embodiments, modified oligonucleotides are 3-10-3 cEt gapmers. In certain embodiments, modified oligonucleotides are 3-10-3 LNA gapmers. In certain embodiments, modified oligonucleotides are 5-8-5 MOE gapmers. In certain embodiments, modified oligonucleotides are 6-10-4 MOE gapmers.


A mixed wing gapmer has at least two different modified sugars in the 5′ and/or 3′ wing. In certain embodiments, modified oligonucleotides are 4-8-5 mixed wing gapmers which has at least two different sugar moieties in the 5′- and/or the 3′-wing. In certain embodiments, the at least two different sugar moieties are selected from 2′-MOE and 2′-cEt sugar moieties.


In certain embodiments, modified oligonucleotides have a sugar motif selected from the following: 5′-eekkddddddddkkeee-3′, 5′-ekekddddddddkekee-3′, 5′-eeeeeddddddddddeeeee-3′, 5′-eeeeddddddddkkeee-3′, 5′-eeeeeddddddddeeeee-3′, and 5′-eeeeeeddddddddddeeee-3′, wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, each “e” represents a 2′-MOE sugar moiety, and each “k” represents a cEt sugar moiety.


2. Certain Nucleobase Motifs

In certain embodiments, oligonucleotides comprise modified and/or unmodified nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or motif. In certain embodiments, each nucleobase is modified. In certain embodiments, none of the nucleobases are modified. In certain embodiments, each purine or each pyrimidine is modified. In certain embodiments, each adenine is modified. In certain embodiments, each guanine is modified. In certain embodiments, each thymine is modified. In certain embodiments, each uracil is modified. In certain embodiments, each cytosine is modified. In certain embodiments, some or all of the cytosine nucleobases in a modified oligonucleotide are 5-methylcytosines. In certain embodiments, all of the cytosine nucleobases are 5-methylcytosines and all of the other nucleobases of the modified oligonucleotide are unmodified nucleobases.


In certain embodiments, modified oligonucleotides comprise a block of modified nucleobases. In certain such embodiments, the block is at the 3′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 3′-end of the oligonucleotide. In certain embodiments, the block is at the 5′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleosides of the 5′-end of the oligonucleotide.


In certain embodiments, oligonucleotides having a gapmer motif comprise a nucleoside comprising a modified nucleobase. In certain such embodiments, one nucleoside comprising a modified nucleobase is in the central gap of an oligonucleotide having a gapmer motif. In certain such embodiments, the sugar moiety of said nucleoside is a 2′-β-D-deoxyribosyl sugar moiety. In certain embodiments, the modified nucleobase is selected from: a 2-thiopyrimidine and a 5-propynepyrimidine.


3. Certain Internucleoside Linkage Motifs

In certain embodiments, oligonucleotides comprise modified and/or unmodified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or motif. In certain embodiments, each internucleoside linking group is a phosphodiester internucleoside linkage (P═O). In certain embodiments, each internucleoside linking group of a modified oligonucleotide is a phosphorothioate internucleoside linkage (P═S). In certain embodiments, each internucleoside linkage of a modified oligonucleotide is independently selected from a phosphorothioate internucleoside linkage and phosphodiester internucleoside linkage. In certain embodiments, each phosphorothioate internucleoside linkage is independently selected from a stereorandom phosphorothioate a (Sp) phosphorothioate, and a (Rp) phosphorothioate.


In certain embodiments, the sugar motif of a modified oligonucleotide is a gapmer and the internucleoside linkages within the gap are all modified. In certain embodiments, some or all of the internucleoside linkages in the wings are unmodified phosphodiester internucleoside linkages. In certain embodiments, the terminal internucleoside linkages are modified. In certain embodiments, the sugar motif of a modified oligonucleotide is a gapmer, and the internucleoside linkage motif comprises at least one phosphodiester internucleoside linkage in at least one wing, wherein the at least one phosphodiester linkage is not a terminal internucleoside linkage, and the remaining internucleoside linkages are phosphorothioate internucleoside linkages. In certain such embodiments, all of the phosphorothioate linkages are stereorandom. In certain embodiments, all of the phosphorothioate linkages in the wings are (Sp) phosphorothioates, and the gap comprises at least one Sp, Sp, or Rp motif. In certain embodiments, populations of modified oligonucleotides are enriched for modified oligonucleotides comprising such internucleoside linkage motifs.


In certain embodiments, modified oligonucleotides have an internucleoside linkage motif selected from: 5′-soosssssssssooss-3′, 5′-sooosssssssssssooss-3′, 5′-sooosssssssssssooos-3′, 5′-sossssssssssssssoss-3′, 5′-ssoosssssssssssooss-3′, 5′-sooosssssssssooss-3′, 5′-sossssssssssssoss-3′, and 5′-sooooossssssssssoss-3′. In certain embodiments, each “s” represents a phosphorothioate internucleoside linkage and each “o” represents a phosphodiester internucleoside linkage.


In certain embodiments, modified oligonucleotides have an internucleoside linkage motif comprising one or more mesyl phosphoramidate linking groups. In certain embodiments, one or more phosphorothioate internucleoside linkages or one or more phosphodiester internucleoside linkages of the internucleoside linkage motifs herein is substituted with a mesyl phosphoramidates linking group.


C. Certain Lengths

It is possible to increase or decrease the length of an oligonucleotide without eliminating activity. For example, in Woolf et al. (Proc. Natl. Acad. Sci. USA 89:7305-7309, 1992), a series of oligonucleotides 13-25 nucleobases in length were tested for their ability to induce cleavage of a target RNA in an oocyte injection model. Oligonucleotides 25 nucleobases in length with 8 or 11 mismatch bases near the ends of the oligonucleotides were able to direct specific cleavage of the target RNA, albeit to a lesser extent than the oligonucleotides that contained no mismatches. Similarly, target specific cleavage was achieved using 13 nucleobase oligonucleotides, including those with 1 or 3 mismatches.


In certain embodiments, oligonucleotides (including modified oligonucleotides) can have any of a variety of ranges of lengths. In certain embodiments, oligonucleotides consist of X to Y linked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number nucleosides in the range. In certain such embodiments, X and Y are each independently selected from 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50; provided that X≤Y. For example, in certain embodiments, oligonucleotides consist of 12 to 13, 12 to 14, 12 to 15, 12 to 16, 12 to 17, 12 to 18, 12 to 19, 12 to 20, 12 to 21, 12 to 22, 12 to 23, 12 to 24, 12 to 25, 12 to 26, 12 to 27, 12 to 28, 12 to 29, 12 to 30, 13 to 14, 13 to 15, 13 to 16, 13 to 17, 13 to 18, 13 to 19, 13 to 20, 13 to 21, 13 to 22, 13 to 23, 13 to 24, 13 to 25, 13 to 26, 13 to 27, 13 to 28, 13 to 29, 13 to 30, 14 to 15, 14 to 16, 14 to 17, 14 to 18, 14 to 19, 14 to 20, 14 to 21, 14 to 22, 14 to 23, 14 to 24, 14 to 25, 14 to 26, 14 to 27, 14 to 28, 14 to 29, 14 to 30, 15 to 16, 15 to 17, 15 to 18, 15 to 19, 15 to 20, 15 to 21, 15 to 22, 15 to 23, 15 to 24, 15 to 25, 15 to 26, 15 to 27, 15 to 28, 15 to 29, 15 to 30, 16 to 17, 16 to 18, 16 to 19, 16 to 20, 16 to 21, 16 to 22, 16 to 23, 16 to 24, 16 to 25, 16 to 26, 16 to 27, 16 to 28, 16 to 29, 16 to 30, 17 to 18, 17 to 19, 17 to 20, 17 to 21, 17 to 22, 17 to 23, 17 to 24, 17 to 25, 17 to 26, 17 to 27, 17 to 28, 17 to 29, 17 to 30, 18 to 19, 18 to 20, 18 to 21, 18 to 22, 18 to 23, 18 to 24, 18 to 25, 18 to 26, 18 to 27, 18 to 28, 18 to 29, 18 to 30, 19 to 20, 19 to 21, 19 to 22, 19 to 23, 19 to 24, 19 to 25, 19 to 26, 19 to 29, 19 to 28, 19 to 29, 19 to 30, 20 to 21, 20 to 22, 20 to 23, 20 to 24, 20 to 25, 20 to 26, 20 to 27, 20 to 28, 20 to 29, 20 to 30, 21 to 22, 21 to 23, 21 to 24, 21 to 25, 21 to 26, 21 to 27, 21 to 28, 21 to 29, 21 to 30, 22 to 23, 22 to 24, 22 to 25, 22 to 26, 22 to 27, 22 to 28, 22 to 29, 22 to 30, 23 to 24, 23 to 25, 23 to 26, 23 to 27, 23 to 28, 23 to 29, 23 to 30, 24 to 25, 24 to 26, 24 to 27, 24 to 28, 24 to 29, 24 to 30, 25 to 26, 25 to 27, 25 to 28, 25 to 29, 25 to 30, 26 to 27, 26 to 28, 26 to 29, 26 to 30, 27 to 28, 27 to 29, 27 to 30, 28 to 29, 28 to 30, or 29 to 30 linked nucleosides.


In certain embodiments, oligonucleotides consist of 16 linked nucleosides. In certain embodiments, oligonucleotides consist of 17 linked nucleosides. In certain embodiments, oligonucleotides consist of 18 linked nucleosides. In certain embodiments, oligonucleotides consist of 19 linked nucleosides. In certain embodiments, oligonucleotides consist of 20 linked nucleosides.


D. Certain Modified Oligonucleotides

In certain embodiments, the above modifications (sugar, nucleobase, internucleoside linkage) are incorporated into a modified oligonucleotide. In certain embodiments, modified oligonucleotides are characterized by their modification motifs and overall lengths. In certain embodiments, such parameters are each independent of one another. Thus, unless otherwise indicated, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications. For example, the internucleoside linkages within the wing regions of a sugar gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region of the sugar motif. Likewise, such sugar gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications. Unless otherwise indicated, all modifications are independent of nucleobase sequence.


E. Certain Populations of Modified Oligonucleotides

Populations of modified oligonucleotides in which all of the modified oligonucleotides of the population have the same molecular formula can be stereorandom populations or chirally enriched populations. All of the chiral centers of all of the modified oligonucleotides are stereorandom in a stereorandom population. In a chirally enriched population, at least one particular chiral center is not stereorandom in the modified oligonucleotides of the population. In certain embodiments, the modified oligonucleotides of a chirally enriched population are enriched for β-D ribosyl sugar moieties, and all of the phosphorothioate internucleoside linkages are stereorandom. In certain embodiments, the modified oligonucleotides of a chirally enriched population are enriched for both β-D ribosyl sugar moieties and at least one, particular phosphorothioate internucleoside linkage in a particular stereochemical configuration.


F. Nucleobase Sequence

In certain embodiments, oligonucleotides (unmodified or modified oligonucleotides) are further described by their nucleobase sequence. In certain embodiments oligonucleotides have a nucleobase sequence that is complementary to a second oligonucleotide or an identified reference nucleic acid, such as a target nucleic acid. In certain such embodiments, a region of an oligonucleotide has a nucleobase sequence that is complementary to a second oligonucleotide or an identified reference nucleic acid, such as a target nucleic acid. In certain embodiments, the nucleobase sequence of a region or entire length of an oligonucleotide is at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% complementary to the second oligonucleotide or nucleic acid, such as a target nucleic acid.


II. Certain Oligomeric Compounds

In certain embodiments, provided herein are oligomeric compounds, which consist of an oligonucleotide (modified or unmodified) and optionally one or more conjugate groups and/or terminal groups. Conjugate groups consist of one or more conjugate moiety and a conjugate linker which links the conjugate moiety to the oligonucleotide. Conjugate groups may be attached to either or both ends of an oligonucleotide and/or at any internal position. In certain embodiments, conjugate groups are attached to the 2′-position of a nucleoside of a modified oligonucleotide. In certain embodiments, conjugate groups that are attached to either or both ends of an oligonucleotide are terminal groups. In certain such embodiments, conjugate groups or terminal groups are attached at the 3′ and/or 5′-end of oligonucleotides. In certain such embodiments, conjugate groups (or terminal groups) are attached at the 3′-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 3′-end of oligonucleotides. In certain embodiments, conjugate groups (or terminal groups) are attached at the 5′-end of oligonucleotides. In certain embodiments, conjugate groups are attached near the 5′-end of oligonucleotides.


Examples of terminal groups include but are not limited to conjugate groups, capping groups, phosphate moieties, protecting groups, modified or unmodified nucleosides, and two or more nucleosides that are independently modified or unmodified.


A. Certain Conjugate Groups

In certain embodiments, oligonucleotides are covalently attached to one or more conjugate groups. In certain embodiments, conjugate groups modify one or more properties of the attached oligonucleotide, including but not limited to pharmacodynamics, pharmacokinetics, stability, binding, absorption, tissue distribution, cellular distribution, cellular uptake, charge and clearance.


In certain embodiments, conjugation of one or more carbohydrate moieties to a modified oligonucleotide can optimize one or more properties of the modified oligonucleotide. In certain embodiments, the carbohydrate moiety is attached to a modified subunit of the modified oligonucleotide. For example, the ribose sugar of one or more ribonucleotide subunits of a modified oligonucleotide can be replaced with another moiety, e.g. a non-carbohydrate (preferably cyclic) carrier to which is attached a carbohydrate ligand. A ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is referred to herein as a ribose replacement modification subunit (RRMS), which is a modified sugar moiety. A cyclic carrier may be a carbocyclic ring system, i.e., one or more ring atoms may be a heteroatom, e.g., nitrogen, oxygen, sulphur. The cyclic carrier may be a monocyclic ring system, or may contain two or more rings, e.g. fused rings. The cyclic carrier may be a fully saturated ring system, or it may contain one or more double bonds. In certain embodiments, the modified oligonucleotide is a gapmer.


In certain embodiments, conjugate groups impart a new property on the attached oligonucleotide, e.g., fluorophores or reporter groups that enable detection of the oligonucleotide. Certain conjugate groups and conjugate moieties have been described previously, for example: cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Lett., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., do-decan-diol or undecyl residues (Saison-Behmoaras et al., EMBO J, 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J Pharmacol. Exp. Ther., 1996, 277, 923-937), a tocopherol group (Nishina et al., Molecular Therapy Nucleic Acids, 2015, 4, e220; and Nishina et al., Molecular Therapy, 2008, 16, 734-740), or a GalNAc cluster (e.g., WO2014/179620).


In certain embodiments, the conjugate group may comprise a conjugate moiety selected from any of a C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, C5 alkyl, C22 alkenyl, C20 alkenyl, C16 alkenyl, C10 alkenyl, C21 alkenyl, C19 alkenyl, C18 alkenyl, C15 alkenyl, C14 alkenyl, C13 alkenyl, C12 alkenyl, C11 alkenyl, C9 alkenyl, C8 alkenyl, C7 alkenyl, C6 alkenyl, or C5 alkenyl.


In certain embodiments, the conjugate group may comprise a conjugate moiety selected from any of a C22 alkyl, C20 alkyl, C16 alkyl, C10 alkyl, C21 alkyl, C19 alkyl, C18 alkyl, C15 alkyl, C14 alkyl, C13 alkyl, C12 alkyl, C11 alkyl, C9 alkyl, C8 alkyl, C7 alkyl, C6 alkyl, or C5 alkyl, where the alkyl chain has one or more unsaturated bonds.


In certain embodiments, a conjugate group is a lipid having the following structure:




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1. Conjugate Moieties

Conjugate moieties include, without limitation, intercalators, reporter molecules, polyamines, polyamides, peptides, carbohydrates, antibodies, vitamin moieties, polyethylene glycols, thioethers, polyethers, cholesterols, thiocholesterols, cholic acid moieties, folate, lipids, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, adamantane, acridine, fluoresceins, rhodamines, coumarins, fluorophores, and dyes.


In certain embodiments, a conjugate moiety comprises an active drug substance, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, fingolimod, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.


2. Conjugate Linkers

Conjugate moieties are attached to oligonucleotides through conjugate linkers. In certain oligomeric compounds, the conjugate linker is a single chemical bond (i.e., the conjugate moiety is attached directly to an oligonucleotide through a single bond). In certain embodiments, the conjugate linker comprises a chain structure, such as a hydrocarbyl chain, or an oligomer of repeating units such as ethylene glycol, nucleosides, or amino acid units.


In certain embodiments, a conjugate linker comprises pyrrolidine.


In certain embodiments, a conjugate linker comprises one or more groups selected from alkyl, amino, oxo, amide, disulfide, polyethylene glycol, ether, thioether, and hydroxylamino. In certain such embodiments, the conjugate linker comprises groups selected from alkyl, amino, oxo, amide and ether groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and amide groups. In certain embodiments, the conjugate linker comprises groups selected from alkyl and ether groups. In certain embodiments, the conjugate linker comprises at least one phosphorus moiety. In certain embodiments, the conjugate linker comprises at least one phosphate group. In certain embodiments, the conjugate linker includes at least one neutral linking group.


In certain embodiments, conjugate linkers, including the conjugate linkers described above, are bifunctional linking moieties, e.g., those known in the art to be useful for attaching conjugate groups to parent compounds, such as the oligonucleotides provided herein. In general, a bifunctional linking moiety comprises at least two functional groups. One of the functional groups is selected to bind to a particular site on a parent compound and the other is selected to bind to a conjugate group. Examples of functional groups used in a bifunctional linking moiety include but are not limited to electrophiles for reacting with nucleophilic groups and nucleophiles for reacting with electrophilic groups. In certain embodiments, bifunctional linking moieties comprise one or more groups selected from amino, hydroxyl, carboxylic acid, thiol, alkyl, alkenyl, and alkynyl.


Examples of conjugate linkers include but are not limited to pyrrolidine, 8-amino-3,6-dioxaoctanoic acid (ADO), succinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and 6-aminohexanoic acid (AHEX or AHA). Other conjugate linkers include but are not limited to substituted or unsubstituted C1-C10 alkyl, substituted or unsubstituted C2-C10 alkenyl or substituted or unsubstituted C2-C10 alkynyl, wherein a nonlimiting list of preferred substituent groups includes hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl.


In certain embodiments, conjugate linkers comprise 1-10 linker-nucleosides. In certain embodiments, conjugate linkers comprise 2-5 linker-nucleosides. In certain embodiments, conjugate linkers comprise exactly 3 linker-nucleosides. In certain embodiments, conjugate linkers comprise the TCA motif. In certain embodiments, such linker-nucleosides are modified nucleosides. In certain embodiments such linker-nucleosides comprise a modified sugar moiety. In certain embodiments, linker-nucleosides are unmodified. In certain embodiments, linker-nucleosides comprise an optionally protected heterocyclic base selected from a purine, substituted purine, pyrimidine or substituted pyrimidine. In certain embodiments, a cleavable moiety is a nucleoside selected from uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N-benzoyl-5-methyl cytosine, adenine, 6-N-benzoyladenine, guanine and 2-N-isobutyrylguanine. It is typically desirable for linker-nucleosides to be cleaved from the oligomeric compound after it reaches a target tissue. Accordingly, linker-nucleosides are typically linked to one another and to the remainder of the oligomeric compound through cleavable bonds. In certain embodiments, such cleavable bonds are phosphodiester bonds.


Herein, linker-nucleosides are not considered to be part of the oligonucleotide. Accordingly, in embodiments in which an oligomeric compound comprises an oligonucleotide consisting of a specified number or range of linked nucleosides and/or a specified percent complementarity to a reference nucleic acid and the oligomeric compound also comprises a conjugate group comprising a conjugate linker comprising linker-nucleosides, those linker-nucleosides are not counted toward the length of the oligonucleotide and are not used in determining the percent complementarity of the oligonucleotide for the reference nucleic acid. For example, an oligomeric compound may comprise (1) a modified oligonucleotide consisting of 8-30 nucleosides and (2) a conjugate group comprising 1-10 linker-nucleosides that are contiguous with the nucleosides of the modified oligonucleotide. The total number of contiguous linked nucleosides in such an oligomeric compound is more than 30. Alternatively, an oligomeric compound may comprise a modified oligonucleotide consisting of 8-30 nucleosides and no conjugate group. The total number of contiguous linked nucleosides in such an oligomeric compound is no more than 30. Unless otherwise indicated conjugate linkers comprise no more than 10 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 5 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 3 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 2 linker-nucleosides. In certain embodiments, conjugate linkers comprise no more than 1 linker-nucleoside.


In certain embodiments, it is desirable for a conjugate group to be cleaved from the oligonucleotide. For example, in certain circumstances oligomeric compounds comprising a particular conjugate moiety are better taken up by a particular cell type, but once the oligomeric compound has been taken up, it is desirable that the conjugate group be cleaved to release the unconjugated or parent oligonucleotide. Thus, certain conjugate linkers may comprise one or more cleavable moieties. In certain embodiments, a cleavable moiety is a cleavable bond. In certain embodiments, a cleavable moiety is a group of atoms comprising at least one cleavable bond. In certain embodiments, a cleavable moiety comprises a group of atoms having one, two, three, four, or more than four cleavable bonds. In certain embodiments, a cleavable moiety is selectively cleaved inside a cell or subcellular compartment, such as a lysosome. In certain embodiments, a cleavable moiety is selectively cleaved by endogenous enzymes, such as nucleases.


In certain embodiments, a cleavable bond is selected from among: an amide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, or a disulfide. In certain embodiments, a cleavable bond is one or both of the esters of a phosphodiester. In certain embodiments, a cleavable moiety comprises a phosphate or phosphodiester. In certain embodiments, the cleavable moiety is a phosphate linkage between an oligonucleotide and a conjugate moiety or conjugate group.


In certain embodiments, a cleavable moiety comprises or consists of one or more linker-nucleosides. In certain such embodiments, the one or more linker-nucleosides are linked to one another and/or to the remainder of the oligomeric compound through cleavable bonds. In certain embodiments, such cleavable bonds are unmodified phosphodiester bonds. In certain embodiments, a cleavable moiety is 2′-deoxynucleoside that is attached to either the 3′ or 5′-terminal nucleoside of an oligonucleotide by a phosphate internucleoside linkage and covalently attached to the remainder of the conjugate linker or conjugate moiety by a phosphate or phosphorothioate linkage. In certain such embodiments, the cleavable moiety is 2′-deoxyadenosine.


3. Cell-Targeting Moieties

In certain embodiments, a conjugate group comprises a cell-targeting moiety. In certain embodiments, a conjugate group has the general formula:




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    • wherein n is from 1 to about 3, m is 0 when n is 1, m is 1 when n is 2 or greater, j is 1 or 0, and k is 1 or 0.





In certain embodiments, n is 1, j is 1 and k is 0. In certain embodiments, n is 1, j is 0 and k is 1. In certain embodiments, n is 1, j is 1 and k is 1. In certain embodiments, n is 2, j is 1 and k is 0. In certain embodiments, n is 2, j is 0 and k is 1. In certain embodiments, n is 2, j is 1 and k is 1. In certain embodiments, n is 3, j is 1 and k is 0. In certain embodiments, n is 3, j is 0 and k is 1. In certain embodiments, n is 3, j is 1 and k is 1.


In certain embodiments, conjugate groups comprise cell-targeting moieties that have at least one tethered ligand. In certain embodiments, cell-targeting moieties comprise two tethered ligands covalently attached to a branching group. In certain embodiments, cell-targeting moieties comprise three tethered ligands covalently attached to a branching group.


In certain embodiments, each ligand of a cell-targeting moiety has an affinity for at least one type of receptor on a target cell. In certain embodiments, each ligand has an affinity for at least one type of receptor on the surface of a mammalian liver cell. In certain embodiments, each ligand has an affinity for the hepatic asialoglycoprotein receptor (ASGP-R). In certain embodiments, each ligand is a carbohydrate.


In certain embodiments, a conjugate group comprises a cell-targeting conjugate moiety. In certain embodiments, a conjugate group has the general formula:




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    • wherein n is from 1 to about 3, m is 0 when n is 1, m is 1 when n is 2 or greater, j is 1 or 0, and k is 1 or 0.





In certain embodiments, n is 1, j is 1 and k is 0. In certain embodiments, n is 1, j is 0 and k is 1. In certain embodiments, n is 1, j is 1 and k is 1. In certain embodiments, n is 2, j is 1 and k is 0. In certain embodiments, n is 2, j is 0 and k is 1. In certain embodiments, n is 2, j is 1 and k is 1. In certain embodiments, n is 3, j is 1 and k is 0. In certain embodiments, n is 3, j is 0 and k is 1. In certain embodiments, n is 3, j is 1 and k is 1.


In certain embodiments, conjugate groups comprise cell-targeting moieties that have at least one tethered ligand. In certain embodiments, cell-targeting moieties comprise two tethered ligands covalently attached to a branching group. In certain embodiments, cell-targeting moieties comprise three tethered ligands covalently attached to a branching group.


In certain embodiments, the cell-targeting moiety targets neurons. In certain embodiments, the cell-targeting moiety targets a neurotransmitter receptor. In certain embodiments, the cell targeting moiety targets a neurotransmitter transporter. In certain embodiments, the cell targeting moiety targets a GABA transporter. See e.g., WO 2011/131693, WO 2014/064257.


In certain embodiments, conjugate groups comprise cell-targeting moieties that have affinities for transferrin receptor (TfR) (also referred to herein as TfR1 and CD71). In certain embodiments, a conjugate group described herein comprises an anti-TfR1 antibody or fragment thereof. In certain embodiments, the conjugate group comprises a protein or peptide capable of binding TfR1. In certain embodiments, the conjugate group comprises an aptamer capable of binding TfR1. In certain embodiments, the anti-TfR1 antibody or fragment thereof can be any known in the art including but not limited to those described in WO1991/004753; WO2013/103800; WO2014/144060; WO2016/081643; WO2016/179257; WO2016/207240; WO2017/221883; WO2018/129384; WO2018/124121; WO2019/151539; WO2020/132584; WO2020/028864; U.S. Pat. Nos. 7,208,174; 9,034,329; and 10,550,188. In certain embodiments, a fragment of an anti-TfR1 antibody is F(ab′)2, Fab, Fab′, Fv, or scFv.


In certain embodiments, the conjugate group comprises a protein or peptide capable of binding TfR1. In certain embodiments, the protein or peptide capable of binding TfR1 can be any known in the art including but not limited to those described in WO2019/140050; WO2020/037150; WO2020/124032; and U.S. Pat. No. 10,138,483.


In certain embodiments, the conjugate group comprises an aptamer capable of binding TfR1. In certain embodiments, the aptamer capable of binding TfR1 can be any known in the art including but not limited to those described in WO2013/163303; WO2019/033051; and WO2020/245198.


B. Certain Terminal Groups

In certain embodiments, oligomeric compounds comprise one or more terminal groups. In certain such embodiments, oligomeric compounds comprise a stabilized 5′-phophate. Stabilized 5′-phosphates include, but are not limited to 5′-phosphanates, including, but not limited to 5′-vinylphosphonates. In certain embodiments, terminal groups comprise one or more abasic nucleosides and/or inverted nucleosides. In certain embodiments, terminal groups comprise one or more 2′-linked nucleosides. In certain such embodiments, the 2′-linked nucleoside is an abasic nucleoside.


III. Oligomeric Duplexes

In certain embodiments, oligomeric compounds described herein comprise an oligonucleotide, having a nucleobase sequence complementary to that of a target nucleic acid. In certain embodiments, an oligomeric compound is paired with a second oligomeric compound to form an oligomeric duplex. Such oligomeric duplexes comprise a first oligomeric compound having a region complementary to a target nucleic acid and a second oligomeric compound having a region complementary to the first oligomeric compound. In certain embodiments, the first oligomeric compound of an oligomeric duplex comprises or consists of (1) a modified or unmodified oligonucleotide and optionally a conjugate group and (2) a second modified or unmodified oligonucleotide and optionally a conjugate group. Either or both oligomeric compounds of an oligomeric duplex may comprise a conjugate group. The oligonucleotides of each oligomeric compound of an oligomeric duplex may include non-complementary overhanging nucleosides.


IV. Antisense Activity

In certain embodiments, oligomeric compounds and oligomeric duplexes are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity; such oligomeric compounds and oligomeric duplexes are antisense compounds. In certain embodiments, antisense compounds have antisense activity when they reduce or inhibit the amount or activity of a target nucleic acid by 25% or more in the standard in vitro assay. In certain embodiments, antisense compounds selectively affect one or more target nucleic acid. Such antisense compounds comprise a nucleobase sequence that hybridizes to one or more target nucleic acid, resulting in one or more desired antisense activity and does not hybridize to one or more non-target nucleic acid or does not hybridize to one or more non-target nucleic acid in such a way that results in significant undesired antisense activity.


In certain antisense activities, hybridization of an antisense compound to a target nucleic acid results in recruitment of a protein that cleaves the target nucleic acid. For example, certain antisense compounds result in RNase H mediated cleavage of the target nucleic acid. RNase H is a cellular endonuclease that cleaves the RNA strand of an RNA:DNA duplex. The DNA in such an RNA:DNA duplex need not be unmodified DNA. In certain embodiments, described herein are antisense compounds that are sufficiently “DNA-like” to elicit RNase H activity. In certain embodiments, one or more non-DNA-like nucleoside in the gap of a gapmer is tolerated.


In certain antisense activities, an antisense compound or a portion of an antisense compound is loaded into an RNA-induced silencing complex (RISC), ultimately resulting in cleavage of the target nucleic acid. For example, certain antisense compounds result in cleavage of the target nucleic acid by Argonaute. Antisense compounds that are loaded into RISC are RNAi agents. RNAi agents may be double-stranded (siRNA or dsRNAi) or single-stranded (ssRNAi).


In certain embodiments, hybridization of an antisense compound to a target nucleic acid does not result in recruitment of a protein that cleaves that target nucleic acid. In certain embodiments, hybridization of the antisense compound to the target nucleic acid results in alteration of splicing of the target nucleic acid. In certain embodiments, hybridization of an antisense compound to a target nucleic acid results in inhibition of a binding interaction between the target nucleic acid and a protein or other nucleic acid. In certain embodiments, hybridization of an antisense compound to a target nucleic acid results in alteration of translation of the target nucleic acid.


Antisense activities may be observed directly or indirectly. In certain embodiments, observation or detection of an antisense activity involves observation or detection of a change in an amount of a target nucleic acid or protein encoded by such target nucleic acid, a change in the ratio of splice variants of a nucleic acid or protein and/or a phenotypic change in a cell or subject.


V. Certain Target Nucleic Acids

In certain embodiments, oligomeric compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid. In certain embodiments, the target nucleic acid is an endogenous RNA molecule. In certain embodiments, the target nucleic acid encodes a protein. In certain such embodiments, the target nucleic acid is selected from: a mature mRNA and a pre-mRNA, including intronic, exonic and untranslated regions. In certain embodiments, the target RNA is a mature mRNA. In certain embodiments, the target nucleic acid is a pre-mRNA. In certain such embodiments, the target region is entirely within an intron. In certain embodiments, the target region spans an intron/exon junction. In certain embodiments, the target region is at least 50% within an intron. In certain embodiments, the target nucleic acid is the RNA transcriptional product of a retrogene. In certain embodiments, the target nucleic acid is a non-coding RNA. In certain such embodiments, the target non-coding RNA is selected from: a long non-coding RNA, a short non-coding RNA, an intronic RNA molecule.


A. Complementarity/Mismatches to the Target Nucleic Acid

In certain embodiments, oligonucleotides are complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99%, 95%, 90%, 85%, or 80% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide and comprise a region that is 100% or fully complementary to a target nucleic acid. In certain embodiments, the region of full complementarity is from 6 to 20, 10 to 18, or 18 to 20 nucleobases in length.


It is possible to introduce mismatch bases without eliminating activity. For example, Gautschi et al (J. Natl. Cancer Inst. 93:463-471, March 2001) demonstrated the ability of an oligonucleotide having 100% complementarity to the bcl-2 mRNA and having 3 mismatches to the bcl-xL mRNA to reduce the expression of both bcl-2 and bcl-xL in vitro and in vivo. Furthermore, this oligonucleotide demonstrated potent anti-tumor activity in vivo. Maher and Dolnick (Nuc. Acid. Res. 16:3341-3358, 1988) tested a series of tandem 14 nucleobase oligonucleotides, and a 28 and 42 nucleobase oligonucleotides comprised of the sequence of two or three of the tandem oligonucleotides, respectively, for their ability to arrest translation of human DHFR in a rabbit reticulocyte assay. Each of the three 14 nucleobase oligonucleotides alone was able to inhibit translation, albeit at a more modest level than the 28 or 42 nucleobase oligonucleotides.


In certain embodiments, oligonucleotides are complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99%, 95%, 90%, 85%, or 80% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide and comprise a region that is 100% or fully complementary to a target nucleic acid. In certain embodiments, the region of full complementarity is from 6 to 20, 10 to 18, or 18 to 20 nucleobases in length.


In certain embodiments, oligonucleotides comprise one or more mismatched nucleobases relative to the target nucleic acid. In certain embodiments, antisense activity against the target is reduced by such mismatch, but activity against a non-target is reduced by a greater amount. Thus, in certain embodiments selectivity of the oligonucleotide is improved. In certain embodiments, the mismatch is specifically positioned within an oligonucleotide having a gapmer motif. In certain embodiments, the mismatch is at position 1, 2, 3, 4, 5, 6, 7, or 8 from the 5′-end of the gap region. In certain embodiments, the mismatch is at position 9, 8, 7, 6, 5, 4, 3, 2, 1 from the 3′-end of the gap region. In certain embodiments, the mismatch is at position 1, 2, 3, or 4 from the 5′-end of the wing region. In certain embodiments, the mismatch is at position 4, 3, 2, or 1 from the 3′-end of the wing region.


B. HTT

In certain embodiments, oligomeric compounds comprise or consist of an oligonucleotide comprising a region that is complementary to an HTT nucleic acid. In certain embodiments, the HTT nucleic acid has the sequence set forth as GENBANK Accession No. NM_002111.6 (incorporated herein as SEQ ID NO: 1), GENBANK Accession No. NT_006081.17 truncated from nucleotides 462000 to 634000 (incorporated herein as SEQ ID NO: 2), GENBANK Accession No. NM_010414.1 (incorporated herein as SEQ ID NO: 3), the complement of GENBANK Accession No. NW_001109716.1 truncated at nucleotides 698000 to 866000 (incorporated herein as SEQ ID NO: 4), and GENBANK Accession No. NM_024357.2 (incorporated herein as SEQ ID NO: 5).


In certain embodiments an oligomeric compound complementary to any one of SEQ ID NOs: 1-5 is capable of reducing HTT RNA in a cell. In certain embodiments an oligomeric compound complementary to any one of SEQ ID NOs: 1-5 is capable of reducing HTT protein in a cell. In certain embodiments, the cell is in vitro. In certain embodiments, the cell is in a subject. In certain embodiments, the oligomeric compound consists of a modified oligonucleotide. In certain embodiments, an oligomeric compound complementary to any one of SEQ ID NOs: 1-5 is capable of ameliorating one or more symptom or hallmark of a neurodegenerative disease when it is introduced to a cell in a subject. In certain embodiments, the neurodegenerative disease is a repeat expansion disease. In certain embodiments, the repeat expansion disease is selected from myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, various polyglutamine disorders, Fragile X syndrome, and a spinocerebellar ataxia (SCA1, SCA2, SCA3, SCA6, SCA7, SCA8, SCA10, SCA17, or Friedrich's ataxia). In certain embodiments, the symptom or hallmark is brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, suicidal behavior, or a combination thereof.


In certain embodiments, an oligomeric compound complementary to any one of SEQ ID NOs: 1-5 is capable of reducing a detectable amount of HTT RNA in the CSF of a subject after the oligomeric compound is administered to the subject. The detectable amount of HTT RNA may be reduced by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%. In certain embodiments, an oligomeric compound complementary to any one of SEQ ID NOs: 1-5 is capable of reducing a detectable amount of HTT protein in the CSF of the subject when the oligomeric compound is administered to the subject. The detectable amount of HTT protein may be reduced by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%. In certain embodiments, an oligomeric compound complementary to any one of SEQ ID NOs: 1-5 is capable of reducing a detectable amount of mHTT protein in the CSF of the subject when the oligomeric compound is administered to the subject. The detectable amount of mHTT protein may be reduced by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%. In certain embodiments, the oligomeric compound is administered into the CSF of the subject.


C. Certain Target Nucleic Acids in Certain Tissues

In certain embodiments, oligomeric compounds comprise or consist of an oligonucleotide comprising a region that is complementary to a target nucleic acid, wherein the target nucleic acid is expressed in a pharmacologically relevant tissue. In certain embodiments, the pharmacologically relevant tissues are the cells and tissues that comprise the central nervous system (CNS). Such tissues include brain tissues, such as, cortex, substantia nigra, striatum, midbrain, and brainstem and spinal cord.


VI. Certain Methods and Uses

Certain embodiments provided herein relate to methods of reducing or inhibiting HTT expression or activity, which can be useful for treating, preventing, or ameliorating a repeat expansion disease. In certain embodiments, the repeat expansion disease is myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, a polyglutamine disorder, Fragile X syndrome, or a spinocerebellar ataxia. In certain embodiments, the repeat expansion disease is Huntington's disease. In certain embodiments, the repeat expansion disease is a spinocerebellar ataxia.


In certain embodiments, a method comprises administering to a subject an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid. In certain embodiments, the subject has or is at risk for developing a repeat expansion disease. In certain embodiments, the subject has or is at risk for developing myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, a polyglutamine disorder, Fragile X syndrome, or a spinocerebellar ataxia. In certain embodiments, the subject has or is at risk for developing Huntington's disease. In certain embodiments, the subject has or is at risk for developing a spinocerebellar ataxia.


In certain embodiments, a method of ameliorating, treating, or preventing a repeat expansion disease comprises administering to a subject an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid. In certain embodiments, a method of ameliorating or preventing a repeat expansion disease comprises administering to a subject an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid. In certain embodiments, the subject has or is at risk for developing a repeat expansion disease. In certain embodiments, the subject has myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, a polyglutamine disorder, Fragile X syndrome, or a spinocerebellar ataxia. In certain embodiments, the subject has Huntington's disease. In certain embodiments, the subject has a spinocerebellar ataxia. In certain embodiments, at least one symptom or hallmark of the repeat expansion disease is ameliorated. In certain embodiments, the symptom or hallmark is selected from brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, suicidal behavior, and a combination thereof. In certain embodiments, administration of the oligomeric compound, the modified oligonucleotide, the oligomeric duplex, or the antisense agent reduces or delays the onset or progression of brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, cardiac failure, impaired glucose tolerance, weight loss, osteoporosis, testicular atrophy, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired learning ability, impaired mental concentration, impaired speech, depression, irritability, anger, impaired mobility, impaired self-care, pain, discomfort, anxiety, suicidal ideation, or suicidal behavior.


In certain embodiments, a method of ameliorating, treating, or preventing Huntington's disease comprises administering to a subject an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid. In certain embodiments, a method of ameliorating or preventing Huntington's disease comprises administering to a subject an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid. In certain embodiments, at least one symptom or hallmark of Huntington's disease is ameliorated. In certain embodiments, the symptom or hallmark is brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, impaired glucose tolerance, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired mental concentration, impaired speech, depression, irritability, impaired mobility, impaired self-care, anxiety, suicidal ideation, or suicidal behavior. In certain embodiments, administration of the oligomeric compound, the modified oligonucleotide, the oligomeric duplex, or the antisense agent reduces or delays the onset or progression of brain atrophy, reduced brain activity, reduced brain connectivity, muscle atrophy, muscle weakness, muscle cramping, difficulty swallowing, seizure, tremor, nerve degeneration, impaired glucose tolerance, impaired global function, impaired motor function, impaired cognitive function, impaired daily function, impaired attention, impaired visuoperceptual processing, impaired working memory, impaired psychomotor speed, impaired verbal motor output, impaired degree of independence, impaired apathy, impaired mental concentration, impaired speech, depression, irritability, impaired mobility, impaired self-care, anxiety, suicidal ideation, or suicidal behavior.


In certain embodiments, a method of reducing expression of HTT nucleic acid, for example RNA, or reducing expression of HTT protein in a cell comprises contacting the cell with an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid. In certain embodiments, the cell is from a subject. In certain embodiments, the subject has or is at risk for developing a repeat expansion disease. In certain embodiments, the subject has or is at risk for developing Huntington's disease. In certain embodiments, the cell is from a brain tissue, optionally from the cortex, substantia nigra, striatum, midbrain, brainstem, or spinal cord. In certain embodiments, the cell is a human cell.


Certain embodiments are drawn to an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid, for use in ameliorating, treating, or preventing a repeat expansion disease or for use in the manufacture of a medicament for ameliorating, treating, or preventing a repeat expansion disease. In certain embodiments, an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid, is for use in ameliorating or preventing a repeat expansion disease or for use in the manufacture of a medicament for ameliorating or preventing a repeat expansion disease. In certain embodiments, the repeat expansion disease is selected from myotonic dystrophy (DM1 and DM2), amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, a polyglutamine disorder, Fragile X syndrome, and a spinocerebellar ataxia. In certain embodiments, the repeat expansion disease is Huntington's disease. In certain embodiments, the repeat expansion disease is a spinocerebellar ataxia.


Certain embodiments are drawn to an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid, for use in ameliorating, treating, or preventing Huntington's disease or for use in the manufacture of a medicament for ameliorating, treating, or preventing Huntington's disease. In certain embodiments, an oligomeric compound, a modified oligonucleotide, an oligomeric duplex, or an antisense agent, any of which having a nucleobase sequence complementary to a HTT nucleic acid, is for use in ameliorating or preventing Huntington's disease or for use in the manufacture of a medicament for ameliorating or preventing Huntington's disease.


In any of the methods or uses described herein, the oligomeric compound, the modified oligonucleotide, the oligomeric duplex, or the antisense agent can be any described herein.


VII. Certain Compositions
Compound No. 1394371

In certain embodiments, Compound No. 1394371 is characterized as a 6-10-4 MOE gapmer, having a sequence of (from 5′ to 3′) CACAGCTTTTATTTCCATAC (incorporated herein as SEQ ID NO: 3619), wherein each of nucleosides 1-6 and 17-20 are 2′-O-methoxyethyl nucleosides, and each of nucleosides 7-16 are β-D-deoxyribonucleosides, wherein the internucleoside linkages between nucleosides 2 to 3, 3 to 4, 4 to 5, 5 to 6, 6 to 7, and 17 to 18 are phosphodiester linkages and the internucleoside linkages between nucleosides 1 to 2, 7 to 8, 8 to 9, 9 to 10, 10 to 11, 11 to 12, 12 to 13, 13 to 14, 14 to 15, 15 to 16, 16 to 17, 18 to 19, and 19 to 20 are phosphorothioate linkages, and wherein each cytosine is a 5-methylcytosine.


In certain embodiments, Compound No. 1394371 is described by the following chemical notation: mCes Aeo mCeo Aeo Geo mCeo Tds Tds Tds Tds Ads Tds Tds Tds mCds mCds Aeo Tes Aes mCe (SEQ ID NO: 3619); wherein, A=an adenine, mC=a 5-methylcytosine, G=a guanine, T=a thymine, e=a 2′-O-methoxyethylribose modified sugar, d=a 2′-deoxyribose sugar moiety, s=a phosphorothioate internucleoside linkage, and o=a phosphodiester internucleoside linkage.


In certain embodiments, Compound No. 1394371 is described by the following chemical structure, or a pharmaceutically acceptable salt thereof:




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In certain embodiments, a pharmaceutically acceptable salt of Compound No. 1394371 described by Structure 1 comprises one or more cations selected from sodium, potassium, calcium, and magnesium.


In certain embodiments, the sodium salt of Compound No. 1394371 is described by the following chemical structure:




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Compound No. 1315578

In certain embodiments, Compound No. 1315578 is characterized as a 5-10-5 MOE gapmer, having a sequence of (from 5′ to 3′) GCTTTGATTTTTACCAGTTA (incorporated herein as SEQ ID NO: 1502), wherein each of nucleosides 1-5 and 16-20 are 2′-O-methoxyethyl nucleosides, and each of nucleosides 6-15 are β-D-deoxyribonucleosides, wherein the internucleoside linkages between nucleosides 2 to 3, 3 to 4, 4 to 5, 16 to 17, and 17 to 18 are phosphodiester linkages and the internucleoside linkages between nucleosides 1 to 2, 5 to 6, 6 to 7, 7 to 8, 8 to 9, 9 to 10, 10 to 11, 11 to 12, 12 to 13, 13 to 14, 14 to 15, 15 to 16, 18 to 19, and 19 to 20 are phosphorothioate linkages, and wherein each cytosine is a 5-methylcytosine.


In certain embodiments, Compound No. 1315578 is described by the following chemical notation: Ges mCeo Teo Teo Tes Gds Ads Tds Tds Tds Tds Tds Ads mCds mCds Aeo Geo Tes Tes Ae (SEQ ID NO: 1502); wherein, A=an adenine, mC=a 5-methylcytosine, G=a guanine, T=a thymine, e=a 2′-O-methoxyethylribose modified sugar, d=a 2′-deoxyribose sugar moiety, s=a phosphorothioate internucleoside linkage, and o=a phosphodiester internucleoside linkage.


In certain embodiments, Compound No. 1315578 is described by the following chemical structure, or a pharmaceutically acceptable salt thereof:




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In certain embodiments, a pharmaceutically acceptable salt of Compound No. 1315578 described by Structure 3 comprises one or more cations selected from sodium, potassium, calcium, and magnesium.


In certain embodiments, the sodium salt of Compound No. 1315578 is described by the following chemical structure:




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Compound No. 1394378

In certain embodiments, Compound No. 1394378 is characterized as a 6-10-4 MOE gapmer, having a sequence of (from 5′ to 3′) ACAGCTTTTATTTCCATACA (incorporated herein as SEQ ID NO: 3646), wherein each of nucleosides 1-6 and 17-20 are 2′-O-methoxyethyl nucleosides, and each of nucleosides 7-16 are β-D-deoxyribonucleosides, wherein the internucleoside linkages between nucleosides 2 to 3, 3 to 4, 4 to 5, 5 to 6, 6 to 7, and 17 to 18 are phosphodiester linkages and the internucleoside linkages between nucleosides 1 to 2, 7 to 8, 8 to 9, 9 to 10, 10 to 11, 11 to 12, 12 to 13, 13 to 14, 14 to 15, 15 to 16, 16 to 17, 18 to 19, and 19 to 20 are phosphorothioate linkages, and wherein each cytosine is a 5-methylcytosine.


In certain embodiments, Compound No. 1394378 is described by the following chemical notation: Aes mCeo Aeo Geo mCeo Teo Tds Tds Tds Ads Tds Tds Tds mCds mCds Ads Teo Aes mCes Ae (SEQ ID NO: 3646); wherein, A=an adenine, mC=a 5-methylcytosine, G=a guanine, T=a thymine, e=a 2′-O-methoxyethylribose modified sugar, d=a 2′-deoxyribose sugar moiety, s=a phosphorothioate internucleoside linkage, and o=a phosphodiester internucleoside linkage.


In certain embodiments, Compound No. 1394378 is described by the following chemical structure, or a pharmaceutically acceptable salt thereof:




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In certain embodiments, a pharmaceutically acceptable salt of Compound No. 1394378 described by Structure 5 comprises one or more cations selected from sodium, potassium, calcium, and magnesium.


In certain embodiments, the sodium salt of Compound No. 1394378 is described by the following chemical structure:




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VIII. Certain Comparator Compositions

In certain embodiments, Compound No: 388241, a 5-10-5 MOE gapmer, having a sequence of (from 5′ to 3′) CTCAGTAACATTGACACCAC (incorporated herein as SEQ ID NO: 858), wherein each internucleoside linkage is a phosphorothioate internucleoside linkage, each cytosine is a 5-methylcytosine, and each of nucleosides 1-5 and 16-20 (from 5′ to 3′) comprise a 2′-MOE modified sugar, which was previously described in WO 2011/032045, incorporated herein by reference, is a comparator compound. Compound No. 388241 was selected as a comparator compound because it was one of the most potent compounds described in WO 2011/032045. Compound No. 388241 and Compound No. 443139, also one of the most potent compounds described in WO 2011/032045, were tested in comparative studies and achieved similar results, as described in WO 2011/032045.


In certain embodiments, compounds described herein, including Compound Nos. 1394371, 1315578, and 1394378, are superior relative to Compound No. 388241 because they demonstrate one or more improved properties, such as, activity and tolerability. Compound Nos. 1394371, 1315578, and 1394378 may be dosed at lower amounts than Compound No. 388241 to achieve a comparable therapeutic effect. Compound Nos. 1394371, 1315578, and 1394378 may be dosed less frequently than Compound No. 388241 to achieve a comparable therapeutic effect.


For example, as provided in Example 8 (hereinbelow), Compound Nos. 1394371, 1315578, and 1394378 demonstrated improved tolerability in rats relative to that of Compound No. 388241. Compound Nos. 1394371, 1315578, and 1394378 demonstrated 3 h FOB scores of 0.00, 0.50, and 0.00, respectively. In contrast, Compound No. 388241 demonstrated a 3 h FOB score of 2.75. See Tables 77 and 78. Therefore, Compound Nos. 1394371, 1315578, and 1394378 are demonstrably more tolerable than Compound No. 388241 in rats.


For example, as provided in Example 9 (hereinbelow), Compound Nos. 1394371, 1315578, and 1394378 demonstrated improved activity in human HTT transgenic mice relative to that of Compound No. 388241. Compound Nos. 1394371, 1315578, and 1394378 reduced HTT RNA levels in spinal cords of mice to 26%, 46% and 28% of HTT RNA levels in untreated control mice, respectively, whereas as Compound No. 388241 only reduced HTT RNA levels in spinal cords of mice to 73% of HTT RNA levels in untreated control mice. Compound Nos. 1394371, 1315578, and 1394378 reduced HTT RNA levels in the cortex of mice to 10% of HTT RNA levels in untreated control mice, respectively, whereas as Compound No. 388241 only reduced HTT RNA levels in the cortex of mice to 56% of HTT RNA levels in untreated control mice.


IX. Certain Hotspot Regions

In certain embodiments, the ranges described in the Table below comprise hotspot regions. Each hotspot region begins with the nucleobase of SEQ ID NO: 2 identified in the “Start Site SEQ ID NO: 2” column and ends with the nucleobase of SEQ ID NO: 2 identified in the “Stop Site SEQ ID NO: 2” column. In certain embodiments, oligomeric compounds comprise modified oligonucleotides that are complementary within any of the hotspot regions 1-10, as defined in the table below. In certain embodiments, modified oligonucleotides are 16 nucleobases in length. In certain embodiments, modified oligonucleotides are 17 nucleobases in length. In certain embodiments, modified oligonucleotides are 18 nucleobases in length. In certain embodiments, modified oligonucleotides are 20 nucleobases in length.


In certain embodiments, oligomeric compounds comprise modified oligonucleotides that are gapmers. In certain embodiments, modified oligonucleotides are 5-10-5 MOE gapmers. In certain embodiments, modified oligonucleotides are 6-10-4 MOE gapmers. In certain embodiments, modified oligonucleotides are 5-8-5 MOE gapmers. In certain embodiments, modified oligonucleotides are gapmers, wherein the wings have a cEt/MOE sugar motif. In certain embodiments, modified oligonucleotides have a sugar motif selected from: eekkddddddddkkeee, ekekddddddddkekee, eeeeeddddddddddeeeee, eeeeddddddddkkeee, and eeeeeeddddddddeeee, wherein each “e” is a nucleoside comprising a 2′-MOE sugar moiety, each “k” is a nucleoside comprising a cEt sugar moiety, and each “d” is a nucleoside comprising a 2′-β-D-deoxyribosyl sugar moiety.


In certain embodiments, oligomeric compounds comprise a modified oligonucleotide comprising a modified internucleoside linkage. In certain embodiments, the modified internucleotides linkage is a phosphorothioate linkage. In certain embodiments, modified oligonucleotides have a internucleoside linkage motif selected from: soosssssssssooss, sooosssssssssssooss, sssssssssssssssssss, sooosssssssssssooos, sossssssssssssssoss, ssoosssssssssssooss, sooosssssssssooss, sooooossssssssssoss, and sossssssssssssoss, wherein each “s” is a phosphorothioate linkage an each “o” is a phosphodiester linkage.


The nucleobase sequences of the oligomeric compounds in the table below are complementary to SEQ ID NO: 2 within the specified hotspot region. In certain embodiments, compounds comprising a modified oligonucleotide complementary to nucleobases within the hotspot region achieve at least “Min. % Red.” (minimum 0 reduction, relative to untreated control cells) of HTT RNA in the standard in vitro assay, as indicated in the table below. In certain embodiments, modified oligonucleotides complementary to nucleobases within the hotspot region achieve an average of “Avg. % Red.” (average % reduction, relative to untreated control cells) of HTT RNA in the standard in vitro assay, as indicated in the table below. In certain embodiments, modified oligonucleotides complementary to nucleobases within the hotspot region achieve a maximum “Max. % Red.” (maximum % reduction, relative to untreated control cells) of HTT RNA in the standard in vitro assay, as indicated in the table below.









TABLE 1







HTT Hotspots















Start
Stop
Min
Max






Site
Site
%
%
Avg %



SEQ
SEQ
Red.
Red.
Red.

SEQ ID


Hotspot
ID
ID
In
In
In
Compound No.
NOs in


ID
NO: 2
NO: 2
vitro
vitro
vitro
in range
range

















1
56443
56500
38
88
72.1
1314697, 1314867,
1184, 1274,








1314999, 1315294,
1331, 1455,








1315702, 1316563,
1481, 1562,








1316677
1684


2
62833
62860
83
92
87.5
1391321, 1314907,
3029, 3104,








1314967, 1391310,
3557, 3562,








1391323, 1391324,
3569, 3586,








1391328, 1391336,
3610, 3620,








1391368, 1394346,
3622, 3623,








1394375, 1394381,
3627, 3634,








1394384, 1394385,
3664, 3687,








1394393, 1394395,
3692, 3697








1394422, 1394428,








1394433, 1394440,








1394451, 1419391,








1419396, 1419403,








1419421


3
69788
69824
52
86
65.8
1315412, 1315885,
2750, 2814,








1315950, 1316385,
2887, 2991,








1317102
3090


4
9984
10008
52
84
73.3
1314829, 1315347,
2581, 2640,








1315586, 1316745,
2736, 2857,








1317017
2917


5
106863
106924
25
75
57.8
1314696, 1315159,
1105, 1232,








1316117, 1316972,
1249, 3330,








1317030, 1318565,
3342, 3344,








1318566, 1318569,
3362, 3382,








1318573, 1318577,
3411, 3419,








1318632, 1318634,
3439, 3456,








1318636, 1318690,
3475, 3488,








1318691, 1318695,
3491, 3511,








1318741, 1318745,
3531, 3550,








1318747
3551


6
115297
115337
65
74
69.2
1315073, 1316061,
2208, 2310,








1316776, 1317084,
2335, 2471,








1391292, 1391293,
3553, 3559,








1391296, 1391299,
3563, 3565,








1391301, 1391304,
3570, 3580,








1391314, 1391316,
3581, 3583,








1391332, 1391333,
3585, 3589,








1391339, 1391351,
3593, 3594,








1391353, 1391356,
3597, 3600,








1391357, 1391364,
3601, 3604,








1391365, 1391366,
3614, 3616,








1394343, 1394373,
3630, 3631,








1394377, 1394382,
3637, 3648,








1394386, 1394392,
3650, 3652,








1394394, 1394419,
3653, 3660,








1394424, 1394441,
3661, 3662,








1394449, 1419387,
3684, 3689








1419393, 1419397,








1419399, 1419404,








1419415, 1419416,








1419418, 1419420,








1419424


7
117868
117902
52
86
73.7
1314540, 1315083,
2644, 2770,








1316639, 1316648,
2786, 2916,








1394315, 1394316,
3574, 3576,








1394317, 1394318,
3578, 3587,








1394320, 1394321,
3665, 3666,








1394323, 1394325,
3667, 3668,








1394326, 1394331,
3669, 3670,








1394335, 1394336,
3671, 3672,








1394349, 1394397,
3673, 3674,








1394398, 1394399,
3675, 3676,








1394400, 1394401,
3686, 3694,








1394402, 1394421,
3698








1394430, 1394434,








1394439, 1394447,








1419408, 1419410,








1419413, 1419422


8
119644
119670
64
81
72.5
1314723, 1316689,
919, 940,








1456397, 1456398,
3677, 3678,








1456399, 1456400,
3679, 3680,








1456401, 1456402,
3681, 3682,








1456403, 1456404,
3705, 3706,








1456405, 1456406,
3707








1456407, 1456408,








1456409, 1456410,








1456411, 1456412,








1456413


9
126780
126829
60
87
72.1
1315214, 1315343,
1576, 1652,








1315670, 1316310,
1771, 1813,








1316802, 1316996,
1933, 1987,








1317163, 1391297,
2078, 3552,








1391308, 1391311,
3555, 3558,








1391313, 1391320,
3560, 3572,








1391329, 1391337,
3573, 3575,








1391346, 1391348,
3579, 3584,








1391352, 1391367,
3598, 3608,








1394345, 1394367,
3611, 3613,








1394368, 1394371,
3619, 3628,








1394378, 1394379,
3635, 3644,








1394387, 1394418,
3646, 3649,








1394423, 1394425,
3663, 3683,








1394444, 1394450,
3688, 3690,








1419360, 1419361,
3700, 3701,








1419362, 1419365,
3702, 3703,








1419370, 1419374,
3704








1419375, 1419376,








1419379, 1419380,








1419383, 1419384,








1419386, 1419389,








1419392, 1419394,








1419406, 1419407,








1419409, 1419414,








1419419


10
130388
130418
52
90
68.6
444652, 1231536,
1343, 1406,








1314810, 1315556,
1539, 3335,








1315878, 1316545,
3401, 3472,








1316803, 1318652,
3477, 3519,








1318742
3591









X. Certain Pharmaceutical Compositions

In certain embodiments, described herein are pharmaceutical compositions comprising one or more oligomeric compounds. In certain embodiments, the one or more oligomeric compounds each consists of a modified oligonucleotide. In certain embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable diluent or carrier. In certain embodiments, a pharmaceutical composition comprises or consists of a sterile saline solution and one or more oligomeric compound. In certain embodiments, the sterile saline is pharmaceutical grade saline. In certain embodiments, a pharmaceutical composition comprises or consists of one or more oligomeric compound and sterile water. In certain embodiments, the sterile water is pharmaceutical grade water. In certain embodiments, a pharmaceutical composition comprises or consists of one or more oligomeric compound and phosphate-buffered saline (PBS). In certain embodiments, the sterile PBS is pharmaceutical grade PBS. In certain embodiments, a pharmaceutical composition comprises or consists of one or more oligomeric compound and artificial cerebrospinal fluid (“artificial CSF” or “aCSF”). In certain embodiments, the artificial cerebrospinal fluid is pharmaceutical grade.


In certain embodiments, a pharmaceutical composition comprises a modified oligonucleotide and artificial cerebrospinal fluid (aCSF). In certain embodiments, a pharmaceutical composition consists of a modified oligonucleotide and artificial cerebrospinal fluid. In certain embodiments, a pharmaceutical composition consists essentially of a modified oligonucleotide and artificial cerebrospinal fluid. In certain embodiments, the artificial cerebrospinal fluid is pharmaceutical grade.


In certain embodiments, aCSF comprises sodium chloride, potassium chloride, sodium dihydrogen phosphate dihydrate, sodium phosphate dibasic anhydrous, calcium chloride dihydrate, and magnesium chloride hexahydrate. In certain embodiments, the pH of an aCSF solution is modulated with a suitable pH-adjusting agent, for example, with acids such as hydrochloric acid and alkalis such as sodium hydroxide, to a range of from about 7.1-7.3, or to about 7.2.


In certain embodiments, pharmaceutical compositions comprise one or more oligomeric compound and one or more excipients. In certain embodiments, excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.


In certain embodiments, oligomeric compounds may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.


In certain embodiments, pharmaceutical compositions comprising an oligomeric compound encompass any pharmaceutically acceptable salts of the oligomeric compound, esters of the oligomeric compound, or salts of such esters. In certain embodiments, pharmaceutical compositions comprising oligomeric compounds comprising one or more oligonucleotide, upon administration to a subject, including a human, are capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to pharmaceutically acceptable salts of oligomeric compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. In certain embodiments, pharmaceutically acceptable salts comprise inorganic salts, such as monovalent or divalent inorganic salts. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium, potassium, calcium, and magnesium salts. In certain embodiments, prodrugs comprise one or more conjugate group attached to an oligonucleotide, wherein the conjugate group is cleaved by endogenous nucleases within the body.


In certain embodiments, oligomeric compounds are lyophilized and isolated as sodium salts. In certain embodiments, the sodium salt of an oligomeric compound is mixed with a pharmaceutically acceptable diluent. In certain embodiments, the pharmaceutically acceptable diluent comprises sterile saline, sterile water, PBS, or aCSF. In certain embodiments, the sodium salt of an oligomeric compound is mixed with PBS. In certain embodiments, the sodium salt of an oligomeric compound is mixed with aCSF.


Lipid moieties have been used in nucleic acid therapies in a variety of methods. In certain such methods, the nucleic acid, such as an oligomeric compound, is introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids. In certain methods, DNA complexes with mono- or poly-cationic lipids are formed without the presence of a neutral lipid. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.


In certain embodiments, pharmaceutical compositions comprise a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds. In certain embodiments, certain organic solvents such as dimethylsulfoxide are used.


In certain embodiments, pharmaceutical compositions comprise one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present invention to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes coated with a tissue-specific antibody.


In certain embodiments, pharmaceutical compositions comprise a co-solvent system. Certain of such co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. In certain embodiments, such co-solvent systems are used for hydrophobic compounds. A non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol comprising 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80™ and 65% w/v polyethylene glycol 300. The proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics. Furthermore, the identity of co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80™; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.


In certain embodiments, pharmaceutical compositions are prepared for administration by intrathecal injection. In certain embodiments, pharmaceutical compositions are prepared for administration by intracerebroventricular injection. In certain of such embodiments, a pharmaceutical composition comprises a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. In certain embodiments, other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives). In certain embodiments, injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like. Certain pharmaceutical compositions for injection are presented in unit dosage form, e.g., in ampoules or in multi-dose containers. Certain pharmaceutical compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes.


Under certain conditions, certain compounds disclosed herein act as acids. Although such compounds may be drawn or described in protonated (free acid) form, or ionized and in association with a cation (salt) form, aqueous solutions of such compounds exist in equilibrium among such forms. For example, a phosphodiester linkage of an oligonucleotide in aqueous solution exists in equilibrium among free acid, anion and salt forms. Unless otherwise indicated, compounds described herein are intended to include all such forms. Moreover, certain oligonucleotides have several such linkages, each of which is in equilibrium. Thus, oligonucleotides in solution exist in an ensemble of forms at multiple positions all at equilibrium. The term “oligonucleotide” is intended to include all such forms. Drawn structures necessarily depict a single form. Nevertheless, unless otherwise indicated, such drawings are likewise intended to include corresponding forms. Herein, a structure depicting the free acid of a compound followed by the term “or a pharmaceutically acceptable salt thereof” expressly includes all such forms that may be fully or partially protonated/de-protonated/in association with a cation or a combination of cations. In certain embodiments, one or more specific cation is identified. The cations include, but are not limited to, sodium, potassium, calcium, and magnesium. In certain embodiments, a structure depicting the free acid of a compound followed by the term “or a pharmaceutically acceptable salt thereof” expressly includes all such forms that may be fully or partially protonated/de-protonated/in association with one or more cations selected from sodium, potassium, calcium, and magnesium.


In certain embodiments, modified oligonucleotides or oligomeric compounds are in aqueous solution with sodium. In certain embodiments, modified oligonucleotides or oligomeric compounds are in aqueous solution with potassium. In certain embodiments, modified oligonucleotides or oligomeric compounds are in aqueous solution with phosphate buffered saline (PBS). In certain embodiments, modified oligonucleotides or oligomeric compounds are in aqueous solution with water. In certain such embodiments, the pH of the solution is adjusted with NaOH and/or HCl to achieve a desired pH.


Herein, certain specific doses are described. A dose may be in the form of a dosage unit. For clarity, a dose (or dosage unit) of a modified oligonucleotide or an oligomeric compound in milligrams indicates the mass of the free acid form of the modified oligonucleotide or oligomeric compound. As described above, in aqueous solution, the free acid is in equilibrium with anionic and salt forms. However, for the purpose of calculating dose, it is assumed that the modified oligonucleotide or oligomeric compound exists as a solvent-free, sodium-acetate free, anhydrous, free acid.


In certain embodiments, where a modified oligonucleotide or an oligomeric compound is in solution comprising sodium (e.g., saline), the modified oligonucleotide or oligomeric compound may be partially or fully de-protonated and in association with sodium ions. However, the mass of the protons is nevertheless counted toward the weight of the dose, and the mass of the sodium ions is not counted toward the weight of the dose. Thus, for example, a dose, or dosage unit, of 10 mg of Compound No. 1127954, equals the number of fully protonated molecules that weighs 10 mg. This would be equivalent to 10.47 mg of solvent-free, sodium acetate-free, anhydrous sodiated Compound No. 1127954.


In certain embodiments, where a modified oligonucleotide or oligomeric compound is in a solution, such as aCSF, comprising sodium, potassium, calcium, and magnesium, the modified oligonucleotide or oligomeric compound may be partially or fully de-protonated and in association with sodium, potassium, calcium, and/or magnesium. However, the mass of the protons is nevertheless counted toward the weight of the dose, and the mass of the sodium, potassium, calcium, and magnesium ions is not counted toward the weight of the dose.


In certain embodiments, when an oligomeric compound comprises a conjugate group, the mass of the conjugate group may be included in calculating the dose of such oligomeric compound. If the conjugate group also has an acid, the conjugate group is likewise assumed to be fully protonated for the purpose of calculating dose.


Nonlimiting Disclosure and Incorporation by Reference

Each of the literature and patent publications listed herein is incorporated by reference in its entirety.


While certain compounds, compositions and methods described herein have been described with specificity in accordance with certain embodiments, the following examples serve only to illustrate the compounds described herein and are not intended to limit the same. Each of the references, GenBank accession numbers, and the like recited in the present application is incorporated herein by reference in its entirety.


Although the sequence listing accompanying this filing identifies each sequence as either “RNA” or “DNA” as required, in reality, those sequences may be modified with any combination of chemical modifications. One of skill in the art will readily appreciate that such designation as “RNA” or “DNA” to describe modified oligonucleotides is, in certain instances, arbitrary. For example, an oligonucleotide comprising a nucleoside comprising a 2′-OH sugar moiety and a thymine base could be described as a DNA having a modified sugar (2′-OH in place of one 2′-H of DNA) or as an RNA having a modified base (thymine (methylated uracil) in place of a uracil of RNA). Accordingly, nucleic acid sequences provided herein, including, but not limited to those in the sequence listing, are intended to encompass nucleic acids containing any combination of natural or modified RNA and/or DNA, including, but not limited to such nucleic acids having modified nucleobases. By way of further example and without limitation, an oligomeric compound having the nucleobase sequence “ATCGATCG” encompasses any oligomeric compounds having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and oligomeric compounds having other modified nucleobases, such as “ATmCGAUCG,” wherein mC indicates a cytosine base comprising a methyl group at the 5-position.


Certain compounds described herein (e.g., modified oligonucleotides) have one or more asymmetric center and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), as a or f such as for sugar anomers, or as (D) or (L), such as for amino acids, etc. Compounds provided herein that are drawn or described as having certain stereoisomeric configurations include only the indicated compounds. Compounds provided herein that are drawn or described with undefined stereochemistry include all such possible isomers, including their stereorandom and optically pure forms, unless specified otherwise. Likewise, tautomeric forms of the compounds herein are also included unless otherwise indicated. Unless otherwise indicated, compounds described herein are intended to include corresponding salt forms.


The compounds described herein include variations in which one or more atoms are replaced with a non-radioactive isotope or radioactive isotope of the indicated element. For example, compounds herein that comprise hydrogen atoms encompass all possible deuterium substitutions for each of the 1H hydrogen atoms. Isotopic substitutions encompassed by the compounds herein include but are not limited to: 2H or 3H in place of 1H, 13C or 14C in place of 2C, 15N in place of 14N, 17O or 18O in place of 16O, and 33S, 34S, 35S or 36S in place of 32S. In certain embodiments, non-radioactive isotopic substitutions may impart new properties on the oligomeric compound that are beneficial for use as a therapeutic or research tool. In certain embodiments, radioactive isotopic substitutions may make the compound suitable for research or diagnostic purposes such as imaging.


EXAMPLES

The following examples illustrate certain embodiments of the present disclosure and are not limiting. Moreover, where specific embodiments are provided, the inventors have contemplated generic application of those specific embodiments. For example, disclosure of an oligonucleotide having a particular motif provides reasonable support for additional oligonucleotides having the same or similar motif And, for example, where a particular high-affinity modification appears at a particular position, other high-affinity modifications at the same position are considered suitable, unless otherwise indicated.


Example 1: Effect of Mixed MOE and cEt, Mixed Backbone Modified Oligonucleotides on Human HTT RNA In Vitro, Single Dose

Modified oligonucleotides complementary to human HTT nucleic acid were designed and tested for their single dose effects on HTT RNA in vitro. The modified oligonucleotides were tested in a series of experiments under the culture conditions indicated in the tables below.


The modified oligonucleotides in the tables below are 17 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eekkddddddddkkeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar, each “e” represents a 2′-MOE sugar moiety, and each “k” represents a cEt sugar moiety. The internucleoside linkage motif for the gapmers is (from 5′ to 3′): soosssssssssooss; wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage. Each cytosine residue is a 5-methylcytosine.


“Start site” indicates the 5′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. Each modified oligonucleotide listed in the tables below is 100% complementary to SEQ ID NO: 1 (GENBANK Accession No. NM_002111.6), to SEQ ID NO: 2 (GENBANK Accession No. NT_006081.17, truncated from 462000 to 634000), or to both. ‘N/A’ indicates that the modified oligonucleotide is not 100% complementary to that particular target nucleic acid sequence.


Cultured HepG2 or Hep3B cells were treated with modified oligonucleotide at a concentration of 2000 nM by electroporation at a density of 20,000 cells per well. After a treatment period of approximately 24 hours, total RNA was isolated from the cells and HTT RNA levels were measured by quantitative real-time RTPCR. HTT RNA levels were measured by human primer probe set RTS2617 (forward sequence CTCCGTCCGGTAGACATGCT, designated herein as SEQ ID NO: 11; reverse sequence GGAAATCAGAACCCTCAAAATGG, designated herein as SEQ ID NO: 12; probe sequence TGAGCACTGTTCAACTGTGGATATCGGGA, designated herein as SEQ ID NO: 13). HTT RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of HTT RNA is presented in the tables below as percent HTT RNA relative to the amount of the HTT RNA in untreated control cells (% UTC). Each table represents results from an individual assay plate.









TABLE 2







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in HepG2 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646201
N/A
N/A
 896
 912
GGCCAGCATGATTGACA
113
 26





646202
N/A
N/A
 900
 916
CGCCGGCCAGCATGATT
 94
 27





646203
N/A
N/A
 904
 920
GCCACGCCGGCCAGCAT
 77
 28





646204
N/A
N/A
 921
 937
GCGCCGGCGGAGGCGGG
 75
 29





 941
 957








646205
N/A
N/A
 922
 938
CGCGCCGGCGGAGGCGG
 89
 30





646206
N/A
N/A
 926
 942
GGGCCGCGCCGGCGGAG
 91
 31





646207
N/A
N/A
 944
 960
GCTGCGCCGGCGGAGGC
 70
 32





646208
 47
 63
1032
1048
GCTCTGGGCCGCAGGTA
 56
 33





646209
181
197
1166
1182
GGAAGGACTTGAGGGAC
 67
 34





646210
185
201
1170
1186
TGCTGGAAGGACTTGAG
 34
 35





646211
189
205
1174
1190
CTGCTGCTGGAAGGACT
 23
 36





646212
254
270
1233
1249
GGCGGCTGTTGCTGCTG
 46
 37





646213
262
278
1241
1257
GCGGCGGTGGCGGCTGT
 81
 38





646214
284
300
1263
1279
TGAGGAGGCGGCGGCGG
 40
 39





646215
288
304
1267
1283
AAGCTGAGGAGGCGGCG
 45
 40





646216
292
308
1271
1287
GAGGAAGCTGAGGAGGC
 54
 41





646217
296
312
1275
1291
GGCTGAGGAAGCTGAGG
 52
 42





646218
300
316
1279
1295
CGGCGGCTGAGGAAGCT
 24
 43





646219
304
320
1283
1299
GCGGCGGCGGCTGAGGA
 26
 44





646220
308
324
1287
1303
GCCTGCGGCGGCGGCTG
 61
 45





646221
312
328
1291
1307
CTGTGCCTGCGGCGGCG
 31
 46





646222
316
332
1295
1311
GCGGCTGTGCCTGCGGC
 36
 47





646223
320
336
1299
1315
AGCAGCGGCTGTGCCTG
 64
 48





646224
324
340
1303
1319
AGGCAGCAGCGGCTGTG
 76
 49





646225
328
344
1307
1323
GCTGAGGCAGCAGCGGC
 63
 50





646226
332
348
1311
1327
TGCGGCTGAGGCAGCAG
 82
 51





646227
336
352
1315
1331
CGGCTGCGGCTGAGGCA
 48
 52





646228
378
394
1357
1373
AGCCACAGCCGGGCCGG
108
 53





646229
382
398
1361
1377
CCTCAGCCACAGCCGGG
 87
 54





646230
N/A
N/A
1402
1418
GGAGCTGCAGCGGGCCC
 90
 55





646231
N/A
N/A
1424
1440
AGCCTGGGACCCGCCGG
 67
 56





646232
N/A
N/A
1425
1441
TAGCCTGGGACCCGCCG
 76
 57





646233
N/A
N/A
1426
1442
GTAGCCTGGGACCCGCC
 68
 58





646234
N/A
N/A
1427
1443
CGTAGCCTGGGACCCGC
 59
 59





646235
N/A
N/A
1428
1444
CCGTAGCCTGGGACCCG
 74
 60





646236
N/A
N/A
1429
1445
GCCGTAGCCTGGGACCC
 83
 61





646237
N/A
N/A
1430
1446
CGCCGTAGCCTGGGACC
 80
 62





646238
N/A
N/A
1431
1447
CCGCCGTAGCCTGGGAC
 71
 63





646239
N/A
N/A
1432
1448
CCCGCCGTAGCCTGGGA
 95
 64





646240
N/A
N/A
1433
1449
CCCCGCCGTAGCCTGGG
 96
 65





646241
N/A
N/A
1434
1450
TCCCCGCCGTAGCCTGG
 78
 66





646242
N/A
N/A
1435
1451
ATCCCCGCCGTAGCCTG
 88
 67





646243
N/A
N/A
1436
1452
CATCCCCGCCGTAGCCT
 72
 68





646244
N/A
N/A
1438
1454
GCCATCCCCGCCGTAGC
 65
 69





646245
N/A
N/A
1439
1455
CGCCATCCCCGCCGTAG
101
 70





646246
N/A
N/A
1440
1456
CCGCCATCCCCGCCGTA
110
 71





646247
N/A
N/A
1441
1457
ACCGCCATCCCCGCCGT
 97
 72





646248
N/A
N/A
1442
1458
TACCGCCATCCCCGCCG
 77
 73





646249
N/A
N/A
1443
1459
TTACCGCCATCCCCGCC
 72
 74





646250
N/A
N/A
1444
1460
GTTACCGCCATCCCCGC
 91
 75





646251
N/A
N/A
1445
1461
GGTTACCGCCATCCCCG
 72
 76





646252
N/A
N/A
1446
1462
GGGTTACCGCCATCCCC
 83
 77





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
 86
 78





646254
N/A
N/A
1448
1464
CAGGGTTACCGCCATCC
 53
 79





646255
N/A
N/A
1449
1465
GCAGGGTTACCGCCATC
 96
 80





646256
N/A
N/A
1450
1466
TGCAGGGTTACCGCCAT
 91
 81





646257
N/A
N/A
1452
1468
GCTGCAGGGTTACCGCC
 81
 82





646258
N/A
N/A
1453
1469
GGCTGCAGGGTTACCGC
 71
 83





646259
N/A
N/A
1454
1470
AGGCTGCAGGGTTACCG
 35
 84





646260
N/A
N/A
1531
1547
GCGGGTGTCCCTCATGG
 98
 85





646261
N/A
N/A
1634
1650
GGACAGGCCCCAACAAG
 92
 86





646262
N/A
N/A
1637
1653
TCAGGACAGGCCCCAAC
 63
 87





646263
N/A
N/A
1640
1656
AATTCAGGACAGGCCCC
 61
 88





646264
N/A
N/A
1643
1659
GTGAATTCAGGACAGGC
 41
 89





646265
N/A
N/A
1646
1662
TCGGTGAATTCAGGACA
 30
 90





646266
N/A
N/A
1649
1665
CCCTCGGTGAATTCAGG
 51
 91





646267
N/A
N/A
1652
1668
CTCCCCTCGGTGAATTC
 69
 92





646268
N/A
N/A
1655
1671
TGACTCCCCTCGGTGAA
 89
 93





646269
N/A
N/A
1658
1674
CCGTGACTCCCCTCGGT
 70
 94





646270
N/A
N/A
1661
1677
AGGCCGTGACTCCCCTC
 87
 95





646271
N/A
N/A
1664
1680
CTGAGGCCGTGACTCCC
 69
 96





646272
N/A
N/A
1667
1683
GGGCTGAGGCCGTGACT
 56
 97





646273
N/A
N/A
1670
1686
AGAGGGCTGAGGCCGTG
 80
 98





646274
N/A
N/A
1673
1689
GCGAGAGGGCTGAGGCC
 78
 99





646275
N/A
N/A
1682
1698
CTGCGAAGGGCGAGAGG
 97
100





646276
N/A
N/A
1685
1701
ATCCTGCGAAGGGCGAG
 76
101





646277
N/A
N/A
1688
1704
CGCATCCTGCGAAGGGC
 88
102





646278
N/A
N/A
1691
1707
CTTCGCATCCTGCGAAG
107
103
















TABLE 3







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in Hep3B cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
 78
 78





646279
N/A
N/A
1694
1710
ACTCTTCGCATCCTGCG
 67
104





646280
N/A
N/A
1697
1713
CCAACTCTTCGCATCCT
 87
105





646281
N/A
N/A
1700
1716
GCCCCAACTCTTCGCAT
 93
106





646282
N/A
N/A
1703
1719
CTCGCCCCAACTCTTCG
 86
107





646283
N/A
N/A
1706
1722
GTTCTCGCCCCAACTCT
 65
108





646284
N/A
N/A
1709
1725
CAAGTTCTCGCCCCAAC
 38
109





646285
N/A
N/A
1712
1728
AAACAAGTTCTCGCCCC
 65
110





646286
N/A
N/A
1715
1731
AAGAAACAAGTTCTCGC
 75
111





646287
N/A
N/A
1725
1741
CGCAAATAAAAAGAAAC
 47
112





646288
N/A
N/A
1728
1744
TCTCGCAAATAAAAAGA
 70
113





646289
N/A
N/A
1731
1747
GTTTCTCGCAAATAAAA
 59
114





646290
N/A
N/A
1734
1750
CTGGTTTCTCGCAAATA
 59
115





646291
N/A
N/A
1737
1753
GCCCTGGTTTCTCGCAA
 71
116





646292
N/A
N/A
1740
1756
CCCGCCCTGGTTTCTCG
 64
117





646293
N/A
N/A
1743
1759
ACCCCCGCCCTGGTTTC
 81
118





646294
N/A
N/A
1746
1762
AGAACCCCCGCCCTGGT
 74
119





646295
N/A
N/A
1749
1765
AAAAGAACCCCCGCCCT
112
120





646296
N/A
N/A
1752
1768
GTTAAAAGAACCCCCGC
124
121





646297
N/A
N/A
1755
1771
GCAGTTAAAAGAACCCC
 54
122





646298
N/A
N/A
1758
1774
AACGCAGTTAAAAGAAC
 90
123





646299
N/A
N/A
1761
1777
CACAACGCAGTTAAAAG
 90
124





646300
N/A
N/A
1764
1780
CTTCACAACGCAGTTAA
 74
125





646301
N/A
N/A
1767
1783
TCTCTTCACAACGCAGT
 43
126





646302
N/A
N/A
1770
1786
AGTTCTCTTCACAACGC
 82
127





646303
N/A
N/A
1773
1789
CCAAGTTCTCTTCACAA
 59
128





646304
N/A
N/A
1776
1792
CCTCCAAGTTCTCTTCA
 85
129





646305
N/A
N/A
1779
1795
GCTCCTCCAAGTTCTCT
 75
130





646306
N/A
N/A
1782
1798
TCGGCTCCTCCAAGTTC
 84
131





646307
N/A
N/A
1785
1801
ATCTCGGCTCCTCCAAG
 53
132





646308
N/A
N/A
1788
1804
CAAATCTCGGCTCCTCC
 71
133





646309
N/A
N/A
1791
1807
GAGCAAATCTCGGCTCC
 78
134





646310
N/A
N/A
1794
1810
ACTGAGCAAATCTCGGC
 79
135





646311
N/A
N/A
1797
1813
GGCACTGAGCAAATCTC
 39
136





646312
N/A
N/A
1800
1816
AGTGGCACTGAGCAAAT
 58
137





646313
N/A
N/A
1803
1819
GGAAGTGGCACTGAGCA
 46
138





646314
N/A
N/A
1806
1822
GAGGGAAGTGGCACTGA
 82
139





646315
N/A
N/A
1809
1825
GAAGAGGGAAGTGGCAC
 81
140





646316
N/A
N/A
1812
1828
CTAGAAGAGGGAAGTGG
100
141





646317
N/A
N/A
1815
1831
AGACTAGAAGAGGGAAG
103
142





646318
N/A
N/A
1818
1834
CTCAGACTAGAAGAGGG
108
143





646319
N/A
N/A
1821
1837
CCTCTCAGACTAGAAGA
104
144





646320
N/A
N/A
1824
1840
TTCCCTCTCAGACTAGA
 81
145





646321
N/A
N/A
1827
1843
CTCTTCCCTCTCAGACT
103
146





646322
N/A
N/A
1830
1846
GCCCTCTTCCCTCTCAG
 85
147





646323
N/A
N/A
1838
1854
CGCCCCCAGCCCTCTTC
 93
148





646324
N/A
N/A
1841
1857
CCGCGCCCCCAGCCCTC
 82
149





646325
N/A
N/A
1844
1860
GTCCCGCGCCCCCAGCC
 92
150





646326
N/A
N/A
1847
1863
AGTGTCCCGCGCCCCCA
 58
151





646327
N/A
N/A
1850
1866
CGAAGTGTCCCGCGCCC
 59
152





646328
N/A
N/A
1853
1869
TCTCGAAGTGTCCCGCG
 95
153





646329
N/A
N/A
1856
1872
TCCTCTCGAAGTGTCCC
 64
154





646330
N/A
N/A
1859
1875
GCCTCCTCTCGAAGTGT
 69
155





646331
N/A
N/A
1862
1878
CCCGCCTCCTCTCGAAG
 75
156





646332
N/A
N/A
1865
1881
AACCCCGCCTCCTCTCG
 65
157





646333
N/A
N/A
1868
1884
CCAAACCCCGCCTCCTC
 71
158





646334
N/A
N/A
1871
1887
GCTCCAAACCCCGCCTC
 76
159





646335
N/A
N/A
1874
1890
CCAGCTCCAAACCCCGC
 59
160





646336
N/A
N/A
1877
1893
TCTCCAGCTCCAAACCC
101
161





646337
N/A
N/A
1880
1896
ATCTCTCCAGCTCCAAA
 67
162





646338
N/A
N/A
1883
1899
CACATCTCTCCAGCTCC
 66
163





646339
N/A
N/A
1889
1905
TGCCCCCACATCTCTCC
 71
164





646340
N/A
N/A
1892
1908
CACTGCCCCCACATCTC
 67
165





646341
N/A
N/A
1895
1911
ATCCACTGCCCCCACAT
 89
166





646342
N/A
N/A
1898
1914
GTCATCCACTGCCCCCA
 44
167





646343
N/A
N/A
1901
1917
TATGTCATCCACTGCCC
 54
168





646344
N/A
N/A
1907
1923
AAGCATTATGTCATCCA
 29
169





646345
N/A
N/A
1910
1926
TAAAAGCATTATGTCAT
 67
170





646346
N/A
N/A
1913
1929
TCCTAAAAGCATTATGT
 97
171





646347
N/A
N/A
1930
1946
CCACTCCCGCCGAGGCG
 74
172





646348
N/A
N/A
1933
1949
CCGCCACTCCCGCCGAG
 71
173





646349
N/A
N/A
1936
1952
GCCCCGCCACTCCCGCC
 80
174





646350
N/A
N/A
1939
1955
CCTGCCCCGCCACTCCC
 78
175





646351
N/A
N/A
1947
1963
GCCCCCCCCCTGCCCCG
 82
176





646352
N/A
N/A
1952
1968
TCCCCGCCCCCCCCCTG
109
177





646353
N/A
N/A
1955
1971
CACTCCCCGCCCCCCCC
 68
178





646354
N/A
N/A
1960
1976
GCCCTCACTCCCCGCCC
 79
179





646355
N/A
N/A
1963
1979
CGCGCCCTCACTCCCCG
 92
180
















TABLE 4







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in HepG2 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
 65
 78





646356
N/A
N/A
1969
1985
ATTGGACGCGCCCTCAC
 38
181





646357
N/A
N/A
1972
1988
CCCATTGGACGCGCCCT
 54
182





646358
N/A
N/A
1975
1991
TCTCCCATTGGACGCGC
 69
183





646359
N/A
N/A
1981
1997
AAGAAATCTCCCATTGG
 55
184





646360
N/A
N/A
1984
2000
GAAAAGAAATCTCCCAT
 58
185





646361
N/A
N/A
1987
2003
TAGGAAAAGAAATCTCC
 87
186





646362
N/A
N/A
1990
2006
CACTAGGAAAAGAAATC
113
187





646363
N/A
N/A
1993
2009
TGCCACTAGGAAAAGAA
 90
188





646364
N/A
N/A
1996
2012
AAGTGCCACTAGGAAAA
 33
189





646365
N/A
N/A
1999
2015
TTTAAGTGCCACTAGGA
 52
190





646366
N/A
N/A
2002
2018
TGTTTTAAGTGCCACTA
 39
191





646367
N/A
N/A
2005
2021
GGCTGTTTTAAGTGCCA
 68
192





646368
N/A
N/A
2008
2024
TCAGGCTGTTTTAAGTG
 69
193





646369
N/A
N/A
2011
2027
ATCTCAGGCTGTTTTAA
 70
194





646370
N/A
N/A
2014
2030
CAAATCTCAGGCTGTTT
 28
195





646371
N/A
N/A
2017
2033
CCTCAAATCTCAGGCTG
 59
196





646372
N/A
N/A
2020
2036
GAGCCTCAAATCTCAGG
 53
197





646373
N/A
N/A
2023
2039
GAAGAGCCTCAAATCTC
 58
198





646374
N/A
N/A
2026
2042
TAGGAAGAGCCTCAAAT
 64
199





646375
N/A
N/A
2029
2045
ATGTAGGAAGAGCCTCA
 50
200





646376
N/A
N/A
2032
2048
ACAATGTAGGAAGAGCC
 31
201





646377
N/A
N/A
2035
2051
CTGACAATGTAGGAAGA
 44
202





646378
N/A
N/A
2038
2054
GTCCTGACAATGTAGGA
 77
203





646379
N/A
N/A
2041
2057
AATGTCCTGACAATGTA
 44
204





646380
N/A
N/A
2044
2060
TGAAATGTCCTGACAAT
 56
205





646381
N/A
N/A
2047
2063
AAATGAAATGTCCTGAC
 47
206





646382
N/A
N/A
2050
2066
ACTAAATGAAATGTCCT
 48
207





646383
N/A
N/A
2057
2073
ATCATGAACTAAATGAA
 84
208





646384
N/A
N/A
2060
2076
GTGATCATGAACTAAAT
 37
209





646385
N/A
N/A
2063
2079
ACCGTGATCATGAACTA
 43
210





646386
N/A
N/A
2066
2082
ACCACCGTGATCATGAA
 46
211





646387
N/A
N/A
2069
2085
ACTACCACCGTGATCAT
 66
212





646388
N/A
N/A
2072
2088
GTTACTACCACCGTGAT
 86
213





646389
N/A
N/A
2075
2091
CGTGTTACTACCACCGT
 50
214





646390
N/A
N/A
2090
2106
GGTGGTGCTTAAAATCG
 74
215





646391
N/A
N/A
2093
2109
TTAGGTGGTGCTTAAAA
 85
216





646392
N/A
N/A
2096
2112
CTCTTAGGTGGTGCTTA
 60
217





646393
N/A
N/A
2099
2115
GATCTCTTAGGTGGTGC
 53
218





646394
N/A
N/A
2102
2118
GCAGATCTCTTAGGTGG
 53
219





646395
N/A
N/A
2105
2121
TGAGCAGATCTCTTAGG
 58
220





646396
N/A
N/A
2111
2127
CTTAGATGAGCAGATCT
 55
221





646397
N/A
N/A
2114
2130
AGGCTTAGATGAGCAGA
 68
222





646398
N/A
N/A
2120
2136
CAACTTAGGCTTAGATG
 35
223





646399
N/A
N/A
2126
2142
GCAGACCAACTTAGGCT
 53
224





646400
N/A
N/A
2129
2145
CCTGCAGACCAACTTAG
 67
225





646401
N/A
N/A
2132
2148
ACGCCTGCAGACCAACT
 31
226





646402
N/A
N/A
2145
2161
ACAACTCATTCAAACGC
 62
227





646403
N/A
N/A
2148
2164
ACCACAACTCATTCAAA
 67
228





646404
N/A
N/A
2151
2167
GCAACCACAACTCATTC
 40
229





646405
N/A
N/A
2154
2170
TTGGCAACCACAACTCA
 63
230





646406
N/A
N/A
2157
2173
TACTTGGCAACCACAAC
 53
231





646407
N/A
N/A
2160
2176
CTTTACTTGGCAACCAC
 44
232





646408
N/A
N/A
2166
2182
TCACCACTTTACTTGGC
 48
233





646409
N/A
N/A
2169
2185
AGTTCACCACTTTACTT
 99
234





646410
N/A
N/A
2172
2188
GTAAGTTCACCACTTTA
 75
235





646411
N/A
N/A
2188
2204
TTTCATTAATCACCACG
 21
236





646412
N/A
N/A
2191
2207
TAATTTCATTAATCACC
 30
237





646413
N/A
N/A
2194
2210
AGATAATTTCATTAATC
 78
238





646414
N/A
N/A
2197
2213
TTAAGATAATTTCATTA
 81
239





646415
N/A
N/A
2205
2221
CCTAATATTTAAGATAA
 82
240





646416
N/A
N/A
2208
2224
CTTCCTAATATTTAAGA
 88
241





646417
N/A
N/A
2211
2227
ACTCTTCCTAATATTTA
 80
242





646418
N/A
N/A
2214
2230
TCAACTCTTCCTAATAT
 72
243





646419
N/A
N/A
2217
2233
CAATCAACTCTTCCTAA
 85
244





646420
N/A
N/A
2220
2236
CTTCAATCAACTCTTCC
 47
245





646421
N/A
N/A
2223
2239
AAACTTCAATCAACTCT
 50
246





646422
N/A
N/A
2226
2242
AAAAAACTTCAATCAAC
 58
247





646423
N/A
N/A
2229
2245
GGCAAAAAACTTCAATC
 46
248





646424
N/A
N/A
2232
2248
ATAGGCAAAAAACTTCA
 66
249





646425
N/A
N/A
2235
2251
CACATAGGCAAAAAACT
 82
250





646426
N/A
N/A
2239
2255
AACACACATAGGCAAAA
 75
251





646427
N/A
N/A
2242
2258
CCCAACACACATAGGCA
 44
252





646428
N/A
N/A
2245
2261
ATTCCCAACACACATAG
 87
253





646429
N/A
N/A
2248
2264
TTTATTCCCAACACACA
 81
254





646430
N/A
N/A
2251
2267
GGTTTTATTCCCAACAC
 95
255





646431
N/A
N/A
2254
2270
GTTGGTTTTATTCCCAA
 91
256





646432
N/A
N/A
2257
2273
CGTGTTGGTTTTATTCC
 85
257









Example 2: Effect of Mixed MOE and cEt, Mixed Backbone Modified Oligonucleotides on Human HTT RNA In Vitro, Single Dose

Modified oligonucleotides complementary to human HTT nucleic acid were designed and tested for their single dose effects on HTT RNA in vitro. The modified oligonucleotides were tested in a series of experiments that had the same culture conditions.


The modified oligonucleotides in the tables below are 17 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): ekekddddddddkekee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar, each “e” represents a 2′-MOE sugar moiety, and each “k” represents a cEt sugar moiety. The internucleoside linkage motif for the gapmers is (from 5′ to 3′): soosssssssssooss; wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage. Each cytosine residue is a 5-methylcytosine.


“Start site” indicates the 5′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. Each modified oligonucleotide listed in the tables below is 100% complementary to SEQ ID NO: 1 (described herein above), to SEQ ID NO: 2 (described herein above), or to both. ‘N/A’ indicates that the modified oligonucleotide is not 100% complementary to that particular target nucleic acid sequence.


Cultured A431 cells were treated with modified oligonucleotide at a concentration of 2000 nM by free uptake at a density of 10,000 cells per well. After a treatment period of approximately 48 hours, total RNA was isolated from the cells and HTT RNA levels were measured by quantitative real-time RTPCR. HTT RNA levels were measured by human primer probe set RTS36485 (forward sequence GAGGAAGTAGATCCAAACACACA, designated herein as SEQ ID NO: 14; reverse sequence GCCGCTATTCCTTTTATGACC, designated herein as SEQ ID NO: 15; probe sequence TCCACCATTTCTGCCACCATCTCA, designated herein as SEQ ID NO: 16). HTT RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of HTT RNA is presented in the tables below as percent HTT RNA relative to the amount of the HTT RNA in untreated control cells (% UTC). Each table represents results from an individual assay plate.


In the tables below, Compound 646253 (described herein above) was used as an inter-experimental control.









TABLE 5







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
140
 78





953797
33
49
1018
1034
GTAAAAGCAGAACCTGA
 93
258





953805
N/A
N/A
1584
1600
ACCCAAGTGAGGGAGCG
115
259





953813
N/A
N/A
1712
1728
AAACAAGTTCTCGCCCC
 85
110





953821
N/A
N/A
1805
1821
AGGGAAGTGGCACTGAG
108
260





953829
N/A
N/A
1906
1922
AGCATTATGTCATCCAC
107
261





953837
N/A
N/A
1984
2000
GAAAAGAAATCTCCCAT
 95
185





953845
N/A
N/A
2045
2061
ATGAAATGTCCTGACAA
 76
262





953853
N/A
N/A
2147
2163
CCACAACTCATTCAAAC
146
263





953861
N/A
N/A
2225
2241
AAAAACTTCAATCAACT
137
264





953869
N/A
N/A
2240
2256
CAACACACATAGGCAAA
 91
265





953877
N/A
N/A
2397
2413
AGCAAACAGAAACCCTT
103
266





953885
N/A
N/A
2426
2442
TCCAAAAAGTAACAAGC
 87
267





953893
N/A
N/A
2468
2484
TCAAAAATTCTCCCCAA
102
268





953901
N/A
N/A
2570
2586
CACCAGAGTACTTCCTA
 85
269





953909
N/A
N/A
2617
2633
CCAGATCGGAAATAGAA
147
270





953917
N/A
N/A
2660
2676
GTCTTAACAGAGATATT
 93
271





953925
N/A
N/A
2714
2730
AGACAAGGATCATAACA
121
272





953933
N/A
N/A
2736
2752
TTCTAATTAAACTTTGA
 94
273





953941
N/A
N/A
2784
2800
CCTAAATTTTATTCCAA
 63
274





953949
N/A
N/A
2827
2843
CCAAATATCCAAAAAGT
107
275





953957
N/A
N/A
2893
2909
CTACAGTAAATTTCTGG
 79
276





953965
N/A
N/A
2906
2922
TCCTAGAAAAGCACTAC
 93
277





953973
N/A
N/A
2952
2968
GTTTACACAAGATACAT
102
278





953981
N/A
N/A
3026
3042
TATTTTTAGAATGATCA
 97
279





953989
N/A
N/A
3055
3071
TGTCAAATCAGCATAAG
 83
280





953997
N/A
N/A
3088
3104
ACCCATATTTTGAAGAT
120
281





954005
N/A
N/A
3134
3150
ACAAAATCTATCTCCTT
 82
282





954013
N/A
N/A
3161
3177
AATCATATATTACCTTA
107
283





954021
N/A
N/A
3515
3531
GTCAATGTATTACTTAT
 60
284





954029
N/A
N/A
3570
3586
GTGGAAGGAAGATATTT
 88
285





954037
N/A
N/A
3647
3663
TTATATCTGGCAGGATA
102
286





954045
N/A
N/A
3674
3690
TTAAATCTATCTTACAA
113
287





954053
N/A
N/A
3748
3764
TGACAATGTGAGACTAC
114
288





954061
N/A
N/A
4068
4084
ATAAATAAACCTAATGC
 92
289





954069
N/A
N/A
4151
4167
AATTAGTGAATACCTCC
 98
290





954077
N/A
N/A
4188
4204
CAAAATCCAAACTTTGT
 89
291





954085
N/A
N/A
4272
4288
ACAGAACAGATACTTTC
 78
292





954093
N/A
N/A
4338
4354
TCATAAACTGAGGCCCA
117
293





954101
N/A
N/A
4441
4457
CTAATTACTGTGAGGAC
 59
294





954109
N/A
N/A
4475
4491
TAAGAAACTGCCAGAAG
 92
295





954117
N/A
N/A
4511
4527
AGTCAGGGAAACACCAG
103
296





954125
N/A
N/A
4548
4564
GTACATGTTTAGTAAAT
102
297





954133
N/A
N/A
4622
4638
ATGAAAGCTTCACGAGG
 80
298





954141
N/A
N/A
4839
4855
CAACACTTAGTGCTACA
 96
299





954149
N/A
N/A
5500
5516
TTAAAATATCAACACTG
 88
300





954157
N/A
N/A
5615
5631
TACGATAGTGATACTGC
102
301





954165
N/A
N/A
5763
5779
CCTTACACTAGACTCTT
 84
302





954173
N/A
N/A
5822
5838
CTGAAACAGGAAGATTT
 91
303





954181
N/A
N/A
5876
5892
TACAAATGTCCCCCTCA
117
304





954189
N/A
N/A
5959
5975
GCCAATATCTTTATTCC
102
305





954197
N/A
N/A
6032
6048
TAAGATTGAAATTCAGA
 89
306





954205
N/A
N/A
6187
6203
TCAAAATCCAGTCAGTC
 46
307





954213
N/A
N/A
6238
6254
TGCTAAATTGTTATACT
 84
308





954221
N/A
N/A
6300
6316
AGCTATTGCAGCAGGAT
 86
309





954229
N/A
N/A
6705
6721
TATAAGAAAGAGCCTGG
 95
310





954237
N/A
N/A
6727
6743
GAACAAGGGTTTGCAAG
109
311





954245
N/A
N/A
6843
6859
GACAATCCAAAGGAAGG
116
312





954253
N/A
N/A
7036
7052
GATCAGACTTAAATGTA
 99
313





954261
N/A
N/A
7163
7179
ACTAAGATAATTCCATG
 91
314





954269
N/A
N/A
7193
7209
AATTAAGGACGATTAAT
135
315





954277
N/A
N/A
7202
7218
AATTTATACAATTAAGG
 88
316





954285
N/A
N/A
7254
7270
TGGCACAGGATCGACAT
111
317





954293
N/A
N/A
7373
7389
CGGAAATGCAAGGGACC
126
318





954301
N/A
N/A
7523
7539
TTACACAAAGTTTGCCC
132
319





954309
N/A
N/A
7597
7613
TACAATGGCAGAGCCGC
115
320





954317
N/A
N/A
7712
7728
TCAAATACTATCTCATG
 74
321





954325
N/A
N/A
7791
7807
AAAACTATAACCTGCAT
142
322





954333
N/A
N/A
8161
8177
AAAGAAATGCTTTCCAG
115
323





954341
N/A
N/A
8292
8308
AGACAAAGATGACAGAC
 83
324





954349
N/A
N/A
8332
8348
GGGAAGAAGACACAAGA
 82
325





954357
N/A
N/A
8365
8381
CATTTAAATGCTTGTAT
 82
326





954365
N/A
N/A
8442
8458
AACAATATCTATGACAC
 56
327





954373
N/A
N/A
8467
8483
ATAAGAATTACAGGTAC
 83
328





954381
N/A
N/A
8490
8506
TCTAAAATATTACATAG
 80
329





954389
N/A
N/A
8551
8567
AGCCACAAAAATGTGAG
116
330





954397
N/A
N/A
8624
8640
ATTTACAGGAAATGGAG
 80
331





954405
N/A
N/A
8679
8695
ACTAAATGTTTTGAGTG
138
332
















TABLE 6







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
140
 78





953798
34
50
1019
1035
GGTAAAAGCAGAACCTG
142
333





953806
N/A
N/A
1595
1611
GACAAGGGAAGACCCAA
122
334





953814
N/A
N/A
1716
1732
AAAGAAACAAGTTCTCG
125
335





953822
N/A
N/A
1809
1825
GAAGAGGGAAGTGGCAC
105
140





953830
N/A
N/A
1911
1927
CTAAAAGCATTATGTCA
 83
336





953838
N/A
N/A
1985
2001
GGAAAAGAAATCTCCCA
 88
337





953846
N/A
N/A
2046
2062
AATGAAATGTCCTGACA
 85
338





953854
N/A
N/A
2163
2179
CCACTTTACTTGGCAAC
105
339





953862
N/A
N/A
2226
2242
AAAAAACTTCAATCAAC
106
247





953870
N/A
N/A
2282
2298
CGGCAATTAACCTCCCC
 94
340





953878
N/A
N/A
2398
2414
AAGCAAACAGAAACCCT
125
341





953886
N/A
N/A
2427
2443
TTCCAAAAAGTAACAAG
105
342





953894
N/A
N/A
2469
2485
TTCAAAAATTCTCCCCA
 94
343





953902
N/A
N/A
2590
2606
TAAGAGAAAGGCCTGAA
 84
344





953910
N/A
N/A
2619
2635
ATCCAGATCGGAAATAG
122
345





953918
N/A
N/A
2669
2685
AATTAATCAGTCTTAAC
 86
346





953926
N/A
N/A
2718
2734
GACGAGACAAGGATCAT
120
347





953934
N/A
N/A
2747
2763
TCCGAATCATTTTCTAA
113
348





953942
N/A
N/A
2785
2801
TCCTAAATTTTATTCCA
 88
349





953950
N/A
N/A
2828
2844
TCCAAATATCCAAAAAG
122
350





953958
N/A
N/A
2895
2911
CACTACAGTAAATTTCT
 84
351





953966
N/A
N/A
2936
2952
TGCAATGTGTGAACTTT
 60
352





953974
N/A
N/A
2959
2975
GTTTAGTGTTTACACAA
114
353





953982
N/A
N/A
3029
3045
GCATATTTTTAGAATGA
159
354





953990
N/A
N/A
3069
3085
GCAAATGCAGGTTCTGT
103
355





953998
N/A
N/A
3103
3119
AGGAAATTTCTTGATAC
124
356





954006
N/A
N/A
3138
3154
TGAAACAAAATCTATCT
 89
357





954014
N/A
N/A
3169
3185
AATAAGGTAATCATATA
117
358





954022
N/A
N/A
3516
3532
TGTCAATGTATTACTTA
 77
359





954030
N/A
N/A
3597
3613
ACAAAGTTAGGTACTCA
 50
360





954038
N/A
N/A
3654
3670
GAACAGGTTATATCTGG
 84
361





954046
N/A
N/A
3675
3691
TTTAAATCTATCTTACA
119
362





954054
N/A
N/A
4018
4034
AGTTATTATTCTAGCCA
 84
363





954062
N/A
N/A
4069
4085
TATAAATAAACCTAATG
 85
364





954070
N/A
N/A
4152
4168
AAATTAGTGAATACCTC
 90
365





954078
N/A
N/A
4189
4205
CCAAAATCCAAACTTTG
118
366





954086
N/A
N/A
4274
4290
AAACAGAACAGATACTT
 92
367





954094
N/A
N/A
4344
4360
AAACACTCATAAACTGA
 91
368





954102
N/A
N/A
4443
4459
TCCTAATTACTGTGAGG
101
369





954110
N/A
N/A
4478
4494
GAATAAGAAACTGCCAG
 89
370





954118
N/A
N/A
4516
4532
AATAAAGTCAGGGAAAC
 71
371





954126
N/A
N/A
4553
4569
ACATAGTACATGTTTAG
 87
372





954134
N/A
N/A
4623
4639
AATGAAAGCTTCACGAG
 84
373





954142
N/A
N/A
4897
4913
TGATAGAGCAAGAACTG
 87
374





954150
N/A
N/A
5504
5520
GTATTTAAAATATCAAC
 88
375





954158
N/A
N/A
5616
5632
CTACGATAGTGATACTG
101
376





954166
N/A
N/A
5781
5797
TACCACTACTTCATACA
 94
377





954174
N/A
N/A
5823
5839
CCTGAAACAGGAAGATT
 92
378





954182
N/A
N/A
5877
5893
CTACAAATGTCCCCCTC
 97
379





954190
N/A
N/A
5965
5981
ATAAATGCCAATATCTT
107
380





954198
N/A
N/A
6034
6050
CTTAAGATTGAAATTCA
 84
381





954206
N/A
N/A
6193
6209
CCGCATTCAAAATCCAG
124
382





954214
N/A
N/A
6244
6260
AGCTACTGCTAAATTGT
 89
383





954222
N/A
N/A
6305
6321
GTTTAAGCTATTGCAGC
101
384





954230
N/A
N/A
6706
6722
GTATAAGAAAGAGCCTG
115
385





954238
N/A
N/A
6732
6748
AATGAGAACAAGGGTTT
 64
386





954246
N/A
N/A
6844
6860
AGACAATCCAAAGGAAG
128
387





954254
N/A
N/A
7043
7059
CAAAATGGATCAGACTT
 85
388





954262
N/A
N/A
7164
7180
TACTAAGATAATTCCAT
134
389





954270
N/A
N/A
7194
7210
CAATTAAGGACGATTAA
 88
390





954278
N/A
N/A
7231
7247
CAACAGGTAGAACTGAC
118
391





954286
N/A
N/A
7286
7302
CACAAACTTCAGTAATC
120
392





954294
N/A
N/A
7374
7390
ACGGAAATGCAAGGGAC
 73
393





954302
N/A
N/A
7525
7541
ATTTACACAAAGTTTGC
 84
394





954310
N/A
N/A
7598
7614
CTACAATGGCAGAGCCG
132
395





954318
N/A
N/A
7723
7739
GACCAAAATAATCAAAT
113
396





954326
N/A
N/A
7792
7808
GAAAACTATAACCTGCA
107
397





954334
N/A
N/A
8167
8183
GCCAAAAAAGAAATGCT
131
398





954342
N/A
N/A
8296
8312
AGTTAGACAAAGATGAC
102
399





954350
N/A
N/A
8340
8356
TAAAATCTGGGAAGAAG
 87
400





954358
N/A
N/A
8368
8384
ACACATTTAAATGCTTG
 92
401





954366
N/A
N/A
8443
8459
GAACAATATCTATGACA
 77
402





954374
N/A
N/A
8469
8485
TAATAAGAATTACAGGT
 78
403





954382
N/A
N/A
8516
8532
CCAAAAGTCCTCTTTTA
 95
404





954390
N/A
N/A
8577
8593
GAGAATATGTCACCAGC
102
405





954398
N/A
N/A
8626
8642
TTATTTACAGGAAATGG
 87
406





954406
N/A
N/A
8680
8696
GACTAAATGTTTTGAGT
 81
407
















TABLE 7







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
130
 78





953799
39
55
1024
1040
CCGCAGGTAAAAGCAGA
 66
408





953807
N/A
N/A
1596
1612
GGACAAGGGAAGACCCA
104
409





953815
N/A
N/A
1725
1741
CGCAAATAAAAAGAAAC
122
112





953823
N/A
N/A
1812
1828
CTAGAAGAGGGAAGTGG
145
141





953831
N/A
N/A
1912
1928
CCTAAAAGCATTATGTC
 83
410





953839
N/A
N/A
1986
2002
AGGAAAAGAAATCTCCC
133
411





953847
N/A
N/A
2051
2067
AACTAAATGAAATGTCC
132
412





953855
N/A
N/A
2165
2181
CACCACTTTACTTGGCA
102
413





953863
N/A
N/A
2227
2243
CAAAAAACTTCAATCAA
117
414





953871
N/A
N/A
2308
2324
GTAAAATGTACACCTCA
 74
415





953879
N/A
N/A
2403
2419
CAATGAAGCAAACAGAA
106
416





953887
N/A
N/A
2446
2462
AGCAACAGAAACCCCTA
115
417





953895
N/A
N/A
2470
2486
TTTCAAAAATTCTCCCC
136
418





953903
N/A
N/A
2592
2608
GGTAAGAGAAAGGCCTG
121
419





953911
N/A
N/A
2623
2639
ACACATCCAGATCGGAA
115
420





953919
N/A
N/A
2670
2686
AAATTAATCAGTCTTAA
 90
421





953927
N/A
N/A
2723
2739
TTGAAGACGAGACAAGG
110
422





953935
N/A
N/A
2766
2782
AAATAAGCTAACACTGC
110
423





953943
N/A
N/A
2797
2813
AGAATAATTTATTCCTA
123
424





953951
N/A
N/A
2855
2871
AGATAAGCCAAATTGTT
129
425





953959
N/A
N/A
2897
2913
AGCACTACAGTAAATTT
105
426





953967
N/A
N/A
2941
2957
ATACATGCAATGTGTGA
111
427





953975
N/A
N/A
2990
3006
CAGAAAGGTCTTCCTTC
131
428





953983
N/A
N/A
3031
3047
AGGCATATTTTTAGAAT
116
429





953991
N/A
N/A
3070
3086
AGCAAATGCAGGTTCTG
 49
430





953999
N/A
N/A
3104
3120
AAGGAAATTTCTTGATA
123
431





954007
N/A
N/A
3139
3155
ATGAAACAAAATCTATC
103
432





954015
N/A
N/A
3170
3186
AAATAAGGTAATCATAT
 89
433





954023
N/A
N/A
3531
3547
ACAGAATTTGTATCATG
 47
434





954031
N/A
N/A
3598
3614
GACAAAGTTAGGTACTC
 81
435





954039
N/A
N/A
3656
3672
ATGAACAGGTTATATCT
101
436





954047
N/A
N/A
3679
3695
GCATTTTAAATCTATCT
 28
437





954055
N/A
N/A
4032
4048
TAAGAACCTTTAAAAGT
109
438





954063
N/A
N/A
4070
4086
CTATAAATAAACCTAAT
104
439





954071
N/A
N/A
4153
4169
AAAATTAGTGAATACCT
 80
440





954079
N/A
N/A
4190
4206
GCCAAAATCCAAACTTT
118
441





954087
N/A
N/A
4280
4296
CCATAAAAACAGAACAG
 93
442





954095
N/A
N/A
4348
4364
GCACAAACACTCATAAA
100
443





954103
N/A
N/A
4454
4470
TATTAATTGCCTCCTAA
 81
444





954111
N/A
N/A
4479
4495
AGAATAAGAAACTGCCA
119
445





954119
N/A
N/A
4517
4533
GAATAAAGTCAGGGAAA
 79
446





954127
N/A
N/A
4555
4571
GCACATAGTACATGTTT
107
447





954135
N/A
N/A
4629
4645
CATTAGAATGAAAGCTT
 74
448





954143
N/A
N/A
4899
4915
GCTGATAGAGCAAGAAC
116
449





954151
N/A
N/A
5505
5521
CGTATTTAAAATATCAA
101
450





954159
N/A
N/A
5618
5634
AGCTACGATAGTGATAC
108
451





954167
N/A
N/A
5786
5802
TGGAATACCACTACTTC
110
452





954175
N/A
N/A
5844
5860
TAAAATGACATCCTTGC
123
453





954183
N/A
N/A
5882
5898
TCTTACTACAAATGTCC
125
454





954191
N/A
N/A
5966
5982
CATAAATGCCAATATCT
120
455





954199
N/A
N/A
6036
6052
CACTTAAGATTGAAATT
122
456





954207
N/A
N/A
6211
6227
CAACAAGTGCAGTTGGT
104
457





954215
N/A
N/A
6249
6265
ACGCAAGCTACTGCTAA
115
458





954223
N/A
N/A
6328
6344
TGATAAGCTCTTGCTTG
107
459





954231
N/A
N/A
6707
6723
AGTATAAGAAAGAGCCT
101
460





954239
N/A
N/A
6802
6818
TGATAAGAATCCAGTAT
 95
461





954247
N/A
N/A
6913
6929
ATAGATAAACTCGACTT
 86
462





954255
N/A
N/A
7044
7060
TCAAAATGGATCAGACT
 97
463





954263
N/A
N/A
7167
7183
GGGTACTAAGATAATTC
100
464





954271
N/A
N/A
7195
7211
ACAATTAAGGACGATTA
 93
465





954279
N/A
N/A
7234
7250
GACCAACAGGTAGAACT
109
466





954287
N/A
N/A
7287
7303
ACACAAACTTCAGTAAT
128
467





954295
N/A
N/A
7423
7439
TCCTACTTGGCTTCTTT
131
468





954303
N/A
N/A
7528
7544
ACCATTTACACAAAGTT
 86
469





954311
N/A
N/A
7618
7634
TGCTTATGGCTACTTTC
108
470





954319
N/A
N/A
7733
7749
TTAAATGGTTGACCAAA
 84
471





954327
N/A
N/A
7793
7809
GGAAAACTATAACCTGC
120
472





954335
N/A
N/A
8222
8238
GTATATGTGTAACTTTT
 64
473





954343
N/A
N/A
8301
8317
TAGGAAGTTAGACAAAG
 56
474





954351
N/A
N/A
8343
8359
TATTAAAATCTGGGAAG
105
475





954359
N/A
N/A
8370
8386
TGACACATTTAAATGCT
126
476





954367
N/A
N/A
8445
8461
TGGAACAATATCTATGA
 85
477





954375
N/A
N/A
8470
8486
TTAATAAGAATTACAGG
 90
478





954383
N/A
N/A
8517
8533
TCCAAAAGTCCTCTTTT
122
479





954391
N/A
N/A
8578
8594
AGAGAATATGTCACCAG
 67
480





954399
N/A
N/A
8629
8645
GACTTATTTACAGGAAA
 77
481





954407
N/A
N/A
8683
8699
TAAGACTAAATGTTTTG
117
482
















TABLE 8







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
 93
 78





953800
287
303
1266
1282
AGCTGAGGAGGCGGCGG
129
483





953808
N/A
N/A
1603
1619
CGCGAGAGGACAAGGGA
114
484





953816
N/A
N/A
1753
1769
AGTTAAAAGAACCCCCG
116
485





953824
N/A
N/A
1814
1830
GACTAGAAGAGGGAAGT
110
486





953832
N/A
N/A
1913
1929
TCCTAAAAGCATTATGT
141
171





953840
N/A
N/A
1987
2003
TAGGAAAAGAAATCTCC
115
186





953848
N/A
N/A
2096
2112
CTCTTAGGTGGTGCTTA
104
217





953856
N/A
N/A
2188
2204
TTTCATTAATCACCACG
115
487





953864
N/A
N/A
2229
2245
GGCAAAAAACTTCAATC
 81
248





953872
N/A
N/A
2309
2325
GGTAAAATGTACACCTC
109
487





953880
N/A
N/A
2405
2421
AGCAATGAAGCAAACAG
 96
488





953888
N/A
N/A
2447
2463
AAGCAACAGAAACCCCT
112
489





953896
N/A
N/A
2494
2510
GTTTTAATGGTCTCTCT
 59
490





953904
N/A
N/A
2603
2619
GAATACTGAGAGGTAAG
101
491





953912
N/A
N/A
2634
2650
TGCCATCTGGGACACAT
117
492





953920
N/A
N/A
2671
2687
AAAATTAATCAGTCTTA
 88
493





953928
N/A
N/A
2730
2746
TTAAACTTTGAAGACGA
 86
494





953936
N/A
N/A
2767
2783
CAAATAAGCTAACACTG
112
495





953944
N/A
N/A
2803
2819
TCCTTTAGAATAATTTA
111
496





953952
N/A
N/A
2859
2875
GAAGAGATAAGCCAAAT
101
497





953960
N/A
N/A
2898
2914
AAGCACTACAGTAAATT
111
498





953968
N/A
N/A
2945
2961
CAAGATACATGCAATGT
121
499





953976
N/A
N/A
2991
3007
GCAGAAAGGTCTTCCTT
114
500





953984
N/A
N/A
3035
3051
GAGAAGGCATATTTTTA
103
501





953992
N/A
N/A
3075
3091
AGATAAGCAAATGCAGG
 97
502





954000
N/A
N/A
3108
3124
AGCAAAGGAAATTTCTT
121
503





954008
N/A
N/A
3148
3164
CTTAAAGTAATGAAACA
132
504





954016
N/A
N/A
3171
3187
TAAATAAGGTAATCATA
125
505





954024
N/A
N/A
3533
3549
TTACAGAATTTGTATCA
138
506





954032
N/A
N/A
3620
3636
TGAAATAGTGCTTGTTC
 91
507





954040
N/A
N/A
3657
3673
TATGAACAGGTTATATC
120
508





954048
N/A
N/A
3701
3717
CTAAACTACTTTTGTTT
 95
509





954056
N/A
N/A
4033
4049
CTAAGAACCTTTAAAAG
135
510





954064
N/A
N/A
4071
4087
ACTATAAATAAACCTAA
117
511





954072
N/A
N/A
4154
4170
CAAAATTAGTGAATACC
 93
512





954080
N/A
N/A
4199
4215
AACAGAACTGCCAAAAT
117
513





954088
N/A
N/A
4288
4304
AGCAAGAGCCATAAAAA
122
514





954096
N/A
N/A
4355
4371
GAGCAGAGCACAAACAC
102
515





954104
N/A
N/A
4455
4471
GTATTAATTGCCTCCTA
110
516





954112
N/A
N/A
4480
4496
GAGAATAAGAAACTGCC
108
517





954120
N/A
N/A
4519
4535
ATGAATAAAGTCAGGGA
105
518





954128
N/A
N/A
4557
4573
AGGCACATAGTACATGT
144
519





954136
N/A
N/A
4632
4648
CTTCATTAGAATGAAAG
123
520





954144
N/A
N/A
4900
4916
GGCTGATAGAGCAAGAA
118
521





954152
N/A
N/A
5506
5522
CCGTATTTAAAATATCA
101
522





954160
N/A
N/A
5679
5695
CAACACATTGTGAGGTT
110
523





954168
N/A
N/A
5815
5831
AGGAAGATTTTGGACCT
108
524





954176
N/A
N/A
5845
5861
CTAAAATGACATCCTTG
 96
525





954184
N/A
N/A
5934
5950
GGCAAGTAGTATTGGTC
102
526





954192
N/A
N/A
5967
5983
ACATAAATGCCAATATC
115
527





954200
N/A
N/A
6046
6062
AGCCAGAGTTCACTTAA
 98
528





954208
N/A
N/A
6221
6237
TAGCAGAGTTCAACAAG
106
529





954216
N/A
N/A
6253
6269
GATAACGCAAGCTACTG
107
530





954224
N/A
N/A
6345
6361
GACTTATTTTTGTCTTC
129
531





954232
N/A
N/A
6709
6725
TAAGTATAAGAAAGAGC
 99
532





954240
N/A
N/A
6823
6839
AGTTTTTACAAATCATC
 91
533





954248
N/A
N/A
6914
6930
AATAGATAAACTCGACT
100
534





954256
N/A
N/A
7086
7102
AATAAAGTTGGACTTCT
121
535





954264
N/A
N/A
7172
7188
AACAAGGGTACTAAGAT
 80
536





954272
N/A
N/A
7196
7212
TACAATTAAGGACGATT
 63
537





954280
N/A
N/A
7239
7255
ATAAAGACCAACAGGTA
118
538





954288
N/A
N/A
7297
7313
TTAAACTGTGACACAAA
 71
539





954296
N/A
N/A
7441
7457
ACACAATCCCTCTCAGA
100
540





954304
N/A
N/A
7543
7559
AATACTTACAATCTGAC
 54
541





954312
N/A
N/A
7626
7642
ATACATATTGCTTATGG
113
542





954320
N/A
N/A
7734
7750
TTTAAATGGTTGACCAA
 94
543





954328
N/A
N/A
7794
7810
GGGAAAACTATAACCTG
121
544





954336
N/A
N/A
8272
8288
CAAGAAGGGCTTTGTTT
116
545





954344
N/A
N/A
8305
8321
TTCTTAGGAAGTTAGAC
107
546





954352
N/A
N/A
8344
8360
ATATTAAAATCTGGGAA
 78
547





954360
N/A
N/A
8407
8423
ACATATGTAATGTGATC
111
548





954368
N/A
N/A
8450
8466
TGCTATGGAACAATATC
135
549





954376
N/A
N/A
8473
8489
CAATTAATAAGAATTAC
110
550





954384
N/A
N/A
8545
8561
AAAAATGTGAGACCTTT
103
551





954392
N/A
N/A
8582
8598
GTAGAGAGAATATGTCA
 66
552





954400
N/A
N/A
8640
8656
ATCAAGTGGTTGACTTA
114
553





954408
N/A
N/A
8688
8704
CTGAATAAGACTAAATG
103
554
















TABLE 9







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
114
 78





953801
329
345
1308
1324
GGCTGAGGCAGCAGCGG
129
555





953809
N/A
N/A
1624
1640
CAACAAGGCTCTGCCTC
119
556





953817
N/A
N/A
1757
1773
ACGCAGTTAAAAGAACC
 88
557





953825
N/A
N/A
1817
1833
TCAGACTAGAAGAGGGA
123
558





953833
N/A
N/A
1942
1958
CCCCCTGCCCCGCCACT
 91
559





953841
N/A
N/A
1993
2009
TGCCACTAGGAAAAGAA
125
188





953849
N/A
N/A
2108
2124
AGATGAGCAGATCTCTT
 99
560





953857
N/A
N/A
2193
2209
GATAATTTCATTAATCA
 92
561





953865
N/A
N/A
2230
2246
AGGCAAAAAACTTCAAT
103
562





953873
N/A
N/A
2310
2326
TGGTAAAATGTACACCT
 88
563





953881
N/A
N/A
2406
2422
CAGCAATGAAGCAAACA
118
564





953889
N/A
N/A
2451
2467
GAACAAGCAACAGAAAC
 99
565





953897
N/A
N/A
2502
2518
CGCTAGATGTTTTAATG
 87
566





953905
N/A
N/A
2608
2624
AAATAGAATACTGAGAG
 67
567





953913
N/A
N/A
2654
2670
ACAGAGATATTCTTACC
104
568





953921
N/A
N/A
2674
2690
CTAAAAATTAATCAGTC
 73
569





953929
N/A
N/A
2731
2747
ATTAAACTTTGAAGACG
110
570





953937
N/A
N/A
2768
2784
ACAAATAAGCTAACACT
105
571





953945
N/A
N/A
2818
2834
CAAAAAGTTTTTCCATC
 90
572





953953
N/A
N/A
2866
2882
ACTTACTGAAGAGATAA
 83
573





953961
N/A
N/A
2902
2918
AGAAAAGCACTACAGTA
105
574





953969
N/A
N/A
2946
2962
ACAAGATACATGCAATG
100
575





953977
N/A
N/A
2993
3009
CAGCAGAAAGGTCTTCC
128
576





953985
N/A
N/A
3036
3052
AGAGAAGGCATATTTTT
 89
577





953993
N/A
N/A
3077
3093
GAAGATAAGCAAATGCA
 70
578





954001
N/A
N/A
3109
3125
CAGCAAAGGAAATTTCT
 92
579





954009
N/A
N/A
3149
3165
CCTTAAAGTAATGAAAC
112
580





954017
N/A
N/A
3172
3188
TTAAATAAGGTAATCAT
 93
581





954025
N/A
N/A
3537
3553
GTAATTACAGAATTTGT
104
582





954033
N/A
N/A
3622
3638
ACTGAAATAGTGCTTGT
 68
583





954041
N/A
N/A
3658
3674
ATATGAACAGGTTATAT
 91
584





954049
N/A
N/A
3703
3719
TTCTAAACTACTTTTGT
 99
585





954057
N/A
N/A
4035
4051
TGCTAAGAACCTTTAAA
 88
586





954065
N/A
N/A
4072
4088
AACTATAAATAAACCTA
107
587





954073
N/A
N/A
4155
4171
TCAAAATTAGTGAATAC
105
588





954081
N/A
N/A
4200
4216
GAACAGAACTGCCAAAA
 78
589





954089
N/A
N/A
4294
4310
CCAAAGAGCAAGAGCCA
110
590





954097
N/A
N/A
4384
4400
CCATAAGGAACTCCTGC
 96
591





954105
N/A
N/A
4457
4473
AAGTATTAATTGCCTCC
 94
592





954113
N/A
N/A
4481
4497
GGAGAATAAGAAACTGC
 86
593





954121
N/A
N/A
4520
4536
AATGAATAAAGTCAGGG
 85
594





954129
N/A
N/A
4570
4586
CTATAACAGTGCCAGGC
 49
595





954137
N/A
N/A
4742
4758
TAACACTCGATTAACCC
 88
596





954145
N/A
N/A
5279
5295
TCACAAGGTCGGCGGAT
 90
597





954153
N/A
N/A
5511
5527
GAACACCGTATTTAAAA
 89
598





954161
N/A
N/A
5726
5742
TCAAAAGCCATCATCTG
 84
599





954169
N/A
N/A
5816
5832
CAGGAAGATTTTGGACC
 95
600





954177
N/A
N/A
5846
5862
ACTAAAATGACATCCTT
113
601





954185
N/A
N/A
5935
5951
AGGCAAGTAGTATTGGT
 81
602





954193
N/A
N/A
5968
5984
CACATAAATGCCAATAT
 90
603





954201
N/A
N/A
6093
6109
CCTAACTGGTTTCTGCT
 89
604





954209
N/A
N/A
6228
6244
TTATACTTAGCAGAGTT
 88
605





954217
N/A
N/A
6254
6270
TGATAACGCAAGCTACT
108
606





954225
N/A
N/A
6350
6366
CCCCAGACTTATTTTTG
 85
607





954233
N/A
N/A
6712
6728
AGGTAAGTATAAGAAAG
 89
608





954241
N/A
N/A
6833
6849
AGGAAGGGAGAGTTTTT
 92
609





954249
N/A
N/A
6917
6933
CAAAATAGATAAACTCG
 97
610





954257
N/A
N/A
7087
7103
GAATAAAGTTGGACTTC
104
611





954265
N/A
N/A
7184
7200
CGATTAATTTTCAACAA
109
612





954273
N/A
N/A
7197
7213
ATACAATTAAGGACGAT
 74
613





954281
N/A
N/A
7241
7257
ACATAAAGACCAACAGG
 87
614





954289
N/A
N/A
7299
7315
ATTTAAACTGTGACACA
109
615





954297
N/A
N/A
7479
7495
TAAGATGCGAATACTCC
 87
616





954305
N/A
N/A
7546
7562
CGAAATACTTACAATCT
 90
617





954313
N/A
N/A
7628
7644
TCATACATATTGCTTAT
 64
618





954321
N/A
N/A
7735
7751
TTTTAAATGGTTGACCA
 88
619





954329
N/A
N/A
7809
7825
TTTTAACCTAGGAGTGG
 79
620





954337
N/A
N/A
8273
8289
GCAAGAAGGGCTTTGTT
102
621





954345
N/A
N/A
8320
8336
CAAGAAACACTTTTGTT
120
622





954353
N/A
N/A
8345
8361
CATATTAAAATCTGGGA
 82
623





954361
N/A
N/A
8409
8425
ATACATATGTAATGTGA
 97
624





954369
N/A
N/A
8462
8478
AATTACAGGTACTGCTA
101
625





954377
N/A
N/A
8474
8490
GCAATTAATAAGAATTA
 93
626





954385
N/A
N/A
8546
8562
CAAAAATGTGAGACCTT
 86
627





954393
N/A
N/A
8584
8600
AGGTAGAGAGAATATGT
109
628





954401
N/A
N/A
8641
8657
TATCAAGTGGTTGACTT
 94
629





954409
N/A
N/A
8689
8705
TCTGAATAAGACTAAAT
111
630
















TABLE 10







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO





646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
111
 78





953802
N/A
N/A
1408
1424
GGACAGGGAGCTGCAGC
 95
631





953810
N/A
N/A
1626
1642
CCCAACAAGGCTCTGCC
 87
632





953818
N/A
N/A
1761
1777
CACAACGCAGTTAAAAG
103
124





953826
N/A
N/A
1886
1902
CCCCACATCTCTCCAGC
109
633





953834
N/A
N/A
1966
1982
GGACGCGCCCTCACTCC
 88
634





953842
N/A
N/A
2016
2032
CTCAAATCTCAGGCTGT
111
635





953850
N/A
N/A
2112
2128
GCTTAGATGAGCAGATC
 97
636





953858
N/A
N/A
2194
2210
AGATAATTTCATTAATC
 95
238





953866
N/A
N/A
2234
2250
ACATAGGCAAAAAACTT
 92
637





953874
N/A
N/A
2316
2332
GAATACTGGTAAAATGT
112
638





953882
N/A
N/A
2417
2433
TAACAAGCTGTCAGCAA
106
639





953890
N/A
N/A
2454
2470
CAAGAACAAGCAACAGA
100
640





953898
N/A
N/A
2525
2541
TTCCAGGGAAAGTCCTG
 86
641





953906
N/A
N/A
2610
2626
GGAAATAGAATACTGAG
 67
642





953914
N/A
N/A
2656
2672
TAACAGAGATATTCTTA
111
643





953922
N/A
N/A
2675
2691
ACTAAAAATTAATCAGT
 91
644





953930
N/A
N/A
2732
2748
AATTAAACTTTGAAGAC
109
645





953938
N/A
N/A
2769
2785
AACAAATAAGCTAACAC
 98
646





953946
N/A
N/A
2819
2835
CCAAAAAGTTTTTCCAT
 86
647





953954
N/A
N/A
2872
2888
GAAATTACTTACTGAAG
 63
648





953962
N/A
N/A
2903
2919
TAGAAAAGCACTACAGT
 79
649





953970
N/A
N/A
2947
2963
CACAAGATACATGCAAT
107
650





953978
N/A
N/A
3014
3030
GATCAAGTGTCTGAAGC
 66
651





953986
N/A
N/A
3044
3060
CATAAGAAAGAGAAGGC
 72
652





953994
N/A
N/A
3078
3094
TGAAGATAAGCAAATGC
 90
653





954002
N/A
N/A
3116
3132
GTCAAGGCAGCAAAGGA
 79
654





954010
N/A
N/A
3150
3166
ACCTTAAAGTAATGAAA
101
655





954018
N/A
N/A
3173
3189
TTTAAATAAGGTAATCA
 96
656





954026
N/A
N/A
3538
3554
TGTAATTACAGAATTTG
 80
657





954034
N/A
N/A
3626
3642
AGGAACTGAAATAGTGC
 89
658





954042
N/A
N/A
3661
3677
ACAATATGAACAGGTTA
 45
659





954050
N/A
N/A
3708
3724
TATTATTCTAAACTACT
102
660





954058
N/A
N/A
4060
4076
ACCTAATGCAGTTGATT
 67
661





954066
N/A
N/A
4106
4122
TGACAAATATGCATTTT
 60
662





954074
N/A
N/A
4156
4172
CTCAAAATTAGTGAATA
103
663





954082
N/A
N/A
4229
4245
GAGAAGAGGATTTTTTG
 89
664





954090
N/A
N/A
4296
4312
CACCAAAGAGCAAGAGC
101
665





954098
N/A
N/A
4386
4402
CCCCATAAGGAACTCCT
113
666





954106
N/A
N/A
4460
4476
AGCAAGTATTAATTGCC
 83
667





954114
N/A
N/A
4487
4503
TCTGAAGGAGAATAAGA
109
668





954122
N/A
N/A
4521
4537
GAATGAATAAAGTCAGG
 82
669





954130
N/A
N/A
4571
4587
CCTATAACAGTGCCAGG
 94
670





954138
N/A
N/A
4749
4765
AATAAGTTAACACTCGA
 92
671





954146
N/A
N/A
5281
5297
GATCACAAGGTCGGCGG
126
672





954154
N/A
N/A
5542
5558
AAAAAAGCTGTCTTCTC
 83
673





954162
N/A
N/A
5727
5743
CTCAAAAGCCATCATCT
 89
674





954170
N/A
N/A
5819
5835
AAACAGGAAGATTTTGG
 87
675





954178
N/A
N/A
5847
5863
AACTAAAATGACATCCT
 88
676





954186
N/A
N/A
5939
5955
TACAAGGCAAGTAGTAT
 95
677





954194
N/A
N/A
5969
5985
TCACATAAATGCCAATA
 67
678





954202
N/A
N/A
6094
6110
TCCTAACTGGTTTCTGC
 82
679





954210
N/A
N/A
6230
6246
TGTTATACTTAGCAGAG
 74
680





954218
N/A
N/A
6263
6279
ATACAAACCTGATAACG
 95
681





954226
N/A
N/A
6370
6386
CTTAACTTATTGTTGAA
107
682





954234
N/A
N/A
6716
6732
TGCAAGGTAAGTATAAG
 79
683





954242
N/A
N/A
6837
6853
CCAAAGGAAGGGAGAGT
 87
684





954250
N/A
N/A
6930
6946
CAGCAACCAAAGACAAA
 88
685





954258
N/A
N/A
7088
7104
AGAATAAAGTTGGACTT
 86
686





954266
N/A
N/A
7185
7201
ACGATTAATTTTCAACA
 64
687





954274
N/A
N/A
7198
7214
TATACAATTAAGGACGA
 63
688





954282
N/A
N/A
7242
7258
GACATAAAGACCAACAG
 83
689





954290
N/A
N/A
7302
7318
TGAATTTAAACTGTGAC
 64
690





954298
N/A
N/A
7502
7518
TCATAGGTGGAAGACAA
 79
691





954306
N/A
N/A
7547
7563
CCGAAATACTTACAATC
 71
692





954314
N/A
N/A
7630
7646
ACTCATACATATTGCTT
 82
693





954322
N/A
N/A
7761
7777
TCACAAGCTAAGAAATG
103
694





954330
N/A
N/A
7816
7832
TATCATATTTTAACCTA
116
695





954338
N/A
N/A
8274
8290
TGCAAGAAGGGCTTTGT
 96
696





954346
N/A
N/A
8322
8338
CACAAGAAACACTTTTG
103
697





954354
N/A
N/A
8346
8362
GCATATTAAAATCTGGG
 73
698





954362
N/A
N/A
8410
8426
AATACATATGTAATGTG
 95
699





954370
N/A
N/A
8463
8479
GAATTACAGGTACTGCT
 71
700





954378
N/A
N/A
8475
8491
AGCAATTAATAAGAATT
 82
701





954386
N/A
N/A
8547
8563
ACAAAAATGTGAGACCT
 72
702





954394
N/A
N/A
8589
8605
TCTCAAGGTAGAGAGAA
 88
703





954402
N/A
N/A
8653
8669
TCAAAGGTAGTTTATCA
 83
704





954410
N/A
N/A
8722
8738
CTTTATAAGGTATTTTA
106
705
















TABLE 11







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
118
78





953803
N/A
N/A
1458
1474
CCGCAGGCTGCAGGGTT
97
706





953811
N/A
N/A
1627
1643
CCCCAACAAGGCTCTGC
136
707





953819
N/A
N/A
1762
1778
TCACAACGCAGTTAAAA
120
708





953827
N/A
N/A
1904
1920
CATTATGTCATCCACTG
76
709





953835
N/A
N/A
1973
1989
TCCCATTGGACGCGCCC
103
710





953843
N/A
N/A
2033
2049
GACAATGTAGGAAGAGC
88
711





953851
N/A
N/A
2117
2133
CTTAGGCTTAGATGAGC
135
712





953859
N/A
N/A
2205
2221
CCTAATATTTAAGATAA
92
240





953867
N/A
N/A
2235
2251
CACATAGGCAAAAAACT
94
250





953875
N/A
N/A
2318
2334
TGGAATACTGGTAAAAT
122
713





953883
N/A
N/A
2424
2440
CAAAAAGTAACAAGCTG
98
714





953891
N/A
N/A
2455
2471
CCAAGAACAAGCAACAG
141
715





953899
N/A
N/A
2544
2560
GTACACTCGACACACAG
86
716





953907
N/A
N/A
2611
2627
CGGAAATAGAATACTGA
109
717





953915
N/A
N/A
2658
2674
CTTAACAGAGATATTCT
123
718





953923
N/A
N/A
2689
2705
GAACAAGAAATATTACT
132
719





953931
N/A
N/A
2733
2749
TAATTAAACTTTGAAGA
92
720





953939
N/A
N/A
2770
2786
CAACAAATAAGCTAACA
105
721





953947
N/A
N/A
2820
2836
TCCAAAAAGTTTTTCCA
93
722





953955
N/A
N/A
2889
2905
AGTAAATTTCTGGATGA
92
723





953963
N/A
N/A
2904
2920
CTAGAAAAGCACTACAG
118
724





953971
N/A
N/A
2948
2964
ACACAAGATACATGCAA
123
725





953979
N/A
N/A
3021
3037
TTAGAATGATCAAGTGT
64
726





953987
N/A
N/A
3045
3061
GCATAAGAAAGAGAAGG
85
727





953995
N/A
N/A
3079
3095
TTGAAGATAAGCAAATG
103
728





954003
N/A
N/A
3117
3133
TGTCAAGGCAGCAAAGG
88
729





954011
N/A
N/A
3156
3172
TATATTACCTTAAAGTA
113
730





954019
N/A
N/A
3217
3233
TCGGATTAAAGGTGTAA
127
731





954027
N/A
N/A
3554
3570
TTAATTATTGCCCTTTT
55
732





954035
N/A
N/A
3633
3649
ATACATGAGGAACTGAA
75
733





954043
N/A
N/A
3662
3678
TACAATATGAACAGGTT
63
734





954051
N/A
N/A
3709
3725
ATATTATTCTAAACTAC
124
735





954059
N/A
N/A
4065
4081
AATAAACCTAATGCAGT
130
736





954067
N/A
N/A
4119
4135
ATACAGAGAAATATGAC
122
737





954075
N/A
N/A
4157
4173
ACTCAAAATTAGTGAAT
137
738





954083
N/A
N/A
4244
4260
CATCAATCTTACTTTGA
106
739





954091
N/A
N/A
4336
4352
ATAAACTGAGGCCCATG
133
740





954099
N/A
N/A
4413
4429
TGCTAGATTTGCTGAGC
120
741





954107
N/A
N/A
4461
4477
AAGCAAGTATTAATTGC
98
742





954115
N/A
N/A
4497
4513
CAGATAGGAATCTGAAG
116
743





954123
N/A
N/A
4524
4540
GATGAATGAATAAAGTC
60
744





954131
N/A
N/A
4572
4588
ACCTATAACAGTGCCAG
103
745





954139
N/A
N/A
4750
4766
AAATAAGTTAACACTCG
83
746





954147
N/A
N/A
5498
5514
AAAATATCAACACTGGC
159
747





954155
N/A
N/A
5585
5601
TTAAAGAGCAAGACCTT
114
748





954163
N/A
N/A
5750
5766
TCTTAACTCGCTTGAGG
118
749





954171
N/A
N/A
5820
5836
GAAACAGGAAGATTTTG
104
750





954179
N/A
N/A
5850
5866
CCCAACTAAAATGACAT
109
751





954187
N/A
N/A
5940
5956
CTACAAGGCAAGTAGTA
92
752





954195
N/A
N/A
5971
5987
ACTCACATAAATGCCAA
110
753





954203
N/A
N/A
6132
6148
ACAGAACCCACCATGCT
103
754





954211
N/A
N/A
6236
6252
CTAAATTGTTATACTTA
102
755





954219
N/A
N/A
6268
6284
GCTGAATACAAACCTGA
79
756





954227
N/A
N/A
6389
6405
AAAGAAAGAGCCTGGGT
85
757





954235
N/A
N/A
6717
6733
TTGCAAGGTAAGTATAA
108
758





954243
N/A
N/A
6838
6854
TCCAAAGGAAGGGAGAG
130
759





954251
N/A
N/A
6951
6967
TTAGATATGACACTTGA
103
760





954259
N/A
N/A
7161
7177
TAAGATAATTCCATGGG
112
761





954267
N/A
N/A
7186
7202
GACGATTAATTTTCAAC
100
762





954275
N/A
N/A
7199
7215
TTATACAATTAAGGACG
101
763





954283
N/A
N/A
7243
7259
CGACATAAAGACCAACA
96
764





954291
N/A
N/A
7304
7320
CATGAATTTAAACTGTG
87
765





954299
N/A
N/A
7520
7536
CACAAAGTTTGCCCATG
75
766





954307
N/A
N/A
7548
7564
CCCGAAATACTTACAAT
106
767





954315
N/A
N/A
7640
7656
GAACACAGACACTCATA
119
768





954323
N/A
N/A
7780
7796
CTGCATATTTTTGGCTA
152
769





954331
N/A
N/A
7830
7846
TCCAAATGTGGTCCTAT
103
770





954339
N/A
N/A
8290
8306
ACAAAGATGACAGACTT
68
771





954347
N/A
N/A
8323
8339
ACACAAGAAACACTTTT
83
772





954355
N/A
N/A
8347
8363
TGCATATTAAAATCTGG
94
773





954363
N/A
N/A
8433
8449
TATGACACATTGTTAAG
147
774





954371
N/A
N/A
8464
8480
AGAATTACAGGTACTGC
116
775





954379
N/A
N/A
8476
8492
TAGCAATTAATAAGAAT
104
776





954387
N/A
N/A
8548
8564
CACAAAAATGTGAGACC
111
777





954395
N/A
N/A
8618
8634
AGGAAATGGAGGTGATG
76
778





954403
N/A
N/A
8654
8670
TTCAAAGGTAGTTTATC
149
779





954411
N/A
N/A
8723
8739
GCTTTATAAGGTATTTT
82
780
















TABLE 12







Reduction of HTT RNA by modified oligonucleotides with a mixed MOE/cEt sugar motif


and mixed PO/PS internucleoside linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















646253
N/A
N/A
1447
1463
AGGGTTACCGCCATCCC
97
78





953804
N/A
N/A
1583
1599
CCCAAGTGAGGGAGCGG
98
781





953812
N/A
N/A
1674
1690
GGCGAGAGGGCTGAGGC
114
782





953820
N/A
N/A
1798
1814
TGGCACTGAGCAAATCT
89
783





953828
N/A
N/A
1905
1921
GCATTATGTCATCCACT
101
784





953836
N/A
N/A
1978
1994
AAATCTCCCATTGGACG
92
785





953844
N/A
N/A
2034
2050
TGACAATGTAGGAAGAG
99
786





953852
N/A
N/A
2123
2139
GACCAACTTAGGCTTAG
97
787





953860
N/A
N/A
2206
2222
TCCTAATATTTAAGATA
133
788





953868
N/A
N/A
2236
2252
ACACATAGGCAAAAAAC
87
789





953876
N/A
N/A
2361
2377
GCCCACGGAGTCTGCGG
100
790





953884
N/A
N/A
2425
2441
CCAAAAAGTAACAAGCT
100
791





953892
N/A
N/A
2456
2472
CCCAAGAACAAGCAACA
87
792





953900
N/A
N/A
2551
2567
TCCTACTGTACACTCGA
91
793





953908
N/A
N/A
2612
2628
TCGGAAATAGAATACTG
145
794





953916
N/A
N/A
2659
2675
TCTTAACAGAGATATTC
89
795





953924
N/A
N/A
2707
2723
GATCATAACAGAAACAA
136
796





953932
N/A
N/A
2735
2751
TCTAATTAAACTTTGAA
86
797





953940
N/A
N/A
2783
2799
CTAAATTTTATTCCAAC
79
798





953948
N/A
N/A
2821
2837
ATCCAAAAAGTTTTTCC
97
799





953956
N/A
N/A
2890
2906
CAGTAAATTTCTGGATG
82
800





953964
N/A
N/A
2905
2921
CCTAGAAAAGCACTACA
109
801





953972
N/A
N/A
2950
2966
TTACACAAGATACATGC
93
802





953980
N/A
N/A
3023
3039
TTTTAGAATGATCAAGT
74
803





953988
N/A
N/A
3054
3070
GTCAAATCAGCATAAGA
118
804





953996
N/A
N/A
3084
3100
ATATTTTGAAGATAAGC
101
805





954004
N/A
N/A
3133
3149
CAAAATCTATCTCCTTT
120
806





954012
N/A
N/A
3159
3175
TCATATATTACCTTAAA
115
807





954020
N/A
N/A
3510
3526
TGTATTACTTATGCAAA
89
808





954028
N/A
N/A
3557
3573
ATTTTAATTATTGCCCT
70
809





954036
N/A
N/A
3634
3650
GATACATGAGGAACTGA
108
810





954044
N/A
N/A
3663
3679
TTACAATATGAACAGGT
46
811





954052
N/A
N/A
3747
3763
GACAATGTGAGACTACA
103
812





954060
N/A
N/A
4066
4082
AAATAAACCTAATGCAG
130
813





954068
N/A
N/A
4124
4140
GCAAAATACAGAGAAAT
63
814





954076
N/A
N/A
4184
4200
ATCCAAACTTTGTGAGC
140
815





954084
N/A
N/A
4269
4285
GAACAGATACTTTCTAA
111
816





954092
N/A
N/A
4337
4353
CATAAACTGAGGCCCAT
118
817





954100
N/A
N/A
4422
4438
TCCCAAGCATGCTAGAT
122
818





954108
N/A
N/A
4465
4481
CCAGAAGCAAGTATTAA
88
819





954116
N/A
N/A
4500
4516
CACCAGATAGGAATCTG
110
820





954124
N/A
N/A
4533
4549
ATATTTACTGATGAATG
95
821





954132
N/A
N/A
4612
4628
CACGAGGGCAGAGCTTT
79
822





954140
N/A
N/A
4751
4767
AAAATAAGTTAACACTC
126
823





954148
N/A
N/A
5499
5515
TAAAATATCAACACTGG
104
824





954156
N/A
N/A
5614
5630
ACGATAGTGATACTGCA
79
825





954164
N/A
N/A
5761
5777
TTACACTAGACTCTTAA
85
826





954172
N/A
N/A
5821
5837
TGAAACAGGAAGATTTT
138
827





954180
N/A
N/A
5851
5867
ACCCAACTAAAATGACA
102
828





954188
N/A
N/A
5942
5958
ATCTACAAGGCAAGTAG
105
829





954196
N/A
N/A
6027
6043
TTGAAATTCAGATCATG
117
830





954204
N/A
N/A
6186
6202
CAAAATCCAGTCAGTCA
77
831





954212
N/A
N/A
6237
6253
GCTAAATTGTTATACTT
82
832





954220
N/A
N/A
6269
6285
AGCTGAATACAAACCTG
80
833





954228
N/A
N/A
6703
6719
TAAGAAAGAGCCTGGGT
148
834





954236
N/A
N/A
6726
6742
AACAAGGGTTTGCAAGG
116
835





954244
N/A
N/A
6839
6855
ATCCAAAGGAAGGGAGA
99
836





954252
N/A
N/A
6988
7004
AGTAAACCTTTTTGACT
105
837





954260
N/A
N/A
7162
7178
CTAAGATAATTCCATGG
109
838





954268
N/A
N/A
7190
7206
TAAGGACGATTAATTTT
126
839





954276
N/A
N/A
7201
7217
ATTTATACAATTAAGGA
126
840





954284
N/A
N/A
7244
7260
TCGACATAAAGACCAAC
125
841





954292
N/A
N/A
7350
7366
GGCCAAATCAATCTTGA
91
842





954300
N/A
N/A
7521
7537
ACACAAAGTTTGCCCAT
80
843





954308
N/A
N/A
7549
7565
GCCCGAAATACTTACAA
125
844





954316
N/A
N/A
7656
7672
TAATAAAATTCTATTGG
128
845





954324
N/A
N/A
7787
7803
CTATAACCTGCATATTT
98
846





954332
N/A
N/A
7976
7992
TACTAGGGAGGCCGTGC
143
847





954340
N/A
N/A
8291
8307
GACAAAGATGACAGACT
100
848





954348
N/A
N/A
8327
8343
GAAGACACAAGAAACAC
129
849





954356
N/A
N/A
8348
8364
ATGCATATTAAAATCTG
102
850





954364
N/A
N/A
8440
8456
CAATATCTATGACACAT
48
851





954372
N/A
N/A
8465
8481
AAGAATTACAGGTACTG
74
852





954380
N/A
N/A
8489
8505
CTAAAATATTACATAGC
96
853





954388
N/A
N/A
8549
8565
CCACAAAAATGTGAGAC
87
854





954396
N/A
N/A
8622
8638
TTACAGGAAATGGAGGT
97
855





954404
N/A
N/A
8655
8671
ATTCAAAGGTAGTTTAT
106
856





954412
N/A
N/A
8724
8740
TGCTTTATAAGGTATTT
78
857









Example 3: Effect of 5-10-5 MOE Mixed Backbone Modified Oligonucleotides on Human HTT RNA In Vitro, Single Dose

Modified oligonucleotides complementary to human HTT nucleic acid were designed and tested for their single dose effects on HTT RNA in vitro. The modified oligonucleotides were tested in a series of experiments that had the same culture conditions.


The modified oligonucleotides in the tables below are 5-10-5 MOE gapmers with mixed PO/PS internucleoside linkages. The gapmers are 20 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar, and each “e” represents a 2′-MOE sugar moiety. The internucleoside linkage motif for the gapmers is (from 5′ to 3′): sooosssssssssssooss; wherein each “o” represents a phosphodiester internucleoside linkage, and each “s” represents a phosphorothioate internucleoside linkage. Each cytosine residue is a 5-methylcytosine.


“Start site” indicates the 5′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. Each modified oligonucleotide listed in the tables below is 100% complementary to SEQ ID NO: 1 (described herein above), to SEQ ID NO: 2 (described herein above), or to both. ‘N/A’ indicates that the modified oligonucleotide is not 100% complementary to that particular target nucleic acid sequence.


Cultured A431 cells were treated with modified oligonucleotide at a concentration of 2000 nM by free uptake at a density of 10,000 cells per well. After a treatment period of approximately 48 hours, total RNA was isolated from the cells and HTT RNA levels were measured by quantitative real-time RTPCR. HTT RNA levels were measured by human primer probe set RTS36478 (forward sequence ACCCTTGCAGAGATTGACTT, designated herein as SEQ ID NO: 17; reverse sequence AGCACTCGTTCTTGCAGTT, designated herein as SEQ ID NO: 18; probe sequence TTTGCCTCCAAAAAGCTCACCAGC, designated herein as SEQ ID NO: 19). HTT RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of HTT RNA is presented in the tables below as percent HTT RNA relative to the amount of the HTT RNA in untreated control cells (% UTC). Each table represents results from an individual assay plate. The values marked with a “t” indicate that the modified oligonucleotide is complementary to the amplicon region of the primer probe set. Additional assays may be used to measure the potency and efficacy of the modified oligonucleotides complementary to the amplicon region.


In the tables below, Compound 388241 was used as a comparator compound. Compound 388241 is 20 nucleosides in length, wherein the sugar motif is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar, and each “e” represents a 2′-MOE sugar moiety. The internucleoside linkage motif for Compound 388241 is (from 5′ to 3′): sssssssssssssssssss; wherein each “s” represents a phosphorothioate internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 13







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
19
858





1314495
N/A
N/A
3136
3155
ATGAAACAAAATCTATCTCC
82
859





1314500
N/A
N/A
129817
129836
AAAACACTTCTTCCCCACTA
54
860





1314528
N/A
N/A
46677
46696
TGAATTTATTCTTTTTCCCT
78
861





1314530
N/A
N/A
117826
117845
CTGAAACCATAATTAAGTCA
46
862





1314541
N/A
N/A
70544
70563
ACAAAAGTTATACTTGCTCA
12
863





1314544
N/A
N/A
60439
60458
GTCATGGTTTCAACTCTCAA
17
864





1314545
N/A
N/A
17085
17104
TATGTATTTATTCTTGCAGT
45
865





1314560
N/A
N/A
81880
81899
TACACATATTTCAAACATCA
55
866





1314580
N/A
N/A
68687
68706
CATGTCAATTTCTATCCCCC
25
867





1314618
N/A
N/A
17819
17838
GTCAATACTTTCCCCAAGTT
32
868





1314639
N/A
N/A
45022
45041
CCCTTTTTTCCCCTTCACCC
73
869





1314667
N/A
N/A
59084
59103
AGCAACAAACATCATCATCT
89
870





1314669
N/A
N/A
100946
100965
GCACTCAGATATACTCCTGC
79
871





1314691
N/A
N/A
34537
34556
TTATTCCAAATCATTCAGCT
68
872





1314751
N/A
N/A
10437
10456
ACCACATTCACCTCCCTCTC
66
873





1314769
N/A
N/A
56771
56790
GCGATTTTAAATCCTCACAC
54
874





1314774
N/A
N/A
111471
111490
GCCAACTTAACCCATTGCCG
40
875





1314793
N/A
N/A
48882
48901
CAGTCAAGTATAACTTTTCA
29
876





1314851
N/A
N/A
53293
53312
AGTTCAAGTTCTTAACCGAC
25
877





1314870
N/A
N/A
130450
130469
AGGCATTTCAAACTTACGAC
25
878





1314943
N/A
N/A
65893
65912
ACTATTTTATCATATTGGTC
19
879





1314955
2872
2891
62554
62573
GGATGACAACATTATTGAGC
3†
880





1314959
N/A
N/A
25031
25050
GTATAACCATATTTCACCCT
46
881





1314969
N/A
N/A
142119
142138
GCCACCATTTTCCTAGTAAA
43
882





1315018
N/A
N/A
56029
56048
CACTCATTCCCACTACATTA
53
883





1315039
N/A
N/A
136561
136580
CCAGATAGTTCTCATCCCAA
10
884





1315041
N/A
N/A
114520
114539
AGACTCACTTTTACTGGCTT
21
885





1315070
N/A
N/A
12554
12573
CTGTATTTCACCAATACTCA
68
886





1315074
N/A
N/A
108167
108186
GCACAAGTTTATTAGTGATC
9
887





1315076
N/A
N/A
7428
7447
TCTCAGAATCCTACTTGGCT
62
888





1315087
N/A
N/A
5891
5910
TTGGACCTTACTTCTTACTA
49
889





1315110
N/A
N/A
104193
104212
GGGAACACTTTCCTTCTGCA
64
890





1315144
3320
3339
73126
73145
GTACAGCTCTTCCTAGACTC
27
891





1315202
N/A
N/A
94641
94660
TCACCTCTCCAGCTACACTT
90
892





1315204
N/A
N/A
133712
133731
CCGTACAAATCTATATCCTT
31
893





1315444
N/A
N/A
45574
45593
TGGATGGTTACTAATTGCCT
49
894





1315451
N/A
N/A
19656
19675
TCTCTTTTTAATATTAGGTA
77
895





1315474
N/A
N/A
41859
41878
TTCACATTCAATCAACCAGT
65
896





1315506
N/A
N/A
20046
20065
TTCATCACTCCAATTTTCAA
88
897





1315527
N/A
N/A
106954
106973
AACATACATTCCTCTTACCT
84
898





1315544
N/A
N/A
134658
134677
CTGATAGGAATTCATGGTCA
25
899





1315615
N/A
N/A
110081
110100
AGTCAGGTATTTACTATGTA
23
900





1315620
N/A
N/A
105918
105937
ACTCTGACCCCTCAGTGACA
94
901





105969
105988








106024
106043








1315688
N/A
N/A
18989
19008
GTCACAAATATAAATATCTA
78
902





1315692
N/A
N/A
69357
69376
GTCATTTACATTCCTGGAGT
16
903





1315714
N/A
N/A
125875
125894
TTCTGATTTTTCTAAGCAGA
91
904





1315804
N/A
N/A
75430
75449
AGGACAGTAGCCATTAACCA
33
905





1315847
N/A
N/A
51146
51165
TGGGAATTTCTAATTTCTGC
23
906





1315992
N/A
N/A
160801
160820
CAGCCCAACACACCAGCACA
92
907





1316076
N/A
N/A
33828
33847
CGACATACAACATACCCCAA
84
908





1316148
N/A
N/A
43578
43597
GCTACACCCTTTTTACTCAA
34
909





1316158
N/A
N/A
26702
26721
AAGCAAAGATTCCCTGGGCA
86
910





1316180
N/A
N/A
149496
149515
GCAAAAGCCCATTTTTCAAA
93
911





1316335
N/A
N/A
9945
9964
TTCTAAATCCTCACCAGCAT
54
912





1316376
N/A
N/A
118118
118137
ACAACTTTAGACATCACCCA
54
913





1316405
N/A
N/A
138747
138766
GACATTGTTCCTCAGTGGCA
53
914





1316523
N/A
N/A
116031
116050
GGTCCTCTTAACTATTTTTA
76
915





1316576
N/A
N/A
40111
40130
ACTTCTCTCCTTGCCAGCCA
55
916





1316597
N/A
N/A
22579
22598
GGCTACTGAAATCTCTATCA
28
917





1316688
N/A
N/A
81002
81021
CCATCACCTGCAACCAGGGA
99
918





1316689
N/A
N/A
119649
119668
AAGCCATATTTTCTCAACTT
36
919





1316695
N/A
N/A
35427
35446
AGGAAGGGAACTACTATCTT
50
920





1316719
N/A
N/A
23097
23116
GCTTGTCATTTTCAAGTTTC
73
921





1316747
N/A
N/A
47423
47442
GACAAAGTTTATACCTTAAC
38
922





1316813
N/A
N/A
52749
52768
GGATTATACAACCAAAACCA
78
923





1316816
N/A
N/A
32332
32351
GGGTTTAGACCACATTCCCA
86
924





1316869
N/A
N/A
83780
83799
ACACGGATCCCTCCAGACTC
97
925





1316872
12480
12499
169229
169248
CTTCACATTTTCCCCTTGAA
68
926





1316933
N/A
N/A
72510
72529
GTAAGTCAAACTACCAAGCA
32
927





1316988
N/A
N/A
127367
127386
AACTAAATTTACCTTTGGTT
85
928





1316999
N/A
N/A
22171
22190
GAAATCTACCATCAAGCTCT
61
929





1317036
N/A
N/A
132358
132377
ACTCTTTTTCCAATTTTGTG
32
930





1317065
N/A
N/A
79756
79775
ATCGAGACTCCCAATGCTCT
79
931





1317087
N/A
N/A
14033
14052
AACATGAATTATTTATTCCA
63
932





1317119
7435
7454
146527
146546
TCTCAGGGAATGCTGTGCCA
47
933





1317177
N/A
N/A
15545
15564
GTAAAGATAACATATAGCTT
51
934





1317181
N/A
N/A
98526
98545
ACAAGATAACTTCCATTTAA
72
935
















TABLE 14







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
27
858





1314513
N/A
N/A
7351
7370
GCATGGCCAAATCAATCTTG
57
936





1314581
N/A
N/A
70467
70486
CCCAAAATTTATCTTGGTGA
49
937





1314632
N/A
N/A
81349
81368
GCAGCAGTCACTTCATGCTT
89
938





1314701
12479
12498
169228
169247
TTCACATTTTCCCCTTGAAA
70
939





1314723
N/A
N/A
119647
119666
GCCATATTTTCTCAACTTTA
19
940





1314754
N/A
N/A
52744
52763
ATACAACCAAAACCACCCTC
84
941





1314780
N/A
N/A
60433
60452
GTTTCAACTCTCAAACAGCA
80
942





1314831
N/A
N/A
20042
20061
TCACTCCAATTTTCAAGGCC
64
943





1314877
N/A
N/A
46668
46687
TCTTTTTCCCTITAATTACA
73
944





1314879
N/A
N/A
59083
59102
GCAACAAACATCATCATCTA
98
945





1314917
N/A
N/A
133711
133730
CGTACAAATCTATATCCTTT
43
946





1314938
N/A
N/A
48879
48898
TCAAGTATAACTTTTCATTA
61
947





1314995
N/A
N/A
138746
138765
ACATTGTTCCTCAGTGGCAC
88
948





1315026
N/A
N/A
18304
18323
ATCTTAAATTTTCAATCCCC
62
949





1315189
N/A
N/A
9909
9928
GATCTTTTCATCTAAATGCA
42
950





1315212
N/A
N/A
130449
130468
GGCATTTCAAACTTACGACA
42
951





1315238
3310
3329
73116
73135
TCCTAGACTCATCTGAGGCA
71
952





1315263
N/A
N/A
34527
34546
TCATTCAGCTAATAAGAGCA
74
953





1315281
N/A
N/A
19563
19582
GCTGAGGTTTTCCACTCCAA
70
954





1315293
N/A
N/A
26588
26607
AAGAACACTTCTTACCACTT
82
955





1315328
N/A
N/A
35423
35442
AGGGAACTACTATCTTTGTT
46
956





1315371
N/A
N/A
15450
15469
ACAGTGTTTCACATGTACCA
55
957





1315479
N/A
N/A
80880
80899
TCTGTGTACATCAGTCATTA
67
958





1315481
N/A
N/A
106953
106972
ACATACATTCCTCTTACCTG
93
959





1315513
N/A
N/A
114499
114518
TCTTGGGTTTCAACTTCCCT
77
960





1315549
N/A
N/A
14032
14051
ACATGAATTATTTATTCCAA
81
961





1315658
N/A
N/A
24894
24913
GTTTAGGCCATCATGCTCCA
57
962





1315673
N/A
N/A
55910
55929
CACAAACAAATTTTACAGCA
49
963





1315726
N/A
N/A
65817
65836
GTAGAATTTTTTCTAGAATA
88
964





1315736
N/A
N/A
62528
62547
TCTTGCAGTTTTAAAAGCTT
 61†
965





1315853
N/A
N/A
45021
45040
CCTTTTTTCCCCTTCACCCT
80
966





1315866
N/A
N/A
94540
94559
AGCAAGGTCACAGATAAGGC
62
967





1315872
N/A
N/A
129797
129816
ACACAGGTTATTTCACTCTA
36
968





1315977
N/A
N/A
79673
79692
GCTCTGCTACTTACTCACTC
89
969





1315983
N/A
N/A
125507
125526
GCATTCCTCCTCTCTCACTG
60
970





1316020
N/A
N/A
40095
40114
GCCACAGGACTCCCTGACAA
78
971





1316034
N/A
N/A
10436
10455
CCACATTCACCTCCCTCTCT
64
972





1316035
N/A
N/A
100944
100963
ACTCAGATATACTCCTGCTC
54
973





1316094
N/A
N/A
115960
115979
CCACCATTCATTTCTAGAAT
59
974





1316095
N/A
N/A
5890
5909
TGGACCTTACTTCTTACTAC
44
975





1316114
N/A
N/A
69334
69353
CTGAGATTCTTTTCACAGAA
66
976





1316190
N/A
N/A
41800
41819
TTTATTTATTTCAAAGGTCT
48
977





1316195
N/A
N/A
17064
17083
AACAAGTTCAAAAATACCTC
72
978





1316207
N/A
N/A
23051
23070
TTGAAATCTTTCTTTCCTAA
81
979





1316234
N/A
N/A
68685
68704
TGTCAATTTCTATCCCCCAT
29
980





1316381
N/A
N/A
12553
12572
TGTATTTCACCAATACTCAA
86
981





1316387
N/A
N/A
17818
17837
TCAATACTTTCCCCAAGTTC
64
982





1316442
N/A
N/A
83711
83730
ACTGTAATCAATCTTAGCTG
64
983





1316457
N/A
N/A
136515
136534
TGGATTTCAAAACAACACCT
93
984





1316466
N/A
N/A
105619
105638
AGGAAACCAAACACCTATGC
71
985





1316469
N/A
N/A
108151
108170
GATCATTTCTAAACAGACAT
47
986





1316476
N/A
N/A
3104
3123
GCAAAGGAAATTTCTTGATA
70
987





1316547
N/A
N/A
75380
75399
GCCAGGAACATCAATTCTGA
62
988





1316553
N/A
N/A
22518
22537
TGCTTCATGTATTTTAGCTC
78
989





1316583
N/A
N/A
43575
43594
ACACCCTTTTTACTCAACAA
71
990





1316626
N/A
N/A
160797
160816
CCAACACACCAGCACAGGCA
72
991





1316650
N/A
N/A
47422
47441
ACAAAGTTTATACCTTAACT
83
992





1316679
N/A
N/A
53292
53311
GTTCAAGTTCTTAACCGACT
32
993





1316681
N/A
N/A
72495
72514
AAGCATTGAACTCCAACCAC
69
994





1316687
N/A
N/A
132283
132302
GTTGAATCCAAAATATGAAT
90
995





1316707
N/A
N/A
111408
111427
CTTCAAGTAAAACCTTTTCC
73
996





1316726
N/A
N/A
45565
45584
ACTAATTGCCTTTTTCTCCC
83
997





1316738
N/A
N/A
149488
149507
CCATTTTTCAAATCAAGGAC
78
998





1316799
N/A
N/A
104192
104211
GGAACACTTTCCTTCTGCAC
80
999





1316856
N/A
N/A
98517
98536
CTTCCATTTAAATTGTGTAA
67
1000





1316873
N/A
N/A
127356
127375
CCTTTGGTTTATTTCTTTTA
57
1001





1316950
N/A
N/A
110053
110072
TTCGATCTCCACTCTACTCA
77
1002





1316956
N/A
N/A
134612
134631
CACAAGATATTTATAATCTT
80
1003





1316998
7419
7438
146511
146530
GCCAAAATCCCCTCCCGGTT
53
1004





1317021
N/A
N/A
33727
33746
CTGAGGCAACAATCATACCT
85
1005





1317056
N/A
N/A
56713
56732
TCACCTTGTTTTCTTGATCA
81
1006





1317108
N/A
N/A
118110
118129
AGACATCACCCATTAACTCT
54
1007





1317124
N/A
N/A
117789
117808
CAGTCATACATTGATTTCAA
33
1008





1317135
N/A
N/A
22161
22180
ATCAAGCTCTTTCTTTCCTT
60
1009





1317191
N/A
N/A
141855
141874
CGAGCATTAATTTCTGAGAA
44
1010





1317220
N/A
N/A
32324
32343
ACCACATTCCCAGTGACTCA
88
1011





1317231
N/A
N/A
51032
51051
TACATGGAATTAACACAGCA
51
1012
















TABLE 15







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
29
858





1314519
N/A
N/A
130441
130460
AAACTTACGACATAATCACA
96
1013





1314577
N/A
N/A
108141
108160
AAACAGACATATCCAGAGCT
64
1014





1314599
N/A
N/A
17807
17826
CCCAAGTTCAATTTACTTTC
68
1015





1314623
N/A
N/A
106952
106971
CATACATTCCTCTTACCTGA
97
1016





1314738
N/A
N/A
55839
55858
GGTTATCTCCTAAATTGCAA
45
1017





1314807
N/A
N/A
62310
62329
GCCTCACTTTCACCTTCTTG
78
1018





1314842
N/A
N/A
43413
43432
CAGCTGTTTATCAACACGCA
90
1019





1314924
N/A
N/A
125053
125072
CGGCAAATTTCTCCACAGCA
39
1020





1314945
N/A
N/A
132174
132193
TCATCTTGATTCATAATCCT
64
1021





1315095
N/A
N/A
118109
118128
GACATCACCCATTAACTCTA
49
1022





1315123
N/A
N/A
39968
39987
GACAAACTTTTTTAGCTGCA
22
1023





1315175
N/A
N/A
14028
14047
GAATTATTTATTCCAAGGGA
50
1024





1315198
N/A
N/A
75376
75395
GGAACATCAATTCTGAGCTT
43
1025





1315199
N/A
N/A
45542
45561
TTGTTGATAATATATGCATA
91
1026





1315217
N/A
N/A
15442
15461
TCACATGTACCATCTGATCC
68
1027





1315221
N/A
N/A
44976
44995
GCAATCCCAATTTAACACAG
76
1028





1315330
N/A
N/A
3100
3119
AGGAAATTTCTTGATACCCA
36
1029





1315344
N/A
N/A
20041
20060
CACTCCAATTTTCAAGGCCA
85
1030





1315443
N/A
N/A
98479
98498
AGGAAAGTTTTCAATTTCTT
88
1031





1315477
N/A
N/A
22491
22510
CGGTGCATAAACATTTCAGC
64
1032





1315504
N/A
N/A
18303
18322
TCTTAAATTTTCAATCCCCT
64
1033





1315510
N/A
N/A
83710
83729
CTGTAATCAATCTTAGCTGT
77
1034





1315545
N/A
N/A
10404
10423
GCCACCACTAACCTACTCTA
83
1035





1315580
N/A
N/A
117436
117455
AAGCAGTATTTACATTATGA
56
1036





1315609
N/A
N/A
47419
47438
AAGTTTATACCTTAACTTCT
101
1037





1315654
N/A
N/A
32219
32238
GCTTTTGTTTCTCAATCCGT
54
1038





1315698
N/A
N/A
48875
48894
GTATAACTTTTCATTAGCGA
16
1039





1315743
12302
12321
169051
169070
GTTTCATTAAAATCTTTCCC
63
1040





1315764
N/A
N/A
149411
149430
CCCTCATACATTTTACAGGC
93
1041





1315806
N/A
N/A
59082
59101
CAACAAACATCATCATCTAA
98
1042





1315818
N/A
N/A
160724
160743
CACTGCACCAACATATGTGC
98
1043





1315819
N/A
N/A
41762
41781
AGACTCTTCCACTCATATGC
93
1044





1315826
N/A
N/A
72494
72513
AGCATTGAACTCCAACCACC
70
1045





1315832
N/A
N/A
79671
79690
TCTGCTACTTACTCACTCCC
89
1046





1315862
N/A
N/A
23033
23052
AAAACAGGCATTTAATGCTA
92
1047





1315920
N/A
N/A
138734
138753
AGTGGCACATCTACACATCC
87
1048





1315942
N/A
N/A
22156
22175
GCTCTTTCTTTCCTTTATTT
70
1049





1315962
N/A
N/A
65571
65590
GCAATAGTTGCAATGAGCCA
67
1050





1315978
N/A
N/A
110048
110067
TCTCCACTCTACTCAGATTA
85
1051





1316000
N/A
N/A
9726
9745
GCAATCCTCCAGCCTCCTCA
62
1052





1316024
2075
2094
56666
56685
ACAAATTTATCAACACTGCT
62
1053





1316064
N/A
N/A
68649
68668
CTCTAATTCCTTTAGAACAC
68
1054





1316080
N/A
N/A
19454
19473
GGTCATTTCCGCACAAGCAA
34
1055





1316096
N/A
N/A
7316
7335
GGAGAACTCACATTTCATGA
31
1056





1316112
N/A
N/A
69329
69348
ATTCTTTTCACAGAAGCACA
64
1057





1316212
N/A
N/A
134511
134530
GTGACAACTTCATAATGCAA
50
1058





1316226
N/A
N/A
52743
52762
TACAACCAAAACCACCCTCA
97
1059





1316246
N/A
N/A
53287
53306
AGTTCTTAACCGACTACTCC
77
1060





1316248
N/A
N/A
141854
141873
GAGCATTAATTTCTGAGAAC
36
1061





1316263
N/A
N/A
114261
114280
CCAGGTATTATTCCAGACTT
41
1062





1316312
N/A
N/A
80876
80895
TGTACATCAGTCATTAGTTT
16
1063





1316327
N/A
N/A
46663
46682
TTCCCTTTAATTACAGTTGC
71
1064





1316356
N/A
N/A
119107
119126
GCTATCTTTTACTCTAAGAT
47
1065





1316383
6512
6531
136200
136219
GGAATCCGATTCACCAGCTC
63
1066





1316390
N/A
N/A
105259
105278
CACTAGCTCCTTCCACAGGC
77
1067





1316425
N/A
N/A
33726
33745
TGAGGCAACAATCATACCTT
100
1068





1316500
N/A
N/A
70457
70476
ATCTTGGTGATTATCTGCCA
31
1069





1316531
N/A
N/A
12544
12563
CCAATACTCAATCAATTTCA
53
1070





1316562
N/A
N/A
35411
35430
TCTTTGTTTATAATCCTGTT
65
1071





1316566
N/A
N/A
51031
51050
ACATGGAATTAACACAGCAA
39
1072





1316598
N/A
N/A
24886
24905
CATCATGCTCCAACTGTCTA
95
1073





1316649
N/A
N/A
129796
129815
CACAGGTTATTTCACTCTAC
40
1074





1316653
N/A
N/A
5889
5908
GGACCTTACTTCTTACTACA
40
1075





1316682
N/A
N/A
100927
100946
CTCAAACCAATTTCACATTC
80
1076





1316848
N/A
N/A
111402
111421
GTAAAACCTTTTCCCAAGTC
77
1077





1316853
N/A
N/A
94516
94535
TAGTTTGTATATCTCAAGCC
89
1078





1316944
N/A
N/A
115953
115972
TCATTTCTAGAATAACTCTC
80
1079





1316987
N/A
N/A
17063
17082
ACAAGTTCAAAAATACCTCT
83
1080





1316992
N/A
N/A
34507
34526
GTAGCAGCTAACATCTAAGC
77
1081





1317053
N/A
N/A
60418
60437
CAGCAACTTCACAAACATTG
94
1082





1317083
N/A
N/A
81283
81302
TGGATGGGAATTCAATAAAC
61
1083





1317088
N/A
N/A
127355
127374
CTTTGGTTTATTTCTTTTAA
71
1084





1317120
N/A
N/A
73081
73100
CTGGAAGCAGACATTTGCAA
94
1085





1317193
N/A
N/A
133708
133727
ACAAATCTATATCCTTTATA
91
1086





1317212
N/A
N/A
104191
104210
GAACACTTTCCTTCTGCACT
79
1087





1317226
N/A
N/A
26582
26601
ACTTCTTACCACTTTGAGGA
93
1088





1317234
N/A
N/A
145879
145898
CCCACAGCCCATCTGCACAA
93
1089
















TABLE 16







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
29
858





1314488
N/A
N/A
73065
73084
GCAAAGTCAAATTATAGACA
92
1090





1314547
N/A
N/A
22153
22172
CTTTCTTTCCTTTATTTGCC
64
1091





1314566
N/A
N/A
127345
127364
TTTCTTTTAAACACTCATCA
63
1092





1314617
N/A
N/A
138731
138750
GGCACATCTACACATCCGTC
62
1093





1314660
N/A
N/A
56541
56560
ACAATTATACATTTATGCTA
72
1094





1314730
N/A
N/A
46661
46680
CCCTTTAATTACAGTTGCCA
69
1095





1314794
N/A
N/A
125052
125071
GGCAAATTTCTCCACAGCAT
44
1096





1314804
N/A
N/A
26552
26571
GCAATTAGTCCTCACACATA
91
1097





1314817
N/A
N/A
117434
117453
GCAGTATTTACATTATGACT
50
1098





1315014
N/A
N/A
80867
80886
GTCATTAGTTTCTAATATCT
28
1099





1315029
N/A
N/A
134371
134390
ACAAGGTACTCTAAAGACTG
53
1100





134404
134423








1315116
N/A
N/A
160723
160742
ACTGCACCAACATATGTGCC
106
1101





1315135
N/A
N/A
149410
149429
CCTCATACATTTTACAGGCC
81
1102





1315137
N/A
N/A
39967
39986
ACAAACTTTTTTAGCTGCAA
27
1103





1315153
N/A
N/A
108139
108158
ACAGACATATCCAGAGCTCA
58
1104





1315159
4850
4869
106905
106924
GACACCACCACCTCTTTTTG
41
1105





1315185
N/A
N/A
20022
20041
AGCACCTTCAAATCTTTCTG
54
1106





1315244
N/A
N/A
141372
141391
AGAAGAATTTCTACACACTT
104
1107





1315391
N/A
N/A
45527
45546
GCATATGCCTTCCCTCTGCC
86
1108





1315454
N/A
N/A
17061
17080
AAGTTCAAAAATACCTCTAC
88
1109





1315518
N/A
N/A
98478
98497
GGAAAGTTTTCAATTTCTTA
70
1110





1315523
N/A
N/A
24836
24855
GCCATGTACATGAAACTGAC
90
1111





1315533
N/A
N/A
130439
130458
ACTTACGACATAATCACAGA
92
1112





1315538
N/A
N/A
23029
23048
CAGGCATTTAATGCTAGAAA
85
1113





1315566
N/A
N/A
55796
55815
GTATGGTATTTCATATGTTT
31
1114





1315588
N/A
N/A
132173
132192
CATCTTGATTCATAATCCTA
74
1115





1315679
N/A
N/A
105211
105230
GGGTTCCTTATTTAAGCTCC
87
1116





1315689
N/A
N/A
52733
52752
ACCACCCTCATATAATCCAG
59
1117





1315713
N/A
N/A
135638
135657
CCAAGGCTCTACCAAGGCTC
86
1118





135649
135668








1315745
N/A
N/A
53280
53299
AACCGACTACTCCAAGCCTT
76
1119





1315824
5164
5183
113978
113997
CCAGAATTCCCGATATCCAC
39
1120





1315840
N/A
N/A
70365
70384
TTCTGCCTTTTTTCACTCAA
56
1121





1315846
N/A
N/A
9588
9607
GCAATCCTCCCACCACACCG
68
1122





1315882
N/A
N/A
133704
133723
ATCTATATCCTTTATATCCT
86
1123





1315918
N/A
N/A
12510
12529
GTTAACATCACTAAAGCCAA
63
1124





1315941
N/A
N/A
109996
110015
GCACCATTCTAAAACCATCT
68
1125





1315943
N/A
N/A
44972
44991
TCCCAATTTAACACAGTTTC
98
1126





1316054
11875
11894
168624
168643
GGTGAAGTCATTTTTACTAA
57
1127





1316079
N/A
N/A
15363
15382
GTTACAGCTTATCTAAAGTC
67
1128





1316102
N/A
N/A
100926
100945
TCAAACCAATTTCACATTCA
89
1129





1316111
N/A
N/A
35389
35408
TACTACTGAATTTCATTGAT
66
1130





1316151
N/A
N/A
60414
60433
AACTTCACAAACATTGATCA
100
1131





1316173
N/A
N/A
94345
94364
GCTTCTACCCTACATATCCC
84
1132





1316220
N/A
N/A
32218
32237
CTTTTGTTTCTCAATCCGTT
67
1133





1316237
N/A
N/A
111363
111382
AACACATTCCCATTAGGGTT
102
1134





1316238
N/A
N/A
81279
81298
TGGGAATTCAATAAACTGCA
37
1135





1316273
N/A
N/A
83587
83606
TCAAAGGGCTTATACATCCT
78
1136





1316289
N/A
N/A
19345
19364
GGTATTCTTCCATATGGGCT
44
1137





1316294
N/A
N/A
3092
3111
TCTTGATACCCATATTTTGA
50
1138





1316304
N/A
N/A
72425
72444
GAACTCATAAATATCAACCC
70
1139





1316309
N/A
N/A
104179
104198
TCTGCACTAAATTTTCCTAA
79
1140





1316350
N/A
N/A
18302
18321
CTTAAATTTTCAATCCCCTT
77
1141





1316363
N/A
N/A
68579
68598
CAGTGGTTTGAATAAAGCCA
84
1142





1316444
N/A
N/A
65481
65500
GAAGTTGCTATCATTTGCAG
56
1143





1316451
N/A
N/A
69321
69340
CACAGAAGCACAATTTCTTA
75
1144





1316463
N/A
N/A
34506
34525
TAGCAGCTAACATCTAAGCC
85
1145





1316480
N/A
N/A
119106
119125
CTATCTTTTACTCTAAGATA
111
1146





1316498
N/A
N/A
13999
14018
AAGGCAACTATTTCACGCAT
64
1147





1316511
N/A
N/A
22489
22508
GTGCATAAACATTTCAGCTT
87
1148





1316512
N/A
N/A
33725
33744
GAGGCAACAATCATACCTTA
103
1149





1316556
N/A
N/A
115930
115949
ATCTTGTAAAAATAACTCCC
93
1150





1316560
N/A
N/A
47418
47437
AGTTTATACCTTAACTTCTC
92
1151





1316589
N/A
N/A
6824
6843
GGAGAGTTTTTACAAATCAT
27
1152





1316594
N/A
N/A
79607
79626
CCCAAATTTATACACTGAAA
83
1153





1316616
N/A
N/A
51029
51048
ATGGAATTAACACAGCAACT
33
1154





1316620
N/A
N/A
129793
129812
AGGTTATTTCACTCTACACT
31
1155





1316665
N/A
N/A
10402
10421
CACCACTAACCTACTCTACT
67
1156





1316676
N/A
N/A
17804
17823
AAGTTCAATTTACTTTCAAT
84
1157





1316705
N/A
N/A
75326
75345
AGCTAGGTATTTCCCTCTTA
46
1158





1316723
N/A
N/A
145835
145854
GACCAGCTAATCTCTTACCT
57
1159





1316731
N/A
N/A
59077
59096
AACATCATCATCTAAACTTA
93
1160





1316852
N/A
N/A
118108
118127
ACATCACCCATTAACTCTAC
67
1161





1316913
N/A
N/A
61811
61830
CCAGATTTATAAACATTCTA
87
1162





1317020
N/A
N/A
43354
43373
AGCATTTTACAAACACTACC
85
1163





1317072
N/A
N/A
41742
41761
CTCCACCTTACCTAAGAGCA
108
1164





1317143
N/A
N/A
5888
5907
GACCTTACTTCTTACTACAA
76
1165





1317178
N/A
N/A
48854
48873
GGGTATTTCCACTCATTATT
33
1166
















TABLE 17







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
27
858





1314521
N/A
N/A
22150
22169
TCTTTCCTTTATTTGCCTCT
47
1167





1314537
N/A
N/A
23018
23037
TGCTAGAAATTTCCATTTAC
69
1168





1314571
N/A
N/A
117433
117452
CAGTATTTACATTATGACTA
62
1169





1314628
N/A
N/A
141361
141380
TACACACTTCCATCAGTGCT
97
1170





1314757
N/A
N/A
129792
129811
GGTTATTTCACTCTACACTG
36
1171





1314789
N/A
N/A
65447
65466
GCAAAATCTCTGAATAGGCA
18
1172





1314798
N/A
N/A
13996
14015
GCAACTATTTCACGCATGCC
66
1173





1314848
N/A
N/A
134292
134311
GCATGATAATTATATTCTCC
25
1174





1314865
N/A
N/A
39369
39388
AGTGCCACTTTTCAACACAT
103
1175





1314946
N/A
N/A
69318
69337
AGAAGCACAATTTCTTAGCA
70
1176





1314950
N/A
N/A
104176
104195
GCACTAAATTTTCCTAATTA
88
1177





1314961
N/A
N/A
73051
73070
TAGACAATTTTTAAGCAAAC
91
1178





1315072
N/A
N/A
19344
19363
GTATTCTTCCATATGGGCTC
56
1179





1315099
N/A
N/A
127335
127354
ACACTCATCATCTAAGCATT
67
1180





1315143
N/A
N/A
50850
50869
GGGTAATTTCCTCAAAGGCA
10
1181





1315207
5039
5058
112922
112941
GTATTTAACACTCCAAGGGC
29
1182





1315253
N/A
N/A
135640
135659
TACCAAGGCTCTACCAAGGC
64
1183





135651
135670








1315294
N/A
N/A
56481
56500
TGATTATTCCTCAATTGGTC
18
1184





1315295
N/A
N/A
74501
74520
GGACATTACCTTTATTGCGG
81
1185





1315307
N/A
N/A
109993
110012
CCATTCTAAAACCATCTGTA
77
1186





1315311
11870
11889
168619
168638
AGTCATTTTTACTAATGAGC
50
1187





1315368
N/A
N/A
72423
72442
ACTCATAAATATCAACCCCT
96
1188





1315386
N/A
N/A
79596
79615
ACACTGAAACTTAATTACCA
80
1189





1315449
N/A
N/A
80866
80885
TCATTAGTTTCTAATATCTT
76
1190





1315457
N/A
N/A
43329
43348
CAGTGCTTAAATTATTAGCA
63
1191





1315468
N/A
N/A
17759
17778
TTGAACTATATTCCACTCAA
77
1192





1315547
N/A
N/A
55763
55782
GGGCATGATTCCACATCACA
77
1193





1315560
N/A
N/A
22485
22504
ATAAACATTTCAGCTTGCTA
99
1194





1315645
N/A
N/A
145833
145852
CCAGCTAATCTCTTACCTCA
72
1195





1315720
N/A
N/A
130438
130457
CTTACGACATAATCACAGAA
98
1196





1315731
N/A
N/A
70353
70372
TCACTCAATATTACAATCCA
75
1197





1315752
N/A
N/A
48853
48872
GGTATTTCCACTCATTATTT
25
1198





1315759
N/A
N/A
59076
59095
ACATCATCATCTAAACTTAA
80
1199





1315761
N/A
N/A
133703
133722
TCTATATCCTTTATATCCTG
62
1200





1315780
N/A
N/A
46628
46647
GCACTCAAATTTAAACTGTA
78
1201





1315953
N/A
N/A
45506
45525
AGCTTCTTAAACATACTATT
87
1202





1315970
N/A
N/A
68426
68445
TCATTGTATCTATCACGCAA
38
1203





1316018
N/A
N/A
105194
105213
TCCAGCAAAATCATCAGGCA
69
1204





1316025
N/A
N/A
15323
15342
AGAGATAGAATTCAAACCTT
57
1205





1316048
N/A
N/A
3056
3075
GTTCTGTCAAATCAGCATAA
66
1206





1316110
N/A
N/A
115715
115734
TCCACTGTAAATATACACCA
57
1207





1316218
N/A
N/A
35333
35352
GCATCTTGTTTTACCACCCA
28
1208





1316299
N/A
N/A
20021
20040
GCACCTTCAAATCTTTCTGT
68
1209





1316314
N/A
N/A
12495
12514
GCCAAACTGCATCTTACAAC
39
1210





1316354
N/A
N/A
32156
32175
ACAACCATATTTTTAACTCA
84
1211





1316366
N/A
N/A
6821
6840
GAGTTTTTACAAATCATCTA
77
1212





1316398
N/A
N/A
53256
53275
GGAGCAATATATAAAGACAT
93
1213





1316403
N/A
N/A
52732
52751
CCACCCTCATATAATCCAGT
75
1214





1316422
N/A
N/A
9019
9038
AACACAGGTCTTCCTCCCAA
55
1215





1316428
N/A
N/A
83581
83600
GGCTTATACATCCTACAAAT
60
1216





1316578
N/A
N/A
26541
26560
TCACACATACACAATTTAAT
98
1217





1316581
N/A
N/A
160500
160519
CAGCATGTCCCAAATCCTGC
81
1218





1316586
N/A
N/A
118105
118124
TCACCCATTAACTCTACCGT
66
1219





1316600
N/A
N/A
10393
10412
CCTACTCTACTACCCCATCT
128
1220





1316632
N/A
N/A
18259
18278
TTTTTAATTTTCTAATGGGA
92
1221





1316659
N/A
N/A
61440
61459
GCTACATTTTTTTAAAAGTT
85
1222





1316678
N/A
N/A
24772
24791
CTTGAAGTAATCCCAAGAAT
109
1223





1316697
N/A
N/A
125051
125070
GCAAATTTCTCCACAGCATC
76
1224





1316702
N/A
N/A
47417
47436
GTTTATACCTTAACTTCTCC
86
1225





1316711
N/A
N/A
94182
94201
GGTGAGTAAATCTACCTTTA
101
1226





1316748
N/A
N/A
111323
111342
AAAGCACTCATCAGTGCCCT
100
1227





1316765
N/A
N/A
5886
5905
CCTTACTTCTTACTACAAAT
84
1228





1316832
N/A
N/A
17059
17078
GTTCAAAAATACCTCTACTA
76
1229





1316843
N/A
N/A
81259
81278
GTCACACCTAAATCCTAGCC
46
1230





1316954
N/A
N/A
119046
119065
GCTTTGATCACAAAAGCACC
95
1231





1316972
4826
4845
106881
106900
TCAAGCTCTTTTCCTGCATC
26
1232





1316977
N/A
N/A
138729
138748
CACATCTACACATCCGTCCA
80
1233





1316986
N/A
N/A
44949
44968
CTGTTCACAAATGTTAGAAA
51
1234





1317018
1019
1038
41729
41748
AAGAGCACATTTAGTAGCCA
60
1235





1317042
N/A
N/A
98440
98459
AAGTCTTGAAATCCAAGTTA
77
1236





1317110
N/A
N/A
131678
131697
GGATAACACCTCTTTCAGTT
46
1237





1317122
N/A
N/A
33722
33741
GCAACAATCATACCTTAATT
88
1238





1317146
N/A
N/A
100923
100942
AACCAATTTCACATTCACAC
76
1239





1317153
N/A
N/A
108109
108128
GGCTGATGAACTCCTCTCCA
34
1240





1317189
N/A
N/A
60362
60381
CCACTTCTAAATAAATCTCA
95
1241





1317201
N/A
N/A
34505
34524
AGCAGCTAACATCTAAGCCC
83
1242





1317208
N/A
N/A
149408
149427
TCATACATTTTACAGGCCTT
86
1243
















TABLE 18







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
25
858





1314572
N/A
N/A
109959
109978
GACCACACTAAAACTGCTGT
89
1244





1314592
N/A
N/A
35332
35351
CATCTTGTTTTACCACCCAT
67
1245





1314619
N/A
N/A
130436
130455
TACGACATAATCACAGAAGA
81
1246





1314648
N/A
N/A
69317
69336
GAAGCACAATTTCTTAGCAA
41
1247





1314651
N/A
N/A
45496
45515
ACATACTATTTATTCAAGAA
88
1248





1314696
4825
4844
106880
106899
CAAGCTCTTTTCCTGCATCA
25
1249





1314706
N/A
N/A
138628
138647
GACCATGTCAATGAATGGCA
96
1250





1314753
N/A
N/A
98429
98448
TCCAAGTTATATACATTACA
68
1251





1314776
N/A
N/A
79592
79611
TGAAACTTAATTACCAGGGT
72
1252





1314790
N/A
N/A
94124
94143
ATCCAGTTATTCTTATGCCA
35
1253





1314802
N/A
N/A
80862
80881
TAGTTTCTAATATCTTGAAC
84
1254





1314825
N/A
N/A
131471
131490
ACAGGAGGTTTTATTTTCCT
97
1255





1314846
N/A
N/A
2987
3006
CAGAAAGGTCTTCCTTCCCA
78
1256





1314881
N/A
N/A
15312
15331
TCAAACCTTTTTTTTTCCTA
75
1257





1314922
N/A
N/A
129017
129036
GCCTATAGATTCTATTTCTA
81
1258





1314930
N/A
N/A
52720
52739
AATCCAGTTATTAGTACCTT
27
1259





1315051
N/A
N/A
26537
26556
ACATACACAATTTAATCCTC
95
1260





1315113
N/A
N/A
53161
53180
TGGTCAGAAACAACTGTCAA
76
1261





1315174
N/A
N/A
17673
17692
TCATTTTTTCACATTTAGGT
26
1262





1315200
N/A
N/A
68258
68277
GCAACAATTTATTCTAAGCT
34
1263





1315319
N/A
N/A
117425
117444
ACATTATGACTATCTGAATC
70
1264





1315335
N/A
N/A
24752
24771
AGCAAATCCCAGTAATACGG
91
1265





1315361
N/A
N/A
22454
22473
TGAACGAATCCCCTTCATCA
77
1266





1315383
N/A
N/A
73038
73057
AGCAAACAACAGTCTTCCTT
94
1267





1315390
N/A
N/A
135639
135658
ACCAAGGCTCTACCAAGGCT
69
1268





135650
135669








1315430
N/A
N/A
13912
13931
GCCTAAATATATTTACCATC
84
1269





1315431
N/A
N/A
18236
18255
AGGGCACTGCACCAATATCA
89
1270





1315639
N/A
N/A
22145
22164
CCTTTATTTGCCTCTTCCCC
75
1271





1315640
N/A
N/A
108108
108127
GCTGATGAACTCCTCTCCAT
53
1272





1315669
N/A
N/A
141360
141379
ACACACTTCCATCAGTGCTT
114
1273





1315702
N/A
N/A
56467
56486
TTGGTCATTTTCATCAGCTA
16
1274





1315757
N/A
N/A
59073
59092
TCATCATCTAAACTTAAACC
105
1275





1315775
N/A
N/A
33719
33738
ACAATCATACCTTAATTTCA
100
1276





1315790
N/A
N/A
112870
112889
GACACCACAAACATTTCTAC
101
1277





1315874
N/A
N/A
70351
70370
ACTCAATATTACAATCCAGA
25
1278





1315880
N/A
N/A
125012
125031
TCATGACTTCATTCTATCCT
73
1279





1315899
11869
11888
168618
168637
GTCATTTTTACTAATGAGCT
68
1280





1315948
N/A
N/A
119021
119040
CCCATCCCTTTTTAAGGCAA
91
1281





1315955
N/A
N/A
149261
149280
CTGCATTCCACAACTTCCCA
81
1282





1315972
N/A
N/A
60292
60311
CACTATGTACTCCACAGCAC
80
1283





1315979
N/A
N/A
105152
105171
GTCAAACTATATCTCCAATA
52
1284





1316010
N/A
N/A
74279
74298
GGCACAGACATTACCTCTCC
93
1285





1316030
N/A
N/A
44880
44899
TTCAGGACCCACCCTTGCTC
90
1286





1316069
N/A
N/A
61169
61188
ACGGCACACACCTATTCTCC
74
1287





1316166
N/A
N/A
46562
46581
TGGAATATACTTACACCATA
93
1288





1316169
N/A
N/A
115658
115677
AGTTGGTTCCACATTTTAGC
24
1289





1316202
N/A
N/A
100921
100940
CCAATTTCACATTCACACGA
81
1290





1316208
N/A
N/A
12494
12513
CCAAACTGCATCTTACAACC
78
1291





1316269
N/A
N/A
47397
47416
CCCTAAATATTTCCCTATCA
101
1292





1316290
N/A
N/A
48829
48848
GGCACGCATTCCATACAGAA
48
1293





1316328
N/A
N/A
19321
19340
CCACCTTGCATCTCTGCACT
86
1294





1316353
N/A
N/A
127297
127316
GGGACACAATTCCCAGATTC
84
1295





1316375
N/A
N/A
17029
17048
CAAGATTATTTTAAATTTCT
92
1296





1316397
N/A
N/A
118104
118123
CACCCATTAACTCTACCGTA
70
1297





1316423
N/A
N/A
158914
158933
TTGCTAATTTTCTTTGCTGA
71
1298





1316426
N/A
N/A
20009
20028
CTTTCTGTTCCATCTTCACA
72
1299





1316450
N/A
N/A
145700
145719
AGGGAACTCCTCAATGCCAG
68
1300





1316468
N/A
N/A
133699
133718
TATCCTTTATATCCTGGGTT
76
1301





1316484
N/A
N/A
10390
10409
ACTCTACTACCCCATCTCTA
87
1302





1316522
N/A
N/A
72375
72394
GGTGTCTACCCATATTTTCT
63
1303





1316524
N/A
N/A
6819
6838
GTTTTTACAAATCATCTATC
80
1304





1316559
N/A
N/A
83580
83599
GCTTATACATCCTACAAATC
81
1305





1316605
N/A
N/A
34504
34523
GCAGCTAACATCTAAGCCCT
86
1306





1316645
N/A
N/A
111084
111103
TGAGTGGACATCTCAGATGC
90
1307





1316759
N/A
N/A
43326
43345
TGCTTAAATTATTAGCATTA
91
1308





1316862
N/A
N/A
55762
55781
GGCATGATTCCACATCACAA
52
1309





1316923
N/A
N/A
5882
5901
ACTTCTTACTACAAATGTCC
91
1310





1316940
N/A
N/A
50762
50781
CCAACACAACTCTACCTTCA
60
1311





1316993
N/A
N/A
22977
22996
AAGTTTAGAAATCTATTGTT
91
1312





1317045
N/A
N/A
41509
41528
TTAGAAGTTTCCAATTCTTG
88
1313





1317046
N/A
N/A
8997
9016
GCTTGCATTGTTATTAGCAA
81
1314





1317089
N/A
N/A
134291
134310
CATGATAATTATATTCTCCT
52
1315





1317105
N/A
N/A
103959
103978
ACCACAAGATTTCATTCCAC
70
1316





1317138
N/A
N/A
65432
65451
AGGCAAGTCATATAAACCTA
32
1317





1317157
N/A
N/A
39367
39386
TGCCACTTTTCAACACATGC
61
1318





1317168
N/A
N/A
81258
81277
TCACACCTAAATCCTAGCCC
85
1319





1317235
N/A
N/A
32081
32100
TGGTACCTCAACCTTCAACA
96
1320
















TABLE 19







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
27
858





1314554
N/A
N/A
65324
65343
ACTTTGGTTTTCTTTTCAGT
36
1321





1314586
N/A
N/A
34471
34490
TATGCTACACTCTAACACAT
96
1322





1314631
N/A
N/A
117377
117396
AAGGATGGCATCTCTTTCTA
94
1323





1314646
N/A
N/A
22966
22985
TCTATTGTTTTTATATCAGT
89
1324





1314668
N/A
N/A
68257
68276
CAACAATTTATTCTAAGCTT
79
1325





1314684
N/A
N/A
6218
6237
TAGCAGAGTTCAACAAGTGC
67
1326





1314688
N/A
N/A
32057
32076
GGCAAGTATCTTTTAAGCAA
50
1327





1314764
4801
4820
106856
106875
TATTTGTTCCTCTTAATACA
78
1328





1314894
N/A
N/A
72302
72321
GTATGTTTACTTGAACGGAT
35
1329





1314936
N/A
N/A
39365
39384
CCACTTTTCAACACATGCAC
83
1330





1314999
N/A
N/A
56466
56485
TGGTCATTTTCATCAGCTAT
12
1331





1315010
N/A
N/A
73034
73053
AACAACAGTCTTCCTTTCTC
89
1332





1315166
N/A
N/A
52714
52733
GTTATTAGTACCTTCAGTTA
53
1333





1315169
N/A
N/A
12487
12506
GCATCTTACAACCAGTGGTA
36
1334





1315284
N/A
N/A
41474
41493
TTGAGGCTTTTCCTACAGCT
51
1335





1315291
N/A
N/A
103559
103578
GCTTCTTTTCCTCCTGCTTA
53
1336





1315355
N/A
N/A
47372
47391
ACCAATGTGATCATTAGCTT
60
1337





1315393
N/A
N/A
134977
134996
GATTCTAGAAATATACACTC
67
1338





1315395
N/A
N/A
17672
17691
CATTTTTTCACATTTAGGTA
81
1339





1315416
N/A
N/A
26536
26555
CATACACAATTTAATCCTCA
99
1340





1315452
N/A
N/A
83551
83570
ACATCAACTATCCATTAGAC
72
1341





1315528
N/A
N/A
131470
131489
CAGGAGGTTTTATTTTCCTC
96
1342





1315556
5816
5835
130399
130418
CGTACTATTTCTCTATTGCA
24
1343





1315559
N/A
N/A
43314
43333
TAGCATTATCTTCAATTCAT
47
1344





1315570
N/A
N/A
33718
33737
CAATCATACCTTAATTTCAT
106
1345





1315605
11868
11887
168617
168636
TCATTTTTACTAATGAGCTC
87
1346





1315608
N/A
N/A
18233
18252
GCACTGCACCAATATCATTA
81
1347





1315613
N/A
N/A
53123
53142
GCTTGCCTTCTTCCAAGCCA
95
1348





1315687
N/A
N/A
119020
119039
CCATCCCTTTTTAAGGCAAC
82
1349





1315706
N/A
N/A
100854
100873
GCAGCATCGCCCTCTTCAGA
90
1350





1315710
N/A
N/A
109957
109976
CCACACTAAAACTGCTGTCA
99
1351





1315719
N/A
N/A
19250
19269
TCTCAGTTTTTCCTCTTGCC
67
1352





1315750
N/A
N/A
22432
22451
ATGAAATGACCATCTCATCC
82
1353





1315756
N/A
N/A
69256
69275
GTAAGATGACCATACAACTA
72
1354





1315811
N/A
N/A
145667
145686
GGAGGAATTTTACCTACAGC
85
1355





1315837
N/A
N/A
149255
149274
TCCACAACTTCCCATTCTGC
70
1356





1315838
N/A
N/A
78919
78938
GTATGAGCCCATCCACAGTA
82
1357





1315875
N/A
N/A
60153
60172
AGCATGCTTCCTTCTGCTCA
95
1358





1315890
N/A
N/A
61167
61186
GGCACACACCTATTCTCCTA
73
1359





1315914
N/A
N/A
45493
45512
TACTATTTATTCAAGAAGAA
100
1360





1316028
N/A
N/A
5783
5802
TGGAATACCACTACTTCATA
77
1361





1316081
N/A
N/A
55682
55701
CTACCAGCAAATTATTACCA
63
1362





1316136
N/A
N/A
44826
44845
TGTCTCACCCTTTCACTCCT
96
1363





1316242
N/A
N/A
133683
133702
GGTTGTCCTAACACAAGGAC
82
1364





1316295
N/A
N/A
15309
15328
AACCTTTTTTTTTCCTACTT
91
1365





1316369
N/A
N/A
22138
22157
TTGCCTCTTCCCCTATTTCT
75
1366





1316371
N/A
N/A
112846
112865
GCCAAAAGAAACGACAGCTT
89
1367





1316388
N/A
N/A
50760
50779
AACACAACTCTACCTTCATC
79
1368





1316393
N/A
N/A
20005
20024
CTGTTCCATCTTCACAGGGC
68
1369





1316427
N/A
N/A
10379
10398
CCATCTCTAACCCCAGGCAA
86
1370





1316445
N/A
N/A
134289
134308
TGATAATTATATTCTCCTTC
63
1371





1316497
N/A
N/A
115610
115629
GGCATGCAAATATCTTTTCA
80
1372





1316509
N/A
N/A
125011
125030
CATGACTTCATTCTATCCTC
78
1373





1316530
N/A
N/A
118070
118089
TAGCTCATTTATACTACCTC
48
1374





1316535
N/A
N/A
158886
158905
TGTGTGCTTTTACCATAACA
29
1375





1316587
N/A
N/A
46550
46569
ACACCATAAAATTACTCATA
102
1376





1316603
N/A
N/A
98424
98443
GTTATATACATTACAACCAT
83
1377





1316701
N/A
N/A
128896
128915
GACAGCACTCCTCTATATCT
53
1378





1316725
N/A
N/A
108043
108062
CAGTTGCTCATTTTCAGACC
19
1379





1316732
N/A
N/A
17028
17047
AAGATTATTTTAAATTTCTG
108
1380





1316744
N/A
N/A
59072
59091
CATCATCTAAACTTAAACCT
99
1381





1316749
N/A
N/A
70341
70360
ACAATCCAGATTATACATCT
62
1382





1316750
N/A
N/A
141349
141368
TCAGTGCTTTTTATTCAACA
103
1383





1316787
N/A
N/A
94007
94026
GATCAACTAACATCAATCTT
81
1384





1316808
N/A
N/A
80861
80880
AGTTTCTAATATCTTGAACC
63
1385





1316811
N/A
N/A
35329
35348
CTTGTTTTACCACCCATGCT
81
1386





1316890
N/A
N/A
138491
138510
TGCAAAGTACTATACTGGCC
78
1387





1316893
N/A
N/A
13897
13916
CCATCTACAGCTACTAGGAA
45
1388





1316898
N/A
N/A
24730
24749
GATGTGCTATTTTTGAAGCA
101
1389





1316911
N/A
N/A
8779
8798
TGTCTCTAACATACATTCTA
70
1390





1316925
N/A
N/A
110976
110995
TGCTACATCCAGACAGGCTC
89
1391





1316970
N/A
N/A
81232
81251
TTCTGACCTTTTCATGGGTA
103
1392





1317063
N/A
N/A
127113
127132
AAGACATCCACCAAGCATTT
75
1393





1317125
N/A
N/A
2979
2998
TCTTCCTTCCCATCAGGAGC
86
1394





1317130
N/A
N/A
105117
105136
TCAAAATTTAATTCACGGCA
32
1395





1317161
N/A
N/A
74278
74297
GCACAGACATTACCTCTCCA
89
1396





1317225
N/A
N/A
48828
48847
GCACGCATTCCATACAGAAA
45
1397
















TABLE 20







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
22
858





1314492
N/A
N/A
106788
106807
AAAGGGTACCCTTATCAGGC
103
1398





1314497
N/A
N/A
52707
52726
GTACCTTCAGTTAATCCTCA
46
1399





1314501
N/A
N/A
43312
43331
GCATTATCTTCAATTCATGA
55
1400





1314522
N/A
N/A
73033
73052
ACAACAGTCTTCCTTTCTCT
91
1401





1314556
N/A
N/A
18231
18250
ACTGCACCAATATCATTACA
86
1402





1314565
N/A
N/A
22425
22444
GACCATCTCATCCTGGGCAA
83
1403





1314695
N/A
N/A
17012
17031
TCTGTGTTAATTTAGAGAAA
77
1404





1314731
N/A
N/A
46048
46067
GCACCCACATTTCCTTCACC
83
1405





1314810
5815
5834
130398
130417
GTACTATTTCTCTATTGCAC
10
1406





1314838
N/A
N/A
109946
109965
CTGCTGTCAATCTCACCAGA
76
1407





1314896
N/A
N/A
48815
48834
ACAGAAAAAAATTCTTCCGT
56
1408





1315009
N/A
N/A
117370
117389
GCATCTCTTTCTATAGGTCT
51
1409





1315027
N/A
N/A
107757
107776
TGTCTTTGAATTCTTATGCC
22
1410





1315069
N/A
N/A
112815
112834
GCTATGTAACTCAAGGGCAA
79
1411





1315094
N/A
N/A
81169
81188
CTCAGATGACTTTATCCCCA
48
1412





1315155
N/A
N/A
145069
145088
ATCATCTTATTTCAGCGGGC
21
1413





1315170
N/A
N/A
34469
34488
TGCTACACTCTAACACATAT
103
1414





1315261
N/A
N/A
100760
100779
TCTGAGCTTTTTTCTGCTAC
76
1415





1315363
N/A
N/A
118069
118088
AGCTCATTTATACTACCTCC
51
1416





1315404
N/A
N/A
45477
45496
AGAATGGTTTCTAATACGAA
78
1417





1315496
N/A
N/A
13547
13566
GTTCAATTACCATAATGGTT
38
1418





1315550
N/A
N/A
141344
141363
GCTTTTTATTCAACATTTTA
81
1419





1315552
N/A
N/A
65282
65301
CGTTTTTTTATATTTTCCTT
28
1420





1315589
N/A
N/A
80835
80854
GGAGAAACTTTCTCTCACTT
78
1421





1315611
N/A
N/A
26533
26552
ACACAATTTAATCCTCACAC
105
1422





1315655
N/A
N/A
53111
53130
CCAAGCCACATTCAAGATCT
80
1423





1315685
N/A
N/A
69250
69269
TGACCATACAACTAACTGGC
64
1424





1315767
N/A
N/A
39207
39226
GCATCAGCAATTCCAAGTGC
79
1425





1315858
N/A
N/A
68246
68265
TCTAAGCTTATCAAATTCCT
58
1426





1315871
N/A
N/A
33714
33733
CATACCTTAATTTCATTGTC
62
1427





1315910
N/A
N/A
128895
128914
ACAGCACTCCTCTATATCTT
45
1428





1315926
N/A
N/A
134916
134935
CTTGTTTAAACCTTTTTCTT
77
1429





1315980
N/A
N/A
60915
60934
TACTTGATAACATCATTCCT
86
1430





1316008
N/A
N/A
15308
15327
ACCTTTTTTTTTCCTACTTT
62
1431





1316011
N/A
N/A
60152
60171
GCATGCTTCCTTCTGCTCAA
97
1432





1316044
N/A
N/A
158859
158878
GCTGAGAGTCTTTCTAGAAA
31
1433





1316063
N/A
N/A
22965
22984
CTATTGTTTTTATATCAGTC
62
1434





1316084
3864
3883
83463
83482
TTTCAGGACATCATGCAGTT
35
1435





1316149
N/A
N/A
115609
115628
GCATGCAAATATCTTTTCAC
81
1436





1316164
N/A
N/A
44799
44818
AGCAAAGACCACATTTTCTG
75
1437





1316170
N/A
N/A
72290
72309
GAACGGATTTTTAACTTTCT
22
1438





1316177
N/A
N/A
133660
133679
CTGTGTTTCCAGCATTACCT
72
1439





1316182
N/A
N/A
55646
55665
AGTTTGTTAACTACTATACT
72
1440





1316187
N/A
N/A
94006
94025
ATCAACTAACATCAATCTTC
105
1441





1316217
N/A
N/A
74103
74122
CCATGACTGTCACCACCACA
58
1442





1316228
N/A
N/A
70339
70358
AATCCAGATTATACATCTCC
39
1443





1316251
N/A
N/A
105074
105093
GTTGCATCGCTTCTTGGCCT
95
1444





1316261
N/A
N/A
41328
41347
CCTCAATTCTAGATACACTC
71
1445





1316296
N/A
N/A
10358
10377
CACTAATCTATTCTCCATCC
91
1446





1316305
11851
11870
168600
168619
CTCATATTCATCTCCGGAGC
57
1447





1316315
N/A
N/A
24691
24710
TCATGATCCCAATCTAACTA
78
1448





1316348
N/A
N/A
2891
2910
ACTACAGTAAATTTCTGGAT
64
1449





1316378
N/A
N/A
59071
59090
ATCATCTAAACTTAAACCTT
88
1450





1316391
N/A
N/A
110920
110939
TCCACAGCCACCCTGTCCTC
93
1451





1316429
N/A
N/A
19249
19268
CTCAGTTTTTCCTCTTGCCA
47
1452





1316494
N/A
N/A
103431
103450
TCAACAACTTTACTATACCC
102
1453





1316534
N/A
N/A
12465
12484
GTTTGATTAGAAACTTTCTT
55
1454





1316563
N/A
N/A
56464
56483
GTCATTTTCATCAGCTATTC
16
1455





1316590
N/A
N/A
50757
50776
ACAACTCTACCTTCATCTGT
75
1456





1316612
N/A
N/A
78813
78832
ACAGAGTTCCTTTATGGGTT
73
1457





1316789
N/A
N/A
47351
47370
CATGTTGTTTTCTAAATTCC
88
1458





1316810
N/A
N/A
131469
131488
AGGAGGTTTTATTTTCCTCC
81
1459





1316824
6757
6776
138424
138443
ACAGATCATTCAACTTGCTC
86
1460





1316834
N/A
N/A
22137
22156
TGCCTCTTCCCCTATTTCTG
61
1461





1316861
N/A
N/A
127078
127097
GTCTGTCTCCTCCAACAGAA
87
1462





1316920
N/A
N/A
149164
149183
GCCTGATAAAATCTCTGCAA
70
1463





1316929
N/A
N/A
6190
6209
CCGCATTCAAAATCCAGTCA
34
1464





1316962
N/A
N/A
5768
5787
TCATACACCCTTACACTAGA
74
1465





1316963
N/A
N/A
98417
98436
ACATTACAACCATTCTTTCA
79
1466





1317027
N/A
N/A
35179
35198
TTTCAGTTTTTTTAGAGATA
81
1467





1317032
N/A
N/A
20004
20023
TGTTCCATCTTCACAGGGCC
65
1468





1317044
N/A
N/A
124824
124843
CTGATTTAAATTTCAGGCCG
81
1469





1317057
N/A
N/A
17658
17677
TAGGTAATTAATCTGAACTT
71
1470





1317145
N/A
N/A
134250
134269
TCTCACACACACAATCCCTG
95
1471





1317173
N/A
N/A
119001
119020
CTACTTGTTATCATTTCTGT
71
1472





1317200
N/A
N/A
8777
8796
TCTCTAACATACATTCTAGC
82
1473





1317213
N/A
N/A
31963
31982
GGCACACATCCCATAAGTCT
76
1474
















TABLE 21







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
27
858





1314477
N/A
N/A
83308
83327
GCCAAGTTTTAAAGAGATTA
65
1475





1314525
N/A
N/A
65281
65300
GTTTTTTTATATTTTCCTTA
40
1476





1314550
N/A
N/A
34465
34484
ACACTCTAACACATATTCCT
94
1477





1314573
N/A
N/A
19248
19267
TCAGTTTTTCCTCTTGCCAT
79
1478





1314587
N/A
N/A
46045
46064
CCCACATTTCCTTCACCTCA
86
1479





1314624
N/A
N/A
112800
112819
GGCAAATCATCATAATCATC
49
1480





1314697
N/A
N/A
56457
56476
TCATCAGCTATTCAGAACTC
48
1481





1314709
11144
11163
167893
167912
ACAGAGTTCCAACATTTCCT
54
1482





1314728
N/A
N/A
53106
53125
CCACATTCAAGATCTCGACT
71
1483





1314755
N/A
N/A
72289
72308
AACGGATTTTTAACTTTCTT
32
1484





1314758
N/A
N/A
60914
60933
ACTTGATAACATCATTCCTT
88
1485





1314777
N/A
N/A
158715
158734
TTCTTCACTTTCAATCTGCT
54
1486





1314869
N/A
N/A
81167
81186
CAGATGACTTTATCCCCACT
40
1487





1314947
N/A
N/A
16983
17002
AGTAATATAAAATCTTCCTA
100
1488





1314991
N/A
N/A
52704
52723
CCTTCAGTTAATCCTCATCT
53
1489





1315007
N/A
N/A
31962
31981
GCACACATCCCATAAGTCTC
73
1490





1315032
N/A
N/A
98412
98431
ACAACCATTCTTTCATGCAT
86
1491





1315042
N/A
N/A
33713
33732
ATACCTTAATTTCATTGTCA
44
1492





1315047
N/A
N/A
17589
17608
GAGAAATGTATCATTTCCCT
101
1493





1315215
N/A
N/A
133652
133671
CCAGCATTACCTCTGAGCGA
94
1494





1315315
N/A
N/A
115526
115545
AGGTGTACTCTTACAGCAAC
43
1495





1315359
N/A
N/A
22397
22416
GCTTTGAAATCCACTTTGTC
91
1496





1315384
N/A
N/A
106787
106806
AAGGGTACCCTTATCAGGCA
90
1497





1315448
6755
6774
138422
138441
AGATCATTCAACTTGCTCCA
94
1498





1315472
N/A
N/A
77967
77986
TTCCACCTCAAATCATCATC
98
1499





1315517
N/A
N/A
141335
141354
TCAACATTTTACATTTGTGC
75
1500





1315577
N/A
N/A
131466
131485
AGGTTTTATTTTCCTCCGTT
82
1501





1315578
N/A
N/A
60025
60044
GCTTTGATTTTTACCAGTTA
13
1502





1315585
N/A
N/A
128815
128834
GTATTGTAAATTATGTGTCA
28
1503





1315587
N/A
N/A
118068
118087
GCTCATTTATACTACCTCCT
43
1504





1315616
N/A
N/A
144457
144476
CCTCAGTTCATTTTAGAAAA
91
1505





1315625
N/A
N/A
35002
35021
ATAGATTTTTTTTAATGCCA
44
1506





1315630
N/A
N/A
6176
6195
CAGTCAGTCATTCCTCACAC
44
1507





1315631
N/A
N/A
41169
41188
GGACTGGAACATCTTCGATC
74
1508





1315643
N/A
N/A
15307
15326
CCTTTTTTTTTCCTACTTTT
72
1509





1315690
N/A
N/A
118972
118991
TGGTAGTTACCTCCAAAATT
87
1510





1315715
N/A
N/A
18230
18249
CTGCACCAATATCATTACAC
71
1511





1315732
N/A
N/A
13500
13519
AGGGAACATTATTCATTTCA
48
1512





1315802
N/A
N/A
94005
94024
TCAACTAACATCAATCTTCA
97
1513





1315808
N/A
N/A
12451
12470
TTTCTTTCTTTCTCAGCAGT
23
1514





1315813
N/A
N/A
70338
70357
ATCCAGATTATACATCTCCA
29
1515





1315836
N/A
N/A
74004
74023
TTCTGCCTCCTTCATTCTCT
101
1516





1315873
N/A
N/A
48780
48799
CAAGGCAGATTAACATTTCC
88
1517





1315929
N/A
N/A
39108
39127
TTGGCAGTTTCTACTGCAGC
114
1518





1315995
N/A
N/A
69249
69268
GACCATACAACTAACTGGCC
88
1519





1315998
N/A
N/A
149127
149146
ACCAGGTACTACTCATGGCC
77
1520





1316038
N/A
N/A
8774
8793
CTAACATACATTCTAGCCCC
75
1521





1316065
N/A
N/A
126944
126963
GTCCAGTATCCATACTGAGC
77
1522





1316075
N/A
N/A
22133
22152
TCTTCCCCTATTTCTGGCTT
87
1523





1316133
N/A
N/A
134194
134213
AAAGTTTAACTTATTCTGCA
53
1524





1316225
N/A
N/A
44798
44817
GCAAAGACCACATTTTCTGT
83
1525





1316267
N/A
N/A
22963
22982
ATTGTTTTTATATCAGTCAA
97
1526





1316298
N/A
N/A
10357
10376
ACTAATCTATTCTCCATCCC
92
1527





1316329
N/A
N/A
134915
134934
TTGTTTAAACCTTTTTCTTC
81
1528





1316345
N/A
N/A
26532
26551
CACAATTTAATCCTCACACA
94
1529





1316399
N/A
N/A
43286
43305
TAAGAATCATTTTAAGCCAC
99
1530





1316456
N/A
N/A
45474
45493
ATGGTTTCTAATACGAACTA
90
1531





1316460
N/A
N/A
24652
24671
TTTCTCTTTATCTCTAGGTA
75
1532





1316467
N/A
N/A
68241
68260
GCTTATCAAATTCCTGATAA
67
1533





1316505
N/A
N/A
2748
2767
GCTCTCCGAATCATTTTCTA
92
1534





1316540
N/A
N/A
103281
103300
GTTTAGTAATAAGATACCCA
68
1535





1316622
N/A
N/A
107598
107617
ACCAACACTGTCAATTGATT
42
1536





1316640
N/A
N/A
55645
55664
GTTTGTTAACTACTATACTA
64
1537





1316768
N/A
N/A
117323
117342
GGAGAACCTTTTTAATATCA
28
1538





1316803
5814
5833
130397
130416
TACTATTTCTCTATTGCACA
25
1539





1316817
2526
2545
59005
59024
TGTGAGGGTTCTAATGGTGC
48
1540





1316865
N/A
N/A
110865
110884
ACATGCCACATCTAAGCCAC
97
1541





1316868
N/A
N/A
73030
73049
ACAGTCTTCCTTTCTCTTGC
85
1542





1316875
N/A
N/A
105008
105027
ACAGGAACTTTATATTCAGA
49
1543





1316897
N/A
N/A
109894
109913
CTCAAGATAACATTCCATTA
51
1544





1316966
N/A
N/A
80834
80853
GAGAAACTTTCTCTCACTTT
79
1545





1317028
N/A
N/A
50599
50618
GGATAAACTCATCTGAGCAA
52
1546





1317038
N/A
N/A
123151
123170
TTGTTTTTCATTTAAGGCTG
76
1547





1317176
N/A
N/A
47264
47283
AATGAAGATCTCTATTTCCC
81
1548





1317182
N/A
N/A
100740
100759
AGGAAACTGACTACTCAGCC
79
1549





1317187
N/A
N/A
19977
19996
TGTGTGTAAAATCTCCCTCT
87
1550





1317188
N/A
N/A
4723
4742
CTGACATTTCCCTATCCCCT
82
1551
















TABLE 22







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
31
858





1314482
N/A
N/A
16953
16972
GGTCACCTATATCTTTCAGA
50
1552





1314539
N/A
N/A
65270
65289
TTTTCCTTAAATTCTGTTCA
43
1553





1314627
N/A
N/A
18229
18248
TGCACCAATATCATTACACA
86
1554





1314635
N/A
N/A
15280
15299
CGTTGTATTCTACAATAGCA
36
1555





1314677
N/A
N/A
118968
118987
AGTTACCTCCAAAATTCTAA
82
1556





1314683
N/A
N/A
53090
53109
GACTCCAGTCCTATTCTCCT
84
1557





1314692
N/A
N/A
107168
107187
AAGGATACACACCAACAACA
81
1558





1314812
N/A
N/A
52703
52722
CTTCAGTTAATCCTCATCTT
74
1559





1314815
N/A
N/A
104960
104979
GTTTCTTGAATTTTTTTCCC
36
1560





1314833
N/A
N/A
68216
68235
TCCTCTTTCACTGCTTCTAC
32
1561





1314867
N/A
N/A
56453
56472
CAGCTATTCAGAACTCAGAA
23
1562





1314874
N/A
N/A
2566
2585
ACCAGAGTACTTCCTAACTC
65
1563





1314886
883
902
N/A
N/A
AAACCTTAATTTCATTGTCA
39
1564





1314910
N/A
N/A
81162
81181
GACTTTATCCCCACTTTCTC
66
1565





1314911
N/A
N/A
58843
58862
GGAGATAAATTGCTCAGCCA
88
1566





1314966
N/A
N/A
128708
128727
GCACTTTGCAATAATACAGC
28
1567





1314994
N/A
N/A
117322
117341
GAGAACCTTTTTAATATCAA
56
1568





1315021
N/A
N/A
19954
19973
TCCTTTTTATATATATGTGA
76
1569





1315035
N/A
N/A
122708
122727
GCAAAATTCAATTCCAGAGA
49
1570





1315138
N/A
N/A
10356
10375
CTAATCTATTCTCCATCCCT
100
1571





1315141
5800
5819
130383
130402
TGCACATTCCAAGTTTGGCT
27
1572





1315152
N/A
N/A
35001
35020
TAGATTTTTTTTAATGCCAA
78
1573





1315161
N/A
N/A
72261
72280
TACATTTTACTCCAATGCCA
52
1574





1315178
N/A
N/A
70337
70356
TCCAGATTATACATCTCCAT
36
1575





1315214
N/A
N/A
126801
126820
GGTCACAGCTTTTATTTCCA
13
1576





1315228
N/A
N/A
22105
22124
TTCACCATTTTTATTATTCT
95
1577





1315259
N/A
N/A
106777
106796
TTATCAGGCATTTCATGGAA
96
1578





1315339
N/A
N/A
43220
43239
GCACAATAAAAACCCTGACA
101
1579





1315345
N/A
N/A
19198
19217
GCTCTCCACATTCATTTTCC
75
1580





1315405
6243
6262
133601
133620
GTTGAGTTCTTCCATTGGCA
26
1581





1315507
N/A
N/A
34464
34483
CACTCTAACACATATTCCTT
98
1582





1315525
N/A
N/A
77966
77985
TCCACCTCAAATCATCATCA
79
1583





1315543
N/A
N/A
12378
12397
ACAGTCTAATACCTACTCTA
77
1584





1315604
N/A
N/A
134191
134210
GTTTAACTTATTCTGCAGTC
31
1585





1315618
N/A
N/A
17582
17601
GTATCATTTCCCTCATTTCC
52
1586





1315659
N/A
N/A
31577
31596
ACGAAGCATTTTCTTTCCTT
73
1587





1315755
N/A
N/A
141297
141316
AGGGATAGACAGACTAGCCT
52
1588





1315772
N/A
N/A
109846
109865
AGGCAGTAACATCAATATCA
82
1589





1315787
N/A
N/A
47190
47209
TCAGCTTGACACACATTTAA
86
1590





1315789
N/A
N/A
60910
60929
GATAACATCATTCCTTGCAT
67
1591





1315798
N/A
N/A
103114
103133
GCCTGGTTTTCTCAGAGCCT
92
1592





1315800
N/A
N/A
80809
80828
TGTGTATTATATTTATTTCT
35
1593





1315968
N/A
N/A
48778
48797
AGGCAGATTAACATTTCCTG
41
1594





1315991
N/A
N/A
44708
44727
GACTGAACTTCTCCAGGCCC
92
1595





1315993
N/A
N/A
73027
73046
GTCTTCCTTTCTCTTGCAAT
82
1596





1315997
N/A
N/A
149126
149145
CCAGGTACTACTCATGGCCT
99
1597





1316003
N/A
N/A
94002
94021
ACTAACATCAATCTTCATTA
80
1598





1316017
N/A
N/A
55642
55661
TGTTAACTACTATACTATTA
65
1599





1316068
N/A
N/A
24525
24544
TTAGCAGTATTTCAGACCTT
70
1600





1316071
N/A
N/A
73997
74016
TCCTTCATTCTCTTACAATC
73
1601





1316074
6653
6672
138320
138339
GCCAGAGTCACCTCACGGGC
89
1602





1316156
N/A
N/A
22960
22979
GTTTTTATATCAGTCAATCC
36
1603





1316172
N/A
N/A
6175
6194
AGTCAGTCATTCCTCACACT
49
1604





1316193
N/A
N/A
83248
83267
ATTCAAGTATTTCCTCTGAC
35
1605





1316201
N/A
N/A
45473
45492
TGGTTTCTAATACGAACTAC
83
1606





1316271
N/A
N/A
118067
118086
CTCATTTATACTACCTCCTA
80
1607





1316276
N/A
N/A
98411
98430
CAACCATTCTTTCATGCATT
86
1608





1316370
N/A
N/A
13495
13514
ACATTATTCATTTCAGTGTC
55
1609





1316373
N/A
N/A
115514
115533
ACAGCAACAAATATTTTCAA
68
1610





1316402
N/A
N/A
8712
8731
AGGTATTTTATTTTTCCTCC
48
1611





1316462
N/A
N/A
50465
50484
ACATTAATTTTTCCTAGAAT
96
1612





1316474
N/A
N/A
26487
26506
GCCACAAAAACATTGATCCC
79
1613





1316481
N/A
N/A
59983
60002
CAGTTGTGACTTATGAGCCA
66
1614





1316506
3138
3157
69111
69130
AAGGTTATTTTCCATAGTGA
22
1615





1316514
N/A
N/A
112799
112818
GCAAATCATCATAATCATCT
68
1616





1316567
N/A
N/A
22381
22400
TGTCTGATATTAACAGAACC
83
1617





1316610
N/A
N/A
110832
110851
TGGTTTTGCTTTCATGCTGC
88
1618





1316647
N/A
N/A
46044
46063
CCACATTTCCTTCACCTCAT
87
1619





1316690
N/A
N/A
134914
134933
TGTTTAAACCTTTTTCTTCA
76
1620





1316724
N/A
N/A
144454
144473
CAGTTCATTTTAGAAAACCC
47
1621





1316739
N/A
N/A
131464
131483
GTTTTATTTTCCTCCGTTTA
82
1622





1316878
N/A
N/A
100616
100635
CATCAATGATATCCCTTCTA
78
1623





1316883
N/A
N/A
4638
4657
GTCTATGTCCTTCATTAGAA
49
1624





1316955
N/A
N/A
158714
158733
TCTTCACTTTCAATCTGCTC
43
1625





1317071
11139
11158
167888
167907
GTTCCAACATTTCCTCCACT
58
1626





1317098
N/A
N/A
41155
41174
TCGATCGGAAATATCTGCAA
87
1627





1317158
N/A
N/A
38809
38828
AGAACACTTAATCCATGGTC
75
1628
















TABLE 23







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
36
858





1314607
N/A
N/A
19197
19216
CTCTCCACATTCATTTTCCT
70
1629





1314611
N/A
N/A
65256
65275
TGTTCATTAAACATGTATTA
64
1630





1314614
N/A
N/A
44660
44679
GGTTTAGTAATTATTTGCTT
61
1631





1314615
N/A
N/A
77963
77982
ACCTCAAATCATCATCAGGC
95
1632





1314719
N/A
N/A
34457
34476
ACACATATTCCTTTATTTTA
91
1633





1314746
N/A
N/A
22104
22123
TCACCATTTTTATTATTCTA
114
1634





1314772
N/A
N/A
48777
48796
GGCAGATTAACATTTCCTGC
74
1635





1314800
N/A
N/A
134912
134931
TTTAAACCTTTTTCTTCACA
89
1636





1314803
N/A
N/A
109841
109860
GTAACATCAATATCACATGC
64
1637





1314837
N/A
N/A
141281
141300
GCCTAGATTCCTTAGAACCA
66
1638





1314859
N/A
N/A
98375
98394
CACTCATTAATTCAATAAAC
107
1639





1314900
N/A
N/A
15242
15261
ATATTTTTATTTTCAGGACA
80
1640





1314903
5778
5797
130361
130380
CAAGTCAGAATCCTCCTCTT
76
1641





1314905
N/A
N/A
8630
8649
GGTTGACTTATTTACAGGAA
9
1642





1314909
N/A
N/A
19939
19958
TGTGATTGCATTTAGTGCCT
64
1643





1315012
N/A
N/A
122518
122537
GAGAAGGATTCATCACTCTC
72
1644





1315016
N/A
N/A
118961
118980
TCCAAAATTCTAACTGCTGT
65
1645





1315020
N/A
N/A
118006
118025
AAGCCTCTATATTTTGGTCT
69
1646





1315034
N/A
N/A
18228
18247
GCACCAATATCATTACACAC
69
1647





1315064
N/A
N/A
149098
149117
TGCCTTTTCATTTTAATTCA
89
1648





1315106
N/A
N/A
133576
133595
GCCATGCTGCTCTAATAGAC
66
1649





1315282
N/A
N/A
17581
17600
TATCATTTCCCTCATTTCCC
42
1650





1315323
N/A
N/A
67762
67781
CATGTGTTTTTTAAAGCAGT
61
1651





1315343
N/A
N/A
126800
126819
GTCACAGCTTTTATTTCCAT
19
1652





1315351
N/A
N/A
22941
22960
CAAAAGACTTTCAAATTTCC
87
1653





1315374
N/A
N/A
83247
83266
TTCAAGTATTTCCTCTGACC
44
1654





1315433
N/A
N/A
24461
24480
GGTCTTTGAAATGATAGATC
86
1655





1315462
N/A
N/A
117318
117337
ACCTTTTTAATATCAAGGGC
94
1656





1315495
N/A
N/A
22378
22397
CTGATATTAACAGAACCAGT
79
1657





1315503
N/A
N/A
13351
13370
TACAAAGTTCTTATTTTCTC
89
1658





1315515
868
887
33698
33717
TGTCATTTGCAAAATTGCCA
64
1659





1315629
N/A
N/A
69010
69029
ACATATATTTTTAAAGATCA
98
1660





1315704
N/A
N/A
59956
59975
TGGAAAGGTTCAACATGCTA
92
1661





1315724
N/A
N/A
81127
81146
CCAAATGTAAATATTCCATT
77
1662





1315765
N/A
N/A
100615
100634
ATCAATGATATCCCTTCTAA
80
1663





1315782
N/A
N/A
41143
41162
ATCTGCAATTTAACTGGACA
84
1664





1315863
N/A
N/A
128650
128669
TTGCAATTCAAATATGAGCA
59
1665





1315916
N/A
N/A
26475
26494
TTGATCCCATTTTATGGTTA
86
1666





1315954
N/A
N/A
158626
158645
GGACACAGAATTCCCATGGA
74
1667





1315982
N/A
N/A
45456
45475
TACGCGCCAAACAGCAATCA
99
1668





1315985
N/A
N/A
52693
52712
TCCTCATCTTTTATAAAGTA
79
1669





1315994
N/A
N/A
10344
10363
CCATCCCTAAAACTGTGCCA
71
1670





1316045
N/A
N/A
34972
34991
AAGGAAGTAATTAACGGATT
79
1671





1316056
N/A
N/A
38581
38600
GGTATGTACATTTCCTGTCA
59
1672





1316057
N/A
N/A
107166
107185
GGATACACACCAACAACACC
69
1673





1316116
N/A
N/A
106764
106783
CATGGAAATTACATTTGGAA
101
1674





1316130
N/A
N/A
60909
60928
ATAACATCATTCCTTGCATC
87
1675





1316229
N/A
N/A
50454
50473
TCCTAGAATCCTTTTGGCTT
41
1676





1316257
N/A
N/A
143913
143932
CTGCAGATTCTACCTTCATA
75
1677





1316278
N/A
N/A
58828
58847
AGCCATGGAACAATTCCCTA
99
1678





1316288
N/A
N/A
31572
31591
GCATTTTCTTTCCTTGTTAC
75
1679





1316331
N/A
N/A
12365
12384
TACTCTATATATACCAGGCT
74
1680





1316389
N/A
N/A
72164
72183
GGGAAAGCAATCATTCTAGA
56
1681





1316609
N/A
N/A
72997
73016
AGGCATGTCACAATACATTT
93
1682





1316628
N/A
N/A
55577
55596
GTAAAAGCAACTCCATTTCT
69
1683





1316677
N/A
N/A
56443
56462
GAACTCAGAAAACAGTATCA
62
1684





1316683
N/A
N/A
16942
16961
TCTTTCAGAAACATTAACAG
83
1685





1316700
N/A
N/A
4262
4281
AGATACTTTCTAAATTGCTT
53
1686





1316708
N/A
N/A
70319
70338
ATATTGTTAAAAATTCTCCA
79
1687





1316727
N/A
N/A
53086
53105
CCAGTCCTATTCTCCTGGAA
91
1688





1316743
6603
6622
138270
138289
AGAAATTTCACTCATCCCTA
59
1689





1316764
N/A
N/A
103067
103086
AGCTCAATAAATCTTTATCA
84
1690





1316855
N/A
N/A
112730
112749
AAGCAAACATTTTTACAACA
86
1691





1316871
N/A
N/A
46040
46059
ATTTCCTTCACCTCATCTGC
91
1692





1316879
N/A
N/A
115513
115532
CAGCAACAAATATTTTCAAC
72
1693





1316903
11138
11157
167887
167906
TTCCAACATTTCCTCCACTT
69
1694





1316949
N/A
N/A
110735
110754
CTCAAGGCTATTCTCAACTC
91
1695





1316976
N/A
N/A
104955
104974
TTGAATTTTTTTCCCTGAGA
88
1696





1316984
N/A
N/A
134190
134209
TTTAACTTATTCTGCAGTCA
32
1697





1317000
N/A
N/A
43184
43203
GTTCAAAAAATCCAATTGCT
79
1698





1317054
N/A
N/A
93976
93995
GACTTATTAATAATTTACTT
98
1699





1317055
N/A
N/A
131436
131455
TTTGTAAATTCTCCATGGTA
87
1700





1317069
N/A
N/A
73990
74009
TTCTCTTACAATCAGTGTCT
65
1701





1317082
N/A
N/A
2565
2584
CCAGAGTACTTCCTAACTCC
88
1702





1317086
N/A
N/A
47189
47208
CAGCTTGACACACATTTAAA
96
1703





1317218
N/A
N/A
80807
80826
TGTATTATATTTATTTCTCT
84
1704





1317224
N/A
N/A
6173
6192
TCAGTCATTCCTCACACTGC
90
1705
















TABLE 24







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
29
858





1314516
N/A
N/A
77962
77981
CCTCAAATCATCATCAGGCA
78
1706





1314578
N/A
N/A
107165
107184
GATACACACCAACAACACCT
81
1707





1314604
N/A
N/A
128216
128235
GCAGCAGGAATTTCTGCAAC
83
1708





1314629
N/A
N/A
48775
48794
CAGATTAACATTTCCTGCTC
82
1709





1314665
N/A
N/A
17573
17592
CCCTCATTTCCCTAATACAT
83
1710





1314742
N/A
N/A
58822
58841
GGAACAATTCCCTACTATCA
91
1711





1314748
N/A
N/A
12326
12345
GTTAACTGACTACAATCAAC
78
1712





1314775
N/A
N/A
22358
22377
CTAGCTTGCATCTAATTCTT
81
1713





1314813
N/A
N/A
8629
8648
GTTGACTTATTTACAGGAAA
20
1714





1314835
N/A
N/A
112729
112748
AGCAAACATTTTTACAACAA
58
1715





1314862
N/A
N/A
131319
131338
ACAAAGAACATCTAACACCT
73
1716





1314893
N/A
N/A
133545
133564
AGTGTGTTTGTAACACCTAA
90
1717





1314978
N/A
N/A
117976
117995
GATGATGTAACCATATAATC
66
1718





1314992
N/A
N/A
31509
31528
TGGTAACTACTTTAAGGTCT
71
1719





1315056
N/A
N/A
4246
4265
GCTTTCATCAATCTTACTTT
19
1720





1315058
N/A
N/A
72161
72180
AAAGCAATCATTCTAGAGCA
86
1721





1315062
N/A
N/A
117317
117336
CCTTTTTAATATCAAGGGCT
98
1722





1315086
N/A
N/A
34455
34474
ACATATTCCTTTATTTTACT
90
1723





1315092
N/A
N/A
100569
100588
ATGCACACACTCACATGCTT
91
1724





1315112
N/A
N/A
19191
19210
ACATTCATTTTCCTGGGATA
74
1725





1315119
N/A
N/A
115509
115528
AACAAATATTTTCAACTGGC
17
1726





1315173
N/A
N/A
72995
73014
GCATGTCACAATACATTTTA
77
1727





1315258
N/A
N/A
18226
18245
ACCAATATCATTACACACTT
64
1728





1315266
N/A
N/A
83246
83265
TCAAGTATTTCCTCTGACCT
45
1729





1315303
N/A
N/A
80806
80825
GTATTATATTTATTTCTCTA
56
1730





1315360
N/A
N/A
134909
134928
AAACCTTTTTCTTCACAGCT
66
1731





1315381
N/A
N/A
26400
26419
AGTGACATTTTCCCAGGAGC
43
1732





1315418
N/A
N/A
110734
110753
TCAAGGCTATTCTCAACTCA
84
1733





1315460
N/A
N/A
55378
55397
TAGGAAGTTCTAACATAGGC
42
1734





1315535
N/A
N/A
149097
149116
GCCTTTTCATTTTAATTCAA
102
1735





1315540
N/A
N/A
6172
6191
CAGTCATTCCTCACACTGCC
89
1736





1315573
N/A
N/A
45998
46017
ACAGCACTGCTTTCATACTA
97
1737





1315597
N/A
N/A
70299
70318
AAGCATCACACTATATACTA
55
1738





1315602
5774
5793
130357
130376
TCAGAATCCTCCTCTTCTCC
74
1739





1315622
N/A
N/A
22103
22122
CACCATTTTTATTATTCTAA
108
1740





1315763
N/A
N/A
22939
22958
AAAGACTTTCAAATTTCCCT
71
1741





1315779
N/A
N/A
93885
93904
ACAGTCATAATAATAAGGTT
79
1742





1315783
N/A
N/A
104939
104958
GAGAAGATTACAAATTGCTG
63
1743





1315805
N/A
N/A
109839
109858
AACATCAATATCACATGCCT
70
1744





1315822
N/A
N/A
143890
143909
GCCTATACCATACAATTCTC
82
1745





1315827
N/A
N/A
103066
103085
GCTCAATAAATCTTTATCAG
59
1746





1315849
N/A
N/A
67687
67706
AGCTGAGTTCCTAATTCAGA
77
1747





1315894
11137
11156
167886
167905
TCCAACATTTCCTCCACTTA
72
1748





1315896
N/A
N/A
73959
73978
CCAAAGCCATTATCTTGCCT
64
1749





1315924
N/A
N/A
118942
118961
TGCTGCTATCCCTTGCAGCA
113
1750





1315936
N/A
N/A
98237
98256
ACACAACTATGATACAGCAA
88
1751





1316033
N/A
N/A
42656
42675
AGTCCACACCTCTAACTCTC
85
1752





1316066
N/A
N/A
44659
44678
GTTTAGTAATTATTTGCTTT
90
1753





1316142
N/A
N/A
45447
45466
AACAGCAATCATCCTAGAAT
82
1754





1316184
N/A
N/A
59893
59912
GGTTGAGTAAATAATCCCTA
46
1755





1316223
N/A
N/A
52691
52710
CTCATCTTTTATAAAGTACA
79
1756





1316240
N/A
N/A
34941
34960
AAAGTGTTAGCATCATCATA
63
1757





1316274
N/A
N/A
158314
158333
GCACGGATTTCACAACGGTG
34
1758





1316319
N/A
N/A
50425
50444
GTTTCACTAAAATCTCAAAC
55
1759





1316340
763
782
33593
33612
GCAGAAGGTTCACCAGGTAA
54
1760





1316347
N/A
N/A
122516
122535
GAAGGATTCATCACTCTCTC
89
1761





1316361
N/A
N/A
10316
10335
AAACATAGAATCATACAGTA
91
1762





1316520
N/A
N/A
15227
15246
GGACATATGCTCATTTGTTA
38
1763





1316528
N/A
N/A
134175
134194
AGTCATGGAAATACACTCAC
51
1764





1316558
N/A
N/A
56406
56425
AGCAAAGATATAATTAAGAT
92
1765





1316564
N/A
N/A
106748
106767
GGAAAACTGCTCTCAACATC
83
1766





1316571
N/A
N/A
68944
68963
GTCTCAACTTTTAAGTGAAA
56
1767





1316737
N/A
N/A
41126
41145
ACATGACCGCATACTACCCA
75
1768





1316755
N/A
N/A
38404
38423
AAGCATATATTTACACGAAC
85
1769





1316770
N/A
N/A
24392
24411
AGCTACACTTTTATATTTCC
67
1770





1316802
N/A
N/A
126799
126818
TCACAGCTTTTATTTCCATA
17
1771





1316830
N/A
N/A
19905
19924
AGATAGCCCCCTCATCTCAA
79
1772





1316851
N/A
N/A
53071
53090
TGGAAGATAAACCTGTAACA
73
1773





1316931
N/A
N/A
138040
138059
TTTGAACAATTTCATTCAAC
77
1774





1316942
N/A
N/A
16926
16945
ACAGAAGTTTTTATAAAGTT
84
1775





1316953
N/A
N/A
141280
141299
CCTAGATTCCTTAGAACCAA
58
1776





1317081
N/A
N/A
47187
47206
GCTTGACACACATTTAAAAA
86
1777





1317091
N/A
N/A
2564
2583
CAGAGTACTTCCTAACTCCT
92
1778





1317104
N/A
N/A
81122
81141
TGTAAATATTCCATTTCCAA
56
1779





1317117
N/A
N/A
13346
13365
AGTTCTTATTTTCTCTAGAC
52
1780





1317205
N/A
N/A
64817
64836
GGCACAATCACATTCTGGTA
19
1781





1317230
N/A
N/A
60882
60901
CCCAGAACTTTCAATTGAGC
76
1782
















TABLE 25







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
31
858





1314562
N/A
N/A
15211
15230
GTTATTTCATTTTCTTCCCA
36
1783





1314576
N/A
N/A
48774
48793
AGATTAACATTTCCTGCTCA
76
1784





1314601
N/A
N/A
31458
31477
GTTACCATTTTTAATTCTCA
72
1785





1314642
N/A
N/A
109838
109857
ACATCAATATCACATGCCTC
72
1786





1314644
N/A
N/A
110729
110748
GCTATTCTCAACTCAGGAAT
91
1787





1314661
N/A
N/A
77961
77980
CTCAAATCATCATCAGGCAT
81
1788





1314724
N/A
N/A
134908
134927
AACCTTTTTCTTCACAGCTA
72
1789





1314779
N/A
N/A
33554
33573
ACGCAAGTCATTCTTCCAGC
91
1790





1314823
N/A
N/A
98187
98206
TTGTCTTAAAATAATCTGCA
81
1791





1314834
N/A
N/A
59871
59890
GCTCACTTTAACTCTTACCA
57
1792





1314855
N/A
N/A
112728
112747
GCAAACATTTTTACAACAAC
52
1793





1314940
N/A
N/A
115508
115527
ACAAATATTTTCAACTGGCA
37
1794





1314954
N/A
N/A
133541
133560
TGTTTGTAACACCTAACAAC
98
1795





1314970
N/A
N/A
149096
149115
CCTTTTCATTTTAATTCAAC
90
1796





1314981
N/A
N/A
128194
128213
GATACAGCAATTTTATGGCT
69
1797





1315063
N/A
N/A
13345
13364
GTTCTTATTTTCTCTAGACA
68
1798





1315091
N/A
N/A
80782
80801
ACCAAGTTACTTAAATCCTA
42
1799





1315097
N/A
N/A
58808
58827
CTATCAACTTTCTAACTCGA
80
1800





1315131
N/A
N/A
24391
24410
GCTACACTTTTATATTTCCT
77
1801





1315171
N/A
N/A
19174
19193
ATAACTATTCTTCTTTGCCT
80
1802





1315379
N/A
N/A
67686
67705
GCTGAGTTCCTAATTCAGAA
61
1803





1315413
N/A
N/A
6130
6149
GACAGAACCCACCATGCTTA
76
1804





1315414
N/A
N/A
16906
16925
TTTGCATATTTATCGATTCC
38
1805





1315466
N/A
N/A
41082
41101
GGAATACTTTCTCATGGGCC
72
1806





1315473
N/A
N/A
68920
68939
CTGAAAATAAATTTTGATCA
92
1807





1315482
N/A
N/A
70297
70316
GCATCACACTATATACTAGC
25
1808





1315505
N/A
N/A
19883
19902
TCCTGAATTTAATCACATCA
82
1809





1315534
N/A
N/A
44646
44665
TTGCTTTTCCCATCAGACCA
76
1810





1315546
N/A
N/A
117975
117994
ATGATGTAACCATATAATCC
75
1811





1315644
N/A
N/A
107164
107183
ATACACACCAACAACACCTC
95
1812





1315670
N/A
N/A
126796
126815
CAGCTTTTATTTCCATACAT
40
1813





1315771
N/A
N/A
47162
47181
AAACACTATTATGAGTGCCA
71
1814





1315829
N/A
N/A
22931
22950
TCAAATTTCCCTTTTGACTT
76
1815





1315841
N/A
N/A
81121
81140
GTAAATATTCCATTTCCAAT
66
1816





1315848
N/A
N/A
133958
133977
ACCTGATAACCTATTTTCCC
69
1817





1315901
N/A
N/A
143889
143908
CCTATACCATACAATTCTCC
97
1818





1315944
N/A
N/A
26339
26358
CGTGCAGGCACAATTGTCAA
70
1819





1315952
N/A
N/A
100565
100584
ACACACTCACATGCTTATTA
59
1820





1315960
11136
11155
167885
167904
CCAACATTTCCTCCACTTAC
67
1821





1315996
N/A
N/A
22354
22373
CTTGCATCTAATTCTTGTAA
82
1822





1316019
N/A
N/A
53062
53081
AACCTGTAACACATTTTCCT
78
1823





1316077
N/A
N/A
12322
12341
ACTGACTACAATCAACATAC
89
1824





1316083
N/A
N/A
42627
42646
GCTTCTCTTCCAAATTAATC
91
1825





1316099
N/A
N/A
130251
130270
GCAGTGAGCTTATTTGCAAA
79
1826





1316115
N/A
N/A
122399
122418
GCCACCACTAATCCCATGGT
93
1827





1316118
N/A
N/A
93812
93831
TAGATGATTTTTATTTCAGT
69
1828





1316191
N/A
N/A
34937
34956
TGTTAGCATCATCATACTCA
61
1829





1316205
N/A
N/A
10299
10318
GTATGTATAACCTTTTGGGA
51
1830





1316214
N/A
N/A
141270
141289
TTAGAACCAATTTTAGACAA
72
1831





1316243
N/A
N/A
83245
83264
CAAGTATTTCCTCTGACCTT
40
1832





1316253
N/A
N/A
60881
60900
CCAGAACTTTCAATTGAGCT
57
1833





1316307
N/A
N/A
52690
52709
TCATCTTTTATAAAGTACAC
85
1834





1316318
N/A
N/A
118929
118948
TGCAGCAGACCATCAGTTAC
101
1835





1316413
N/A
N/A
8564
8583
CACCAGCACATTCTACAGCC
78
1836





1316418
N/A
N/A
45977
45996
GGAGATTTCCATTTACATGC
46
1837





1316464
N/A
N/A
45446
45465
ACAGCAATCATCCTAGAATT
98
1838





1316489
N/A
N/A
72052
72071
AGTCACCAAAATCATTCTCA
64
1839





1316519
N/A
N/A
38350
38369
GGTGTCAACAAAACTTCGGA
63
1840





1316541
N/A
N/A
138039
138058
TTGAACAATTTCATTCAACA
68
1841





1316546
N/A
N/A
64257
64276
GTCTACACAAAATCTTGCAG
50
1842





1316570
N/A
N/A
106743
106762
ACTGCTCTCAACATCTACAA
92
1843





1316613
N/A
N/A
17572
17591
CCTCATTTCCCTAATACATA
77
1844





1316629
N/A
N/A
2558
2577
ACTTCCTAACTCCTACTGTA
80
1845





1316657
N/A
N/A
157506
157525
CCACCATGCCATTCTCACCA
85
1846





1316780
N/A
N/A
56350
56369
ACCTGTAGTCCACATACCCA
77
1847





1316885
N/A
N/A
103064
103083
TCAATAAATCTTTATCAGCA
55
1848





1316887
N/A
N/A
72991
73010
GTCACAATACATTTTATACC
48
1849





1316909
N/A
N/A
131314
131333
GAACATCTAACACCTTTTCT
77
1850





1316922
N/A
N/A
4145
4164
TAGTGAATACCTCCTTTCTC
49
1851





1316937
N/A
N/A
34452
34471
TATTCCTTTATTTTACTCTC
68
1852





1316964
N/A
N/A
18225
18244
CCAATATCATTACACACTTT
54
1853





1316968
N/A
N/A
117297
117316
TCCAACAGATCAACTGCTGA
93
1854





1316979
N/A
N/A
104875
104894
AGTACCTTCACATACACAGA
81
1855





1317074
N/A
N/A
73939
73958
TAGCATCAACATTAATCTCC
70
1856





1317115
N/A
N/A
50380
50399
GACGCAAATATTATAGATTC
29
1857





1317128
N/A
N/A
55377
55396
AGGAAGTTCTAACATAGGCT
27
1858





1317174
N/A
N/A
22102
22121
ACCATTTTTATTATTCTAAT
95
1859
















TABLE 26







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
32
858





1314490
N/A
N/A
22921
22940
CTTTTGACTTCACTTCTGAC
83
1860





1314518
N/A
N/A
107163
107182
TACACACCAACAACACCTCC
82
1861





1314531
N/A
N/A
112727
112746
CAAACATTTTTACAACAACA
96
1862





1314552
N/A
N/A
18222
18241
ATATCATTACACACTTTCCT
69
1863





1314555
N/A
N/A
33552
33571
GCAAGTCATTCTTCCAGCTC
113
1864





1314640
N/A
N/A
6122
6141
CCACCATGCTTATCTGAGCA
95
1865





1314662
N/A
N/A
19134
19153
CCACTGTTACATATATTTCT
71
1866





1314693
N/A
N/A
133957
133976
CCTGATAACCTATTTTCCCA
69
1867





1314710
N/A
N/A
110701
110720
TCCTGCTAAAACCTACACCA
94
1868





1314752
N/A
N/A
72990
73009
TCACAATACATTTTATACCA
75
1869





1314821
N/A
N/A
71905
71924
CAGTAGTTCCTAAATCATCA
65
1870





1314863
N/A
N/A
157438
157457
GAAATGAGTTTCCATTGCTA
44
1871





1314888
N/A
N/A
50377
50396
GCAAATATTATAGATTCCAA
26
1872





1314902
N/A
N/A
19882
19901
CCTGAATTTAATCACATCAT
72
1873





1315055
N/A
N/A
48749
48768
CTGGCAAACATTTATGTTCA
49
1874





1315057
N/A
N/A
44565
44584
GCATATAGTTTCAATACTTT
46
1875





1315157
N/A
N/A
52689
52708
CATCTTTTATAAAGTACACA
51
1876





1315194
N/A
N/A
47130
47149
TACCAGACATTTTAAAGGCA
85
1877





1315251
N/A
N/A
131313
131332
AACATCTAACACCTTTTCTA
90
1878





1315272
N/A
N/A
102989
103008
CTGTACTGAATCTTAAGAAC
89
1879





1315285
N/A
N/A
68907
68926
TTGATCATTATTCCATAACA
81
1880





1315380
N/A
N/A
8563
8582
ACCAGCACATTCTACAGCCA
68
1881





1315401
N/A
N/A
149095
149114
CTTTTCATTTTAATTCAACC
98
1882





1315476
N/A
N/A
24386
24405
ACTTTTATATTTCCTAGCTG
94
1883





1315486
N/A
N/A
70296
70315
CATCACACTATATACTAGCA
57
1884





1315539
N/A
N/A
31454
31473
CCATTTTTAATTCTCATCTC
102
1885





1315558
N/A
N/A
98130
98149
ACAAGCATTTTTATCAACAT
54
1886





1315569
N/A
N/A
45442
45461
CAATCATCCTAGAATTGCTT
107
1887





1315624
N/A
N/A
133540
133559
GTTTGTAACACCTAACAACC
86
1888





1315675
N/A
N/A
4144
4163
AGTGAATACCTCCTTTCTCA
49
1889





1315697
N/A
N/A
93811
93830
AGATGATTTTTATTTCAGTA
68
1890





1315735
N/A
N/A
134904
134923
TTTTTCTTCACAGCTATCTT
94
1891





1315781
N/A
N/A
55126
55145
AATGTATTTAATACCAGCGA
24
1892





1315788
N/A
N/A
26266
26285
GCATCTCCAAACCATACAAT
77
1893





1315803
N/A
N/A
83107
83126
GCTTTGTGAGAAATCAGTTA
34
1894





1315821
N/A
N/A
2555
2574
TCCTAACTCCTACTGTACAC
92
1895





1315852
N/A
N/A
128125
128144
TCTAGTAATTCATTTTTCTC
66
1896





1315959
N/A
N/A
22070
22089
TTCATTAGCTATAATTCCTT
93
1897





1315966
N/A
N/A
58806
58825
ATCAACTTTCTAACTCGAAA
85
1898





1316001
N/A
N/A
118881
118900
AGACCAGCCCCACCTCCTCA
86
1899





1316067
N/A
N/A
16841
16860
GTTATATTTTCTAGCTGATT
53
1900





1316107
N/A
N/A
117974
117993
TGATGTAACCATATAATCCC
83
1901





1316123
N/A
N/A
53061
53080
ACCTGTAACACATTTTCCTA
88
1902





1316224
N/A
N/A
80778
80797
AGTTACTTAAATCCTATGTT
74
1903





1316241
N/A
N/A
15207
15226
TTTCATTTTCTTCCCACAAC
99
1904





1316258
N/A
N/A
100559
100578
TCACATGCTTATTAATACCC
93
1905





1316264
N/A
N/A
56349
56368
CCTGTAGTCCACATACCCAT
90
1906





1316323
N/A
N/A
130244
130263
GCTTATTTGCAAAATACTGA
57
1907





1316324
N/A
N/A
117258
117277
GTTTGCCTCATATTTGGACC
32
1908





1316326
N/A
N/A
106741
106760
TGCTCTCAACATCTACAAAA
86
1909





1316344
N/A
N/A
34449
34468
TCCTTTATTTTACTCTCAGA
58
1910





1316396
N/A
N/A
64229
64248
TCACAGTACCATAATTCATA
36
1911





1316415
N/A
N/A
22333
22352
CACAGTGAACTTCTTTCCGT
77
1912





1316417
N/A
N/A
12320
12339
TGACTACAATCAACATACCA
72
1913





1316565
N/A
N/A
34936
34955
GTTAGCATCATCATACTCAA
48
1914





1316568
N/A
N/A
81114
81133
TTCCATTTCCAATCAGAATT
77
1915





1316585
11132
11151
167881
167900
CATTTCCTCCACTTACCACA
92
1916





1316601
N/A
N/A
115507
115526
CAAATATTTTCAACTGGCAC
54
1917





1316634
N/A
N/A
17547
17566
TACACCCATCATAAATTCAT
93
1918





1316654
N/A
N/A
59860
59879
CTCTTACCATACTATGGGCC
93
1919





1316713
N/A
N/A
41024
41043
TGATGGCCATTTAAATCTTG
95
1920





1316718
N/A
N/A
73938
73957
AGCATCAACATTAATCTCCT
67
1921





1316729
N/A
N/A
10278
10297
TGGCTTTTTTCATTAGCATA
54
1922





1316774
N/A
N/A
122319
122338
CTGTTTTTATCCTCACAGAA
105
1923





1316800
N/A
N/A
77713
77732
GGCACTCTCCTTTCTCCCTC
69
1924





1316809
N/A
N/A
143883
143902
CCATACAATTCTCCCCATTT
68
1925





1316854
N/A
N/A
45884
45903
AGTATGTATCTTACACATCA
75
1926





1316938
442
461
13271
13290
GACAATGATTCACACGGTCT
46
1927





1316973
N/A
N/A
42624
42643
TCTCTTCCAAATTAATCGGT
104
1928





1317001
N/A
N/A
104874
104893
GTACCTTCACATACACAGAC
74
1929





1317058
N/A
N/A
109830
109849
ATCACATGCCTCTAAGTTTA
79
1930





1317061
N/A
N/A
67659
67678
ATCAAGTGATCATTTAAGCT
27
1931





1317111
N/A
N/A
60880
60899
CAGAACTTTCAATTGAGCTT
73
1932





1317163
N/A
N/A
126795
126814
AGCTTTTATTTCCATACATA
32
1933





1317190
N/A
N/A
141233
141252
GAGGTACCAATCTCTTGGTT
55
1934





1317211
N/A
N/A
37845
37864
GAGTAATTTCCTTCCAGGGA
53
1935





1317219
N/A
N/A
138016
138035
GCTTAGTAAAATATATATCT
76
1936
















TABLE 27







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
35
858





1314503
N/A
N/A
45374
45393
CCTCTATTTTTCAATTTATT
97
1937





1314508
N/A
N/A
10272
10291
TTTTCATTAGCATAACTTCA
69
1938





1314514
N/A
N/A
15206
15225
TTCATTTTCTTCCCACAACA
95
1939





1314523
N/A
N/A
83030
83049
GCCTAAGATTCCTTAGTGGC
114
1940





1314574
N/A
N/A
12319
12338
GACTACAATCAACATACCAC
88
1941





1314620
N/A
N/A
117243
117262
GGACCATGACTTAATGCTGT
39
1942





1314633
N/A
N/A
45816
45835
ACAAATGTTATTCACTGCAA
53
1943





1314636
N/A
N/A
22018
22037
ACTATGTATCTTCATCACAA
64
1944





1314650
433
452
13262
13281
TCACACGGTCTTTCTTGGTA
31
1945





1314672
N/A
N/A
107160
107179
ACACCAACAACACCTCCTGC
98
1946





1314685
N/A
N/A
130188
130207
AGTTGTTTTAAATATTGCCA
25
1947





1314694
N/A
N/A
133953
133972
ATAACCTATTTTCCCACTCA
77
1948





1314735
N/A
N/A
2298
2317
GTACACCTCATTCATCCCTC
46
1949





1314744
N/A
N/A
137926
137945
GGTATGACAATTTTAATTCA
33
1950





1314826
N/A
N/A
34447
34466
CTTTATTTTACTCTCAGAGT
94
1951





1314850
N/A
N/A
106740
106759
GCTCTCAACATCTACAAAAT
88
1952





1314901
N/A
N/A
70295
70314
ATCACACTATATACTAGCAT
53
1953





1314933
N/A
N/A
52672
52691
ACAGAGAATTTCATTAGATA
75
1954





1314937
N/A
N/A
80767
80786
TCCTATGTTTCTACATGACA
90
1955





1314939
N/A
N/A
104859
104878
CAGACACACATGCAGAGCCT
89
1956





1314951
N/A
N/A
6043
6062
AGCCAGAGTTCACTTAAGAT
71
1957





1314987
N/A
N/A
22919
22938
TTTGACTTCACTTCTGACCC
92
1958





1315068
N/A
N/A
72988
73007
ACAATACATTTTATACCAGC
54
1959





1315105
N/A
N/A
112716
112735
ACAACAACACTGTATAGCTA
96
1960





1315142
N/A
N/A
8562
8581
CCAGCACATTCTACAGCCAC
77
1961





1315160
N/A
N/A
19133
19152
CACTGTTACATATATTTCTT
72
1962





1315193
N/A
N/A
117973
117992
GATGTAACCATATAATCCCA
54
1963





1315241
N/A
N/A
33547
33566
TCATTCTTCCAGCTCTCCTT
106
1964





1315269
N/A
N/A
44497
44516
CAGATATAAAATATACACTA
103
1965





1315304
N/A
N/A
131312
131331
ACATCTAACACCTTTTCTAC
92
1966





1315399
N/A
N/A
47129
47148
ACCAGACATTTTAAAGGCAG
95
1967





1315442
N/A
N/A
53057
53076
GTAACACATTTTCCTAGTTG
54
1968





1315445
N/A
N/A
128119
128138
AATTCATTTTTCTCATCTCA
42
1969





1315446
N/A
N/A
58739
58758
TCCAAATTCAGAAATGACTT
84
1970





1315447
N/A
N/A
115478
115497
GGCAGAGTTTCTACCGGGCA
36
1971





1315617
N/A
N/A
19881
19900
CTGAATTTAATCACATCATA
94
1972





1315642
N/A
N/A
59579
59598
GCCCATAGTCTTGAACTCCT
67
1973





1315686
N/A
N/A
81081
81100
AATCAGTTTTTTCACTCACT
46
1974





1315742
N/A
N/A
37844
37863
AGTAATTTCCTTCCAGGGAT
90
1975





1315886
N/A
N/A
60864
60883
GCTTAGTTCATGAAATCTAA
34
1976





1315923
N/A
N/A
143387
143406
AGAAGGACTTCTCATTGGAC
47
1977





1315933
1974
1993
56308
56327
CGAGGCTTCATCAGGAAGAA
77
1978





1315946
N/A
N/A
141189
141208
ACTTCAGATTTCATTCAGAT
80
1979





1315957
N/A
N/A
118805
118824
GTTTATGGTCACCCATATTA
106
1980





1315986
N/A
N/A
17546
17565
ACACCCATCATAAATTCATA
115
1981





1316002
N/A
N/A
110696
110715
CTAAAACCTACACCACATCA
108
1982





1316090
N/A
N/A
22332
22351
ACAGTGAACTTCTTTCCGTT
74
1983





1316196
N/A
N/A
73934
73953
TCAACATTAATCTCCTGAGT
97
1984





1316270
N/A
N/A
41021
41040
TGGCCATTTAAATCTTGATA
97
1985





1316281
N/A
N/A
93765
93784
ATAGTATTTTCCATTTTGCT
64
1986





1316310
N/A
N/A
126794
126813
GCTTTTATTTCCATACATAT
34
1987





1316357
N/A
N/A
156630
156649
GTAGCATTTCCACCATCTAC
112
1988





1316431
N/A
N/A
149093
149112
TTTCATTTTAATTCAACCTA
119
1989





1316433
N/A
N/A
109708
109727
GGCAACCTCAAGCTGTGCCA
96
1990





1316515
N/A
N/A
42623
42642
CTCTTCCAAATTAATCGGTT
91
1991





1316579
N/A
N/A
18221
18240
TATCATTACACACTTTCCTA
84
1992





1316625
N/A
N/A
98129
98148
CAAGCATTTTTATCAACATC
95
1993





1316758
N/A
N/A
4138
4157
TACCTCCTTTCTCAACAGCA
55
1994





1316771
11128
11147
167877
167896
TCCTCCACTTACCACATTCA
95
1995





1316785
N/A
N/A
64198
64217
ACATGAACTCTATAATATCC
79
1996





1316796
N/A
N/A
133538
133557
TTGTAACACCTAACAACCCA
109
1997





1316833
N/A
N/A
34871
34890
ATACCATCTATCATCTGAGC
95
1998





1316874
N/A
N/A
16607
16626
TTAACAAATTTTCCAGATGA
102
1999





1316880
N/A
N/A
134899
134918
CTTCACAGCTATCTTCTCAT
76
2000





1316881
N/A
N/A
100557
100576
ACATGCTTATTAATACCCCA
47
2001





1316886
N/A
N/A
121393
121412
GCTACACTCACCACTATCAA
100
2002





1316889
N/A
N/A
50338
50357
ACTTAATTCAATGAAGGCTA
46
2003





1316905
N/A
N/A
67657
67676
CAAGTGATCATTTAAGCTTA
73
2004





1316943
N/A
N/A
24238
24257
GTATATCTCAATTCAGACAC
73
2005





1316946
N/A
N/A
71903
71922
GTAGTTCCTAAATCATCACC
68
2006





1316952
N/A
N/A
102912
102931
GTCTTTGTTCTTACTAGAAT
73
2007





1316959
N/A
N/A
48722
48741
CAGCAGTAAGACTTCAGTCA
56
2008





1317005
N/A
N/A
77686
77705
CCTCTCAATCTTTCTTTTTC
106
2009





1317010
N/A
N/A
31384
31403
ACAGCATTTCCTTCTAACAT
87
2010





1317112
N/A
N/A
68888
68907
AATGGCTGAATTTATTCCCT
49
2011





1317167
N/A
N/A
26106
26125
TGCAAACCATACAATAGAGC
95
2012





1317227
N/A
N/A
55125
55144
ATGTATTTAATACCAGCGAA
29
2013
















TABLE 28







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
24
858





1314502
N/A
N/A
110691
110710
ACCTACACCACATCAGCGCA
100
2014





1314542
1963
1982
56297
56316
CAGGAAGAATACCTGTGGCT
46
2015





1314548
N/A
N/A
55067
55086
GTTACACATATTTAACCACA
19
2016





1314553
N/A
N/A
52296
52315
TTCAAGTTAAACTATCCATA
82
2017





1314605
N/A
N/A
13241
13260
CTGAAAGTTCTTTCTTTCTA
94
2018





1314621
N/A
N/A
2294
2313
ACCTCATTCATCCCTCGGCA
49
2019





1314663
N/A
N/A
22882
22901
GGGTTTTTCCACATATCTGA
60
2020





1314698
N/A
N/A
25930
25949
TCCAAACCATACAAGAGCAC
84
2021





25951
25970








26062
26081








26083
26102








26150
26169








26171
26190








26238
26257








1314704
N/A
N/A
106736
106755
TCAACATCTACAAAATGCTT
92
2022





1314795
N/A
N/A
149092
149111
TTCATTTTAATTCAACCTAC
85
2023





1314801
N/A
N/A
134897
134916
TCACAGCTATCTTCTCATCA
63
2024





1314964
N/A
N/A
72986
73005
AATACATTTTATACCAGCTC
30
2025





1314980
N/A
N/A
15205
15224
TCATTTTCTTCCCACAACAT
93
2026





1314986
N/A
N/A
22014
22033
TGTATCTTCATCACAATCTA
69
2027





1315003
N/A
N/A
127983
128002
GATTTATTTTTTCCTTCCAC
46
2028





1315090
N/A
N/A
53042
53061
AGTTGACTTTCTAAATTACC
76
2029





1315107
N/A
N/A
117970
117989
GTAACCATATAATCCCAACA
36
2030





1315177
N/A
N/A
117197
117216
CTTTCTATTTTCTTGAGAGA
85
2031





1315277
N/A
N/A
98128
98147
AAGCATTTTTATCAACATCT
52
2032





1315283
N/A
N/A
68886
68905
TGGCTGAATTTATTCCCTCC
61
2033





1315305
N/A
N/A
58723
58742
ACTTCACTATAATAACCCTA
66
2034





1315321
N/A
N/A
130187
130206
GTTGTTTTAAATATTGCCAT
11
2035





1315385
N/A
N/A
6029
6048
TAAGATTGAAATTCAGATCA
77
2036





1315392
N/A
N/A
34421
34440
ATATGGGTCCCATTAAGGCT
53
2037





1315420
N/A
N/A
100455
100474
CATGGGTATTTTCCTTGACT
63
2038





1315424
N/A
N/A
12318
12337
ACTACAATCAACATACCACA
101
2039





1315529
N/A
N/A
17542
17561
CCATCATAAATTCATACAGA
76
2040





1315575
N/A
N/A
19132
19151
ACTGTTACATATATTTCTTC
49
2041





1315636
N/A
N/A
48604
48623
GCAGAAGTTTATCCATAGCC
29
2042





1315661
N/A
N/A
30256
30275
ATATACATTTACATGTACCT
112
2043





1315691
N/A
N/A
50287
50306
ACTGCAAATAATATTAGGCA
34
2044





1315727
N/A
N/A
19870
19889
CACATCATAAAACAATTTTC
79
2045





1315814
N/A
N/A
81079
81098
TCAGTTTTTTCACTCACTAC
41
2046





1315869
N/A
N/A
156305
156324
CCTGTCACTTACCATCCCAA
78
2047





1315906
N/A
N/A
37202
37221
CCAACATCCAACTAACCAAT
82
2048





1315909
N/A
N/A
112707
112726
CTGTATAGCTACATTTTTCC
68
2049





1315921
N/A
N/A
67642
67661
GCTTAGAAGTCATTTAGTCC
6
2050





1316004
N/A
N/A
16585
16604
TTGATGCTCATCCATACTTA
73
2051





1316021
N/A
N/A
93764
93783
TAGTATTTTCCATTTTGCTA
77
2052





1316047
N/A
N/A
22306
22325
CCTGTAGGTTATTTTTGCCT
56
2053





1316078
N/A
N/A
33539
33558
CCAGCTCTCCTTCAGGAGAA
93
2054





1316121
N/A
N/A
64192
64211
ACTCTATAATATCCATCTGA
63
2055





1316145
N/A
N/A
70279
70298
GCATATGTACATAATTTAAT
72
2056





1316171
N/A
N/A
131308
131327
CTAACACCTTTTCTACAAAT
79
2057





1316186
N/A
N/A
47128
47147
CCAGACATTTTAAAGGCAGT
61
2058





1316372
N/A
N/A
77684
77703
TCTCAATCTTTCTTTTTCTC
86
2059





1316461
N/A
N/A
107158
107177
ACCAACAACACCTCCTGCCA
91
2060





1316584
N/A
N/A
18171
18190
GGTCAGACATATAATAATCT
45
2061





1316606
N/A
N/A
83029
83048
CCTAAGATTCCTTAGTGGCC
72
2062





1316607
N/A
N/A
44472
44491
GACAAGGCTTTTCCTCCAAT
38
2063





1316637
N/A
N/A
141147
141166
CTGTTGGCCATCTCTCACCC
89
2064





1316662
N/A
N/A
115458
115477
GCACAGCTCCTACACTCTGA
60
2065





1316666
N/A
N/A
34870
34889
TACCATCTATCATCTGAGCT
81
2066





1316686
N/A
N/A
24225
24244
CAGACACTAAATTTTCATCA
57
2067





1316694
N/A
N/A
133537
133556
TGTAACACCTAACAACCCAA
87
2068





1316720
N/A
N/A
143372
143391
TGGACTTAAGCAATTAAGCC
84
2069





1316721
N/A
N/A
109548
109567
GCCAGGCCATTTCCTTCCAC
81
2070





1316778
N/A
N/A
4051
4070
TGCAGTTGATTTCAGAGCAT
64
2071





1316791
N/A
N/A
121302
121321
GGCACAGGATCTTTTAGAAC
33
2072





1316823
N/A
N/A
42593
42612
CAGTCATTCACATGCAGGGC
33
2073





1316836
N/A
N/A
80718
80737
ACGCTGTTTCCTACCTGCAC
95
2074





1316919
N/A
N/A
45371
45390
CTATTTTTCAATTTATTCCT
92
2075





1316935
N/A
N/A
45777
45796
GAGTCCAGTCACAATAACCT
97
2076





1316978
N/A
N/A
118800
118819
TGGTCACCCATATTACTCAT
37
2077





1316996
N/A
N/A
126780
126799
ACATATACAAATAATGGAGT
40
2078





1317023
N/A
N/A
137925
137944
GTATGACAATTTTAATTCAT
56
2079





1317037
N/A
N/A
73882
73901
TTGGATGAATGATCTTATTA
71
2080





1317100
11122
11141
167871
167890
ACTTACCACATTCAATACCC
84
2081





1317106
N/A
N/A
133952
133971
TAACCTATTTTCCCACTCAT
97
2082





1317121
N/A
N/A
102713
102732
TAGACGGATTTTCTTCGGAC
39
2083





1317140
N/A
N/A
60844
60863
TGGATGTGACTCACTTACCT
111†
2084





1317141
N/A
N/A
10243
10262
TTGCATGCTATCAGTAGCTC
44
2085





1317148
N/A
N/A
59495
59514
GCCCAGCATATTCAACAGAC
89
2086





1317172
N/A
N/A
104782
104801
GCCAAGCACATCACGACACC
63
2087





1317180
N/A
N/A
71902
71921
TAGTTCCTAAATCATCACCA
58
2088





1317198
N/A
N/A
41019
41038
GCCATTTAAATCTTGATAAA
99
2089





1317206
N/A
N/A
8488
8507
TTCTAAAATATTACATAGCA
100
2090
















TABLE 29







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
27
858





1314527
N/A
N/A
34404
34423
GCTTATTTTTCAGAATACGA
41
2091





1314570
N/A
N/A
19128
19147
TTACATATATTTCTTCCGTT
32
2092





1314797
N/A
N/A
26052
26071
ACAAGAGCACTTCCAAACCA
85
2093





26140
26159








1314806
N/A
N/A
142925
142944
AAGCATAATCATCTTCACCC
41
2094





1314824
N/A
N/A
48603
48622
CAGAAGTTTATCCATAGCCT
26
2095





1314841
N/A
N/A
10209
10228
CTGAGTAGTTTAACCATTCA
59
2096





1314872
2750
2769
60811
60830
GCAAGGGTTTCCAGAAGCTC
731
2097





1314919
N/A
N/A
45776
45795
AGTCCAGTCACAATAACCTA
104
2098





1314982
N/A
N/A
126685
126704
GTAAGCCTTTTTGAATGGTA
30
2099





1314983
N/A
N/A
77634
77653
TCTCTCTTTTTCCTGTGGGC
55
2100





1315011
N/A
N/A
72985
73004
ATACATTTTATACCAGCTCA
41
2101





1315025
N/A
N/A
137869
137888
TCAGTGATACACCAACCACC
74
2102





1315075
N/A
N/A
33519
33538
ACAGAAGCAATTCATTCCCT
84
2103





1315088
N/A
N/A
81077
81096
AGTTTTTTCACTCACTACAT
62
2104





1315176
4740
4759
104727
104746
TGTCACAGCCTTCCTTCCAC
69
2105





1315179
N/A
N/A
6024
6043
TTGAAATTCAGATCATGCTA
60
2106





1315188
N/A
N/A
83013
83032
GGCCAACAACTTCATGAGCA
86
2107





1315190
1947
1966
56281
56300
GGCTTCCTCATCTTCATCCT
49
2108





1315234
666
685
N/A
N/A
ACCATTCTTTTTAATTTCCT
27
2109





1315278
N/A
N/A
19869
19888
ACATCATAAAACAATTTTCC
74
2110





1315301
N/A
N/A
68884
68903
GCTGAATTTATTCCCTCCCT
55
2111





1315320
N/A
N/A
112705
112724
GTATAGCTACATTTTTCCCA
69
2112





1315324
N/A
N/A
133950
133969
ACCTATTTTCCCACTCATCA
83
2113





1315325
3703
3722
80650
80669
CTGGTTCTTTCTCCTTCCCC
51
2114





1315403
N/A
N/A
58666
58685
TAGAGATTCATCATATTGCC
43
2115





1315429
N/A
N/A
107157
107176
CCAACAACACCTCCTGCCAC
68
2116





1315493
1212
1231
N/A
N/A
CAGTTCATAAACCTGGACAA
63
2117





1315583
N/A
N/A
34869
34888
ACCATCTATCATCTGAGCTC
107
2118





1315660
N/A
N/A
22261
22280
GGCAGCAGCATATACCGAGT
53
2119





1315693
N/A
N/A
15200
15219
TTCTTCCCACAACATTTCCA
68
2120





1315711
N/A
N/A
24156
24175
CGTATACCATTTCCAACCAC
60
2121





1315725
N/A
N/A
47110
47129
GTATGCCATATTTATTAGCA
80
2122





1315741
N/A
N/A
59493
59512
CCAGCATATTCAACAGACTT
67
2123





1315831
N/A
N/A
13194
13213
TGTGTTGAATTACCCACTCC
92
2124





1315864
N/A
N/A
121270
121289
CGGGAAATACTTCACAGAGC
48
2125





1315870
N/A
N/A
45314
45333
TGCATATCTAAAATTATCAA
88
2126





1315877
N/A
N/A
54999
55018
GTAGCAAACATTATTAGACT
17
2127





1315927
N/A
N/A
52293
52312
AAGTTAAACTATCCATAGGC
68
2128





1315989
N/A
N/A
127982
128001
ATTTATTTTTTCCTTCCACC
43
2129





1316005
N/A
N/A
18169
18188
TCAGACATATAATAATCTAA
76
2130





1316031
N/A
N/A
149091
149110
TCATTTTAATTCAACCTACA
111
2131





1316060
N/A
N/A
87154
87173
GAGACTTTTAACTCAGGCTC
68
2132





1316087
N/A
N/A
71901
71920
AGTTCCTAAATCATCACCAT
69
2133





1316093
N/A
N/A
134895
134914
ACAGCTATCTTCTCATCAAT
72
2134





1316098
N/A
N/A
16582
16601
ATGCTCATCCATACTTAGGA
33
2135





1316120
N/A
N/A
22879
22898
TTTTTCCACATATCTGAGGC
76
2136





1316155
N/A
N/A
102145
102164
GTAATATTTCTAACTCACAA
68
2137





1316176
N/A
N/A
64128
64147
GCCAATAAAAATGAACAAAC
78
2138





1316216
N/A
N/A
44471
44490
ACAAGGCTTTTCCTCCAATT
64
2139





1316219
N/A
N/A
98127
98146
AGCATTTTTATCAACATCTA
67
2140





1316292
11121
11140
167870
167889
CTTACCACATTCAATACCCA
109
2141





1316333
N/A
N/A
22010
22029
TCTTCATCACAATCTACCTT
74
2142





1316336
N/A
N/A
50286
50305
CTGCAAATAATATTAGGCAT
50
2143





1316377
N/A
N/A
41009
41028
TCTTGATAAAAATATCCTAA
93
2144





1316401
8300
8319
156196
156215
GTCACATACATCAGCTCAAA
48
2145





1316404
N/A
N/A
73872
73891
GATCTTATTAAAATACTCAT
66
2146





1316483
N/A
N/A
133536
133555
GTAACACCTAACAACCCAAA
86
2147





1316510
N/A
N/A
110690
110709
CCTACACCACATCAGCGCAA
89
2148





1316516
N/A
N/A
117149
117168
GGCTTCTAGCTATTTAGTCA
76
2149





1316518
N/A
N/A
70274
70293
TGTACATAATTTAATTATTC
100
2150





1316551
N/A
N/A
67530
67549
ACAAGTCTTATCACTTCTGC
20
2151





1316658
N/A
N/A
17539
17558
TCATAAATTCATACAGATAC
79
2152





1316691
N/A
N/A
141140
141159
CCATCTCTCACCCTGAGGTT
80
2153





1316709
N/A
N/A
12295
12314
ACCTCAGTAAAATATAAGCA
85
2154





1316710
N/A
N/A
117968
117987
AACCATATAATCCCAACAAT
77
2155





1316769
N/A
N/A
100453
100472
TGGGTATTTTCCTTGACTCC
82
2156





1316772
N/A
N/A
130155
130174
TATGTGTAATATATACTCTC
29
2157





1316857
N/A
N/A
131302
131321
CCTTTTCTACAAATTAACTT
96
2158





1316901
N/A
N/A
53041
53060
GTTGACTTTCTAAATTACCA
69
2159





1316904
N/A
N/A
108878
108897
GGAGAACTGCTATCAAGGCA
65
2160





1317006
N/A
N/A
118798
118817
GTCACCCATATTACTCATGC
47
2161





1317015
N/A
N/A
37074
37093
GTACCTAGCACTTCACCTCC
82
2162





1317041
N/A
N/A
2278
2297
GGCAATTAACCTCCCCATCA
51
2163





1317078
5486
5505
115364
115383
TGGATCAGACACATTAGCAG
54
2164





1317099
N/A
N/A
106700
106719
ACCCTTACACATACTTGGTT
88
2165





1317204
N/A
N/A
8344
8363
TGCATATTAAAATCTGGGAA
22
2166





1317210
N/A
N/A
4014
4033
GTTATTATTCTAGCCAGGCA
68
2167
















TABLE 30







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
 4862
 4881
106917
106936
CTCAGTAACATTGACACCAC
 24
 858





1314479
N/A
N/A
22878
22897
TTTTCCACATATCTGAGGCT
 78
2168





1314486
 2697
 2716
60758
60777
AGTCAGCACATCGATGATCA
 75
2169





1314487
N/A
N/A
10160
10179
GTTCTTAGATATTATGGGTA
 17
2170





1314582
N/A
N/A
48405
48424
CAGACGGATTTTCTCAAGTC
 84
2171





1314670
N/A
N/A
26046
26065
GCACTTCCAAACCATACAAT
 65
2172





26134
26153








1314674
N/A
N/A
45772
45791
CAGTCACAATAACCTAGACT
 90
2173





1314703
 4739
 4758
104726
104745
GTCACAGCCTTCCTTCCACT
 52
2174





1314711
N/A
N/A
142923
142942
GCATAATCATCTTCACCCAA
 42
2175





1314784
N/A
N/A
24155
24174
GTATACCATTTCCAACCACA
 66
2176





1314840
N/A
N/A
47107
47126
TGCCATATTTATTAGCACTT
 73
2177





1314868
N/A
N/A
118797
118816
TCACCCATATTACTCATGCA
 63
2178





1314904
N/A
N/A
8261
8280
GCTTTGTTTTTCATCTGTGC
 21
2179





1314929
N/A
N/A
52292
52311
AGTTAAACTATCCATAGGCA
 65
2180





1314956
N/A
N/A
2254
2273
CGTGTTGGTTTTATTCCCAA
 67
2181





1314962
N/A
N/A
106660
106679
GGTTATCAATCATTATACCA
 85
2182





1314993
N/A
N/A
67526
67545
GTCTTATCACTTCTGCAATC
 37
2183





1315080
N/A
N/A
130141
130160
ACTCTCAGTTATCTATTCCT
 42
2184





1315208
N/A
N/A
13193
13212
GTGTTGAATTACCCACTCCA
 88
2185





1315255
N/A
N/A
153568
153587
GTGGCACTGTCCTTCAGCCC
 73
2186





153636
153655








153670
153689








153704
153723








153738
153757








153772
153791








153806
153825








153840
153859








153874
153893








153908
153927








153942
153961








153976
153995








154010
154029








154044
154063








154078
154097








1315280
N/A
N/A
22260
22279
GCAGCAGCATATACCGAGTC
 54
2187





1315336
N/A
N/A
19114
19133
TCCGTTTTCAACTATTTCAA
 54
2188





1315342
N/A
N/A
117135
117154
TAGTCATTTATTTAAAGCAA
 77
2189





1315400
N/A
N/A
100416
100435
TTGTAGCTATTTAATCGCTA
 94
2190





1315428
N/A
N/A
107008
107027
CACATGGCACTTCCTTCCAT
 70
2191





1315439
N/A
N/A
45313
45332
GCATATCTAAAATTATCAAT
 93
2192





1315500
N/A
N/A
72947
72966
ATCAACTAACATCTTTCCTA
 98
2193





1315674
N/A
N/A
126670
126689
TGGTAAAATAACATTTCCAA
 81
2194





1315681
N/A
N/A
34748
34767
GAGCACCTACTCCCATTCCA
 69
2195





1315696
N/A
N/A
133527
133546
AACAACCCAAAATAACCTCA
 80
2196





1315718
N/A
N/A
19868
19887
CATCATAAAACAATTTTCCA
105
2197





1315733
N/A
N/A
16581
16600
TGCTCATCCATACTTAGGAA
 28
2198





1315737
N/A
N/A
133948
133967
CTATTTTCCCACTCATCACA
 91
2199





1315740
N/A
N/A
15199
15218
TCTTCCCACAACATTTCCAC
 84
2200





1315760
N/A
N/A
33515
33534
AAGCAATTCATTCCCTGTTA
 82
2201





1315778
10934
10953
167683
167702
CACTTCCATTTTAATGACTT
 82
2202





1315876
N/A
N/A
17526
17545
CAGATACACACATACACTCT
 85
2203





1315922
N/A
N/A
121269
121288
GGGAAATACTTCACAGAGCA
 32
2204





1315937
N/A
N/A
137723
137742
GTTTAGCCATTTAAAGATTG
 82
2205





1315949
N/A
N/A
81076
81095
GTTTTTTCACTCACTACATC
 72
2206





1315988
N/A
N/A
37032
37051
GAAAAGTACATTCATAGGTT
 89
2207





1316061
 5436
 5455
115314
115333
TTGCTGCTCACTCATTTCCA
 26
2208





1316132
N/A
N/A
3714
3733
ATAGATATATATTATTCTAA
116
2209





1316153
N/A
N/A
130780
130799
TACTTTGTTTTTTAAATCAT
 95
2210





1316154
N/A
N/A
58665
58684
AGAGATTCATCATATTGCCA
 25
2211





1316255
N/A
N/A
6012
6031
TCATGCTACTCCTCTGCTCT
 64
2212





1316256
N/A
N/A
34403
34422
CTTATTTTTCAGAATACGAA
 75
2213





1316262
N/A
N/A
68832
68851
AGCCATACTCCCCTTACAGC
 36
2214





1316285
N/A
N/A
108824
108843
ACCCACCTTTCACAAGGACC
 87
2215





1316286
N/A
N/A
44419
44438
AGGTGTTAATTTACACAGTG
 84
2216





1316320
N/A
N/A
64097
64116
GCTACAACAAGAACCAATCT
 75
2217





1316334
N/A
N/A
30175
30194
GCCCACCTTTTTAATTTCCT
 90
2218





1316367
N/A
N/A
149088
149107
TTTTAATTCAACCTACACTC
 98
2219





1316453
N/A
N/A
50263
50282
GCTCTCAATTAAATACTCAA
 36
2220





1316459
N/A
N/A
134891
134910
CTATCTTCTCATCAATACTC
 87
2221





1316492
N/A
N/A
97718
97737
CCATTCTGAATGCCTAGATA
107
2222





1316521
N/A
N/A
110505
110524
CCCAGGTATCTCCTAGGCTT
 89
2223





1316543
N/A
N/A
53038
53057
GACTTTCTAAATTACCATTT
 45
2224





1316582
N/A
N/A
77632
77651
TCTCTTTTTCCTGTGGGCCA
 49
2225





1316604
 1175
 1194
42524
42543
GAGACTTCCATTTCTTTCCT
 19
2226





1316611
 3702
 3721
80649
80668
TGGTTCTTTCTCCTTCCCCT
 41
2227





1316646
 1912
 1931
56246
56265
GCAGGCCCAAATACTGGTTG
 49
2228





1316651
N/A
N/A
73838
73857
CACGAAACTCTCCTATAGCC
 85
2229





1316699
N/A
N/A
87068
87087
GCTCTGTTACTTCCTCAGGC
 71
2230





1316760
N/A
N/A
71900
71919
GTTCCTAAATCATCACCATT
 80
2231





1316818
N/A
N/A
70273
70292
GTACATAATTTAATTATTCT
 87
2232





1316840
N/A
N/A
18154
18173
TCTAAAGCTTTATATTTTCC
 79
2233





1316842
N/A
N/A
59479
59498
AGACTTTACACTTAATGATA
 72
2234





1316896
N/A
N/A
40948
40967
ACTATGTTACTTAAGAACAT
 85
2235





1316900
N/A
N/A
83012
83031
GCCAACAACTTCATGAGCAC
 98
2236





1316947
N/A
N/A
117966
117985
CCATATAATCCCAACAATGC
 93
2237





1317003
N/A
N/A
22009
22028
CTTCATCACAATCTACCTTA
 75
2238





1317137
N/A
N/A
127953
127972
CCTTAGACACTCACATGCTT
 49
2239





1317139
N/A
N/A
54878
54897
AGTTCTTAAAATAATGCACA
 43
2240





1317171
N/A
N/A
141101
141120
TACTATCAAAATCATCACTA
 82
2241





1317184
N/A
N/A
12168
12187
AGATGCCTCCTTCCCATCCA
 84
2242





1317209
N/A
N/A
112701
112720
AGCTACATTTTTCCCATAAC
 60
2243





1317222
N/A
N/A
101905
101924
GCAGAGCCACACAGCTCCCA
 90
2244
















TABLE 31







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
 4862
 4881
106917
106936
CTCAGTAACATTGACACCAC
 31
 858





1314483
N/A
N/A
130779
130798
ACTTTGTTTTTTAAATCATT
 89
2245





1314484
N/A
N/A
45770
45789
GTCACAATAACCTAGACTCA
 95
2246





1314622
  665
  684
N/A
N/A
CCATTCTTTTTAATTTCCTT
 36
2247





1314625
N/A
N/A
118780
118799
GCAAGGCCAATCACATAGGC
 93
2248





1314666
N/A
N/A
8212
8231
TGTAACTTTTATAATTTTCA
 47
2249





1314808
N/A
N/A
19110
19129
TTTTCAACTATTTCAAGGCA
 85
2250





1314830
N/A
N/A
106565
106584
GCTCCTATAATTTAACACCA
 69
2251





1314878
N/A
N/A
16580
16599
GCTCATCCATACTTAGGAAC
 54
2252





1314884
N/A
N/A
26045
26064
CACTTCCAAACCATACAATA
 92
2253





26133
26152








1314915
N/A
N/A
52281
52300
CCATAGGCAATTTTTCATCC
 40
2254





1314944
N/A
N/A
36952
36971
GGAAAATGATTTCTACCCCA
 83
2255





1314963
N/A
N/A
110471
110490
TGCAAATTCACTCAAATGTC
 78
2256





1314990
N/A
N/A
126632
126651
ACACTGTTACTTCATTATCT
 62
2257





1315013
N/A
N/A
24152
24171
TACCATTTCCAACCACACTT
 94
2258





1315023
N/A
N/A
130140
130159
CTCTCAGTTATCTATTCCTA
 46
2259





1315066
N/A
N/A
71875
71894
TGCTAGGTCACAATTAAGTG
 49
2260





1315108
N/A
N/A
13191
13210
GTTGAATTACCCACTCCACT
 90
2261





1315132
N/A
N/A
73728
73747
GGCCACATCCTCCATTATCA
 96
2262





1315210
N/A
N/A
60655
60674
CAGGTTAGTCCCACTCAGTA
 91
2263





1315220
N/A
N/A
53037
53056
ACTTTCTAAATTACCATTTA
 74
2264





1315225
N/A
N/A
2250
2269
TTGGTTTTATTCCCAACACA
 90
2265





1315229
N/A
N/A
112700
112719
GCTACATTTTTCCCATAACA
 52
2266





1315265
N/A
N/A
68831
68850
GCCATACTCCCCTTACAGCG
 51
2267





1315267
N/A
N/A
22867
22886
TCTGAGGCTTTTCCAGGTTA
 48
2268





1315292
N/A
N/A
137675
137694
TCTTAGTTTAATACTCAGAA
 84
2269





1315296
N/A
N/A
44393
44412
GAAGCAGTATATCAGACCAC
 66
2270





1315302
N/A
N/A
22250
22269
ATACCGAGTCTTACTTTTCC
 49
2271





1315326
N/A
N/A
17520
17539
CACACATACACTCTTCTTTC
 77
2272





1315394
N/A
N/A
141093
141112
AAATCATCACTATAACCTCC
 84
2273





1315417
N/A
N/A
42357
42376
AGCAAGACATCTTAACATCT
 98
2274





1315511
N/A
N/A
134883
134902
TCATCAATACTCAAACAGGT
 51
2275





1315541
N/A
N/A
107007
107026
ACATGGCACTTCCTTCCATC
 78
2276





1315562
N/A
N/A
108445
108464
AACACAAGTTCCTCTAGGGC
 28
2277





1315671
N/A
N/A
40940
40959
ACTTAAGAACATCCATTTCC
 80
2278





1315747
N/A
N/A
10100
10119
ATTAAGGTTTCATTTCTCTA
 18
2279





1315754
N/A
N/A
54865
54884
ATGCACAGTATTAATCACAT
 25
2280





1315766
N/A
N/A
56227
56246
GTCGGTACCGTCTAACACCT
 76
2281





1315843
N/A
N/A
100379
100398
ACAAGGGATTCTATTATTGC
 46
2282





1315861
N/A
N/A
142801
142820
TGAGTATTCATAACAAGACT
 71
2283





1315868
N/A
N/A
19867
19886
ATCATAAAACAATTTTCCAT
 97
2284





1315902
N/A
N/A
45281
45300
CTTGCTTAATAGTTTGGCCA
 86
2285





1315907
N/A
N/A
117964
117983
ATATAATCCCAACAATGCTA
 89
2286





1315947
N/A
N/A
15198
15217
CTTCCCACAACATTTCCACA
 91
2287





1315956
N/A
N/A
80421
80440
ACACTGTACACATTTTATTT
 84
2288





1315999
N/A
N/A
82942
82961
GCACAAACATTATCATTAAA
 58
2289





1316016
N/A
N/A
127949
127968
AGACACTCACATGCTTGTTA
 41
2290





1316104
N/A
N/A
97693
97712
GCATTCAGAATGCACAGCCT
111
2291





1316134
N/A
N/A
58633
58652
TACCACAGACTTTCTGGATT
 84
2292





1316141
N/A
N/A
86309
86328
TTCCTAACTTTCTTTCATAA
114
2293





1316179
N/A
N/A
47093
47112
GCACTTTTAATACTATATCA
 79
2294





1316197
N/A
N/A
18151
18170
AAAGCTTTATATTTTCCCAA
 45
2295





1316215
N/A
N/A
153260
153279
TGGTCATTTTCACTTATCTT
 48
2296





1316303
N/A
N/A
81070
81089
TCACTCACTACATCTATTCC
 84
2297





1316317
N/A
N/A
22003
22022
CACAATCTACCTTATTACAC
 87
2298





1316439
N/A
N/A
133943
133962
TTCCCACTCATCACAGGACA
103
2299





1316536
N/A
N/A
72939
72958
ACATCTTTCCTATAAATCAG
 85
2300





1316555
N/A
N/A
148916
148935
GTCAAGACACCATTCAGCTA
 83
2301





1316561
N/A
N/A
133522
133541
CCCAAAATAACCTCATGCTC
 61
2302





1316573
N/A
N/A
70222
70241
TGTCAGCAACATAAATTCTT
 44
2303





1316631
N/A
N/A
59475
59494
TTTACACTTAATGATAGGTT
 65
2304





1316633
N/A
N/A
121128
121147
CAATGTCAACTTTATTACTA
 89
2305





1316636
N/A
N/A
11756
11775
GTAGTCACTTTCACTTCACC
 35
2306





1316685
N/A
N/A
3678
3697
GAGCATTTTAAATCTATCTT
 37
2307





1316742
N/A
N/A
77458
77477
GAACGAACTCATACACGCTC
 76
2308





1316757
N/A
N/A
64094
64113
ACAACAAGAACCAATCTCAC
100
2309





1316776
 5432
 5451
115310
115329
TGCTCACTCATTTCCACCTT
 35
2310





1316841
N/A
N/A
117134
117153
AGTCATTTATTTAAAGCAAA
 85
2311





1316882
N/A
N/A
33511
33530
AATTCATTCCCTGTTAGGGA
 98
2312





1316891
10930
10949
167679
167698
TCCATTTTAATGACTTGGCT
 66
2313





1316965
N/A
N/A
50196
50215
GTGACAGCAATTCTTTTCCT
 29
2314





1316994
 4736
 4755
104723
104742
ACAGCCTTCCTTCCACTGGC
 98
2315





1317035
N/A
N/A
48404
48423
AGACGGATTTTCTCAAGTCA
 98
2316





1317079
N/A
N/A
101851
101870
CCTGCTAAATTCCATTCCTT
 66
2317





1317147
N/A
N/A
34330
34349
GAGGACAGAATTCTAATCCA
 81
2318





1317149
N/A
N/A
67048
67067
CTGAAGCTTTTTTCTAGAAA
 51
2319





1317166
N/A
N/A
6011
6030
CATGCTACTCCTCTGCTCTA
 85
2320





1317228
N/A
N/A
34747
34766
AGCACCTACTCCCATTCCAA
 80
2321
















TABLE 32







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
 4862
 4881
106917
106936
CTCAGTAACATTGACACCAC
 24
 858





1314533
N/A
N/A
33490
33509
AAGCCAGTTTTATATTCCAA
 47
2322





1314567
N/A
N/A
3677
3696
AGCATTTTAAATCTATCTTA
 80
2323





1314590
N/A
N/A
53006
53025
GGCTATATAAAAATTATGGC
 74
2324





1314596
N/A
N/A
130139
130158
TCTCAGTTATCTATTCCTAA
 26
2325





1314657
N/A
N/A
133521
133540
CCAAAATAACCTCATGCTCA
 57
2326





1314681
N/A
N/A
15195
15214
CCCACAACATTTCCACAAAT
 90
2327





1314687
N/A
N/A
2249
2268
TGGTTTTATTCCCAACACAC
 77
2328





1314712
 3090
 3109
N/A
N/A
GCCTCTATATATTCTGGTTA
 66
2329





1314739
N/A
N/A
126630
126649
ACTGTTACTTCATTATCTAA
 54
2330





1314763
N/A
N/A
68813
68832
CGTTGCCTACTATCTGTTTA
 36
2331





1314819
N/A
N/A
80417
80436
TGTACACATTTTATTTACTT
 94
2332





1314873
N/A
N/A
22244
22263
AGTCTTACTTTTCCATTCAA
 44
2333





1314899
N/A
N/A
108444
108463
ACACAAGTTCCTCTAGGGCA
 24
2334





1315073
 5428
 5447
115306
115325
CACTCATTTCCACCTTCAGC
 29
2335





1315115
N/A
N/A
19109
19128
TTTCAACTATTICAAGGCAA
 57
2336





1315121
N/A
N/A
30084
30103
GGAAGACACATCCCATCACT
 93
2337





1315148
N/A
N/A
70218
70237
AGCAACATAAATTCTTATTA
 62
2338





1315211
N/A
N/A
47028
47047
GACAATTTTTCCACAGGGCC
 65
2339





1315213
N/A
N/A
34329
34348
AGGACAGAATTCTAATCCAA
 80
2340





1315239
N/A
N/A
148850
148869
CCTTATTTTATTCCCCACCA
 77
2341





1315249
N/A
N/A
22856
22875
TCCAGGTTATCTTCCTATAA
 58
2342





1315289
N/A
N/A
16531
16550
AAGCAGACTACATTTTCACA
 63
2343





1315434
N/A
N/A
130775
130794
TGTTTTTTAAATCATTAGTT
 84
2344





1315441
N/A
N/A
77383
77402
TGCTTGCTCACTTCTTCCTG
 70
2345





1315485
N/A
N/A
142746
142765
ACTGATTGATTTCAATCCAC
 39
2346





1315571
N/A
N/A
26043
26062
CTTCCAAACCATACAATAGA
 95
2347





26131
26150








1315581
N/A
N/A
17517
17536
ACATACACTCTTCTTTCTGT
 59
2348





1315590
N/A
N/A
44344
44363
TTCTCAATAAATGAACTCTA
 70
2349





1315619
N/A
N/A
60653
60672
GGTTAGTCCCACTCAGTACC
 97
2350





1315641
N/A
N/A
106414
106433
CCACATAATACATTTAGTCA
 45
2351





1315664
N/A
N/A
18148
18167
GCTTTATATTTTCCCAAATT
 46
2352





1315672
N/A
N/A
127938
127957
TGCTTGTTACATATTATCTT
 18
2353





1315707
N/A
N/A
140849
140868
GCCACTTTTATTTTACAGTA
 75
2354





1315708
N/A
N/A
107004
107023
TGGCACTTCCTTCCATCTGC
 51
2355





1315730
N/A
N/A
86303
86322
ACTTTCTTTCATAATGAGAA
 93
2356





1315809
N/A
N/A
45741
45760
AAAGATTTCAGTACTACTCC
 53
2357





1315815
N/A
N/A
117936
117955
TTTTAGTTCCCCTTCCACTC
 89
2358





1315839
N/A
N/A
6005
6024
ACTCCTCTGCTCTAATCCTC
 82
2359





1315930
N/A
N/A
73678
73697
TGCTCTTTCCTACCAGCCCA
 76
2360





1315935
N/A
N/A
82902
82921
GCCAAGCACTATATACAACT
 58
2361





1315964
N/A
N/A
10094
10113
GTTTCATTTCTCTAGGATTA
 14
2362





1315965
N/A
N/A
34746
34765
GCACCTACTCCCATTCCAAA
 79
2363





1315990
N/A
N/A
81069
81088
CACTCACTACATCTATTCCT
 87
2364





1316052
10190
10209
166939
166958
TCACATACTTTACACGGGCA
 34
2365





1316073
N/A
N/A
59459
59478
GGTTATTTCTAAATATATCC
 76
2366





1316088
N/A
N/A
50195
50214
TGACAGCAATTCTTTTCCTA
 29
2367





1316119
N/A
N/A
101840
101859
CCATTCCTTTTTAAAGAGGT
 60
2368





1316126
N/A
N/A
133918
133937
TACAGGCATTCTAAATGCTA
 86
2369





1316140
N/A
N/A
52279
52298
ATAGGCAATTTTTCATCCCA
 43
2370





1316157
N/A
N/A
40939
40958
CTTAAGAACATCCATTTCCC
 74
2371





1316250
N/A
N/A
117119
117138
GCAAAGCATTCTCATTACAA
 29
2372





1316254
N/A
N/A
54861
54880
ACAGTATTAATCACATTTCA
 24
2373





1316316
N/A
N/A
56127
56146
AAAGAGCACATTTTACACAC
 80
2374





1316358
N/A
N/A
19859
19878
ACAATTTTCCATATAAAGTA
110
2375





1316365
N/A
N/A
152925
152944
GCTTTCACTAAATCAGGAAC
 63
2376





1316416
N/A
N/A
13184
13203
TACCCACTCCACTTAGTTCT
 86
2377





1316465
N/A
N/A
45260
45279
GCCTAGGATTATATTAAATT
 91
2378





1316542
N/A
N/A
72933
72952
TTCCTATAAATCAGAGCTCC
 76
2379





1316572
N/A
N/A
24064
24083
AGCTTATCTATATCTTCTTG
 67
2380





1316638
 4717
 4736
104704
104723
CCATGATGCCATCACAGAGC
 30
2381





1316652
N/A
N/A
11415
11434
GCCAGCCTCCTCTAATTGTG
 86
2382





1316669
N/A
N/A
137634
137653
TTGAAGCTTTCTTTTACAGT
 45
2383





1316692
N/A
N/A
7818
7837
GGTCCTATCATATTTTAACC
 60
2384





1316698
N/A
N/A
36896
36915
TGGCATTTTTATGAATGCAA
 85
2385





1316714
N/A
N/A
118749
118768
GCTGAGAACACAGCCTGCTA
 95
2386





1316716
N/A
N/A
121124
121143
GTCAACTTTATTACTATAGA
 24
2387





1316752
N/A
N/A
71846
71865
TCCTAAACTTCTAATTCACA
103
2388





1316761
N/A
N/A
100345
100364
GCAACTCAAATACCTGTTCA
 49
2389





1316838
N/A
N/A
64085
64104
ACCAATCTCACAATTAAGTA
 47
2390





1316860
N/A
N/A
22002
22021
ACAATCTACCTTATTACACC
 76
2391





1316884
N/A
N/A
58620
58639
CTGGATTATAATTCTAGGTT
 59
2392





1316941
N/A
N/A
110470
110489
GCAAATTCACTCAAATGTCA
 74
2393





1317052
N/A
N/A
48299
48318
CCTACTGTTTTCATTTCTCA
 61
2394





1317113
N/A
N/A
134881
134900
ATCAATACTCAAACAGGTCA
 56
2395





1317129
N/A
N/A
42356
42375
GCAAGACATCTTAACATCTG
 97
2396





1317195
N/A
N/A
97647
97666
AACTGGTTTCCATCAGCTGC
 91
2397





1317197
N/A
N/A
112697
112716
ACATTTTTCCCATAACAGAA
 82
2398
















TABLE 33







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 42
 858





1314526
N/A
N/A
59378
59397
GAAGCATTAACTTTACTGGC
 45
2399





1314536
N/A
N/A
25828
25847
AACAGAGCACCTCCAAACCA
 96
2400





25851
25870








25897
25916








25962
25981








26182
26201








26205
26224








1314549
N/A
N/A
22243
22262
GTCTTACTTTTCCATTCAAT
 42
2401





1314551
N/A
N/A
50190
50209
GCAATTCTTTTCCTATGCAA
 74
2402





1314594
N/A
N/A
133914
133933
GGCATTCTAAATGCTACCTC
 72
2403





1314653
N/A
N/A
30083
30102
GAAGACACATCCCATCACTA
105
2404





1314713
N/A
N/A
18117
18136
AGGTTGTATCACCTCTGACA
 83
2405





1314734
N/A
N/A
56125
56144
AGAGCACATTTTACACACAG
 70
2406





1314796
N/A
N/A
53005
53024
GCTATATAAAAATTATGGCA
100
2407





1314822
N/A
N/A
16529
16548
GCAGACTACATTTTCACAAT
 33
2408





1314854
N/A
N/A
22846
22865
CTTCCTATAATATATTCCAA
 95
2409





1314898
N/A
N/A
24063
24082
GCTTATCTATATCTTCTTGA
 83
2410





1314960
N/A
N/A
34681
34700
GCATGAAGAAATATTACACT
 59
2411





1314979
N/A
N/A
118732
118751
CTAGAGGTCATCTTCGGTCA
 44
2412





1314989
N/A
N/A
19076
19095
GTCCTTGTTATTCTATCTTA
 56
2413





1315030
N/A
N/A
3676
3695
GCATTTTAAATCTATCTTAC
 45
2414





1315044
N/A
N/A
33475
33494
TCCAACAGTCCCTAATGGGA
 90
2415





1315050
N/A
N/A
48296
48315
ACTGTTTTCATTTCTCAGCA
 56
2416





1315089
N/A
N/A
52278
52297
TAGGCAATTTTTCATCCCAT
 40
2417





1315100
N/A
N/A
106068
106087
CCTCAGTGACACATACGCTC
 93
2418





106124
106143








106180
106199








1315126
N/A
N/A
13176
13195
CCACTTAGTTCTACACCTCA
 77
2419





1315180
N/A
N/A
82901
82920
CCAAGCACTATATACAACTA
 83
2420





1315288
N/A
N/A
15165
15184
CAGAACAGAATCATACACAG
 69
2421





1315318
N/A
N/A
42352
42371
GACATCTTAACATCTGACTC
 94
2422





1315332
N/A
N/A
2247
2266
GTTTTATTCCCAACACACAT
 82
2423





1315358
N/A
N/A
112576
112595
CTGACACAATCATTACCAAC
156
2424





1315407
N/A
N/A
142745
142764
CTGATTGATTTCAATCCACA
 55
2425





1315453
N/A
N/A
86216
86235
GTCCTATTCCTTATACACTA
 86
2426





1315455
N/A
N/A
45735
45754
TTCAGTACTACTCCATGTCA
 83
2427





1315456
N/A
N/A
19845
19864
AAAGTAATATTTACAGGCTC
 78
2428





1315469
N/A
N/A
5998
6017
TGCTCTAATCCTCCAGTGAC
 89
2429





1315516
N/A
N/A
117915
117934
CCACCTCTATCTCTACCATC
 91
2430





1315607
N/A
N/A
133480
133499
TGTACAGTTCATCCTAGTAA
 92
2431





1315663
N/A
N/A
106980
106999
GTCAATAAAGTATCCACGAC
 88
2432





1315667
N/A
N/A
81068
81087
ACTCACTACATCTATTCCTA
 75
2433





1315717
N/A
N/A
45257
45276
TAGGATTATATTAAATTCTA
 101
2434





1315723
N/A
N/A
117026
117045
ATCTTATGACTTTCTTGGGT
 29
2435





1315796
N/A
N/A
130136
130155
CAGTTATCTATTCCTAAGCT
 79
2436





1315797
N/A
N/A
140553
140572
GATGCATATTTTATCTACCT
 47
2437





1315835
N/A
N/A
104554
104573
TTCTTTTAAAATTAAGATAC
 95
2438





1315867
3009
3028
66873
66892
ACTGCTTTGATCTCTTGCCA
 20
2439





1315883
N/A
N/A
58326
58345
GCTTTAGGTTTAAATCCGAT
 32
2440





1315911
N/A
N/A
54852
54871
ATCACATTTCATTAAGACCA
 36
2441





1315987
N/A
N/A
64053
64072
TGCAAAAGTCCATCTATACT
 76
2442





1316106
N/A
N/A
108443
108462
CACAAGTTCCTCTAGGGCAC
 34
2443





1316144
N/A
N/A
40937
40956
TAAGAACATCCATTTCCCAT
 85
2444





1316159
N/A
N/A
126625
126644
TACTTCATTATCTAAGGATA
 84
2445





1316183
N/A
N/A
77035
77054
GTCCGGTTTTTAACAGAGGT
 80
2446





1316185
N/A
N/A
11357
11376
GGGCATGTAAACTCAAGGAC
 52
2447





1316200
N/A
N/A
72918
72937
GCTCCATAAAAATCATTTGA
 84
2448





1316209
N/A
N/A
36874
36893
CCTCATACAATTTCCCTCCC
 97
2449





1316227
N/A
N/A
17494
17513
ATACCTGTTTTAACATCCAA
 78
2450





1316230
N/A
N/A
60616
60635
AGAACCGTCACTCTTCAACA
117
2451





1316287
N/A
N/A
21999
22018
ATCTACCTTATTACACCATT
 73
2452





1316338
N/A
N/A
110398
110417
GCAGACACCACCTAACTCTC
 83
2453





1316374
N/A
N/A
134846
134865
CCCTAGTTTACTTTTAAGTA
 88
2454





1316395
N/A
N/A
121123
121142
TCAACTTTATTACTATAGAA
 92
2455





1316436
N/A
N/A
97545
97564
CTTGTTGGTTTCAAATACTC
 68
2456





1316479
N/A
N/A
34313
34332
CCAAGTCCATCTGATTCCAC
 67
2457





1316538
N/A
N/A
10051
10070
TGGGCTGTATACTAACGGTA
 71
2458





1316550
N/A
N/A
70217
70236
GCAACATAAATTCTTATTAT
 78
2459





1316591
N/A
N/A
80405
80424
ATTTACTTTTACCCACACAA
 71
2460





1316614
N/A
N/A
99836
99855
CTGTTCTTTCATCCTTGTTA
 50
2461





1316664
N/A
N/A
137618
137637
CAGTCAGAACTTTTACAGCT
 55
2462





1316675
N/A
N/A
152835
152854
CCAGCATACACCTGTAGGGC
 68
2463





1316795
N/A
N/A
44299
44318
AACCAGTTCATCAAAGAGAT
 95
2464





1316804
N/A
N/A
47027
47046
ACAATTTTTCCACAGGGCCA
 89
2465





1316814
N/A
N/A
148560
148579
GCAGTGAGTCCCTTAAACCT
 77
2466





1316858
N/A
N/A
165381
165400
TGTCAGCATTTTACTTCCCT
 47
2467





1316877
N/A
N/A
7813
7832
TATCATATTTTAACCTAGGA
 94
2468





1316980
N/A
N/A
71708
71727
TGGCATTCATTTCCCACAGC
 62
2469





1317024
4486
4505
101339
101358
GCAAATCTAAAACCTGCTTC
 62
2470





1317084
5427
5446
115305
115324
ACTCATTTCCACCTTCAGCT
 33
2471





1317090
N/A
N/A
127937
127956
GCTTGTTACATATTATCTTA
 16
2472





1317094
N/A
N/A
130764
130783
TCATTAGTTATTATTATTCC
 53
2473





1317216
N/A
N/A
68794
68813
AAGTTGAAATACATGCTTCA
 73
2474





1317236
N/A
N/A
73559
73578
GTCCATACATTATACTTTCT
 46
2475
















TABLE 34







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 27
 858





1314506
N/A
N/A
133876
133895
TGCAAACTGCCTCCACTCAC
 85
2476





1314509
N/A
N/A
44288
44307
CAAAGAGATTTACAATCCTT
 90
2477





1314532
N/A
N/A
21995
22014
ACCTTATTACACCATTTCAC
 69
2478





1314557
N/A
N/A
22242
22261
TCTTACTTTTCCATTCAATC
 41
2479





1314584
N/A
N/A
19073
19092
CTTGTTATTCTATCTTAGCC
 80
2480





1314598
N/A
N/A
121103
121122
AGGACCACTTTCTCTCTCTT
 70
2481





1314613
N/A
N/A
2226
2245
GGCAAAAAACTTCAATCAAC
 41
2482





1314641
N/A
N/A
56124
56143
GAGCACATTTTACACACAGA
 37
2483





1314690
N/A
N/A
97432
97451
TTTTTGTTTTTACTAGCTCC
 70
2484





1314761
N/A
N/A
7724
7743
GGTTGACCAAAATAATCAAA
 55
2485





1314778
N/A
N/A
164361
164380
GTAGGGACCAGAACTCCTAA
 92
2486





164423
164442








1314791
N/A
N/A
59377
59396
AAGCATTAACTTTACTGGCA
 34
2487





1314849
N/A
N/A
58282
58301
GCTGAGGTTTCTACTTTTCT
 13
2488





1314880
N/A
N/A
40935
40954
AGAACATCCATTTCCCATTA
 67
2489





1314882
N/A
N/A
130135
130154
AGTTATCTATTCCTAAGCTA
 81
2490





1314908
N/A
N/A
73558
73577
TCCATACATTATACTTTCTT
 63
2491





1314948
N/A
N/A
72840
72859
GGAATGCTTTTACTAGGGCA
 45
2492





1314968
N/A
N/A
60613
60632
ACCGTCACTCTTCAACACAC
 75
2493





1315201
N/A
N/A
13171
13190
TAGTTCTACACCTCATTCAT
 73
2494





1315256
N/A
N/A
140551
140570
TGCATATTTTATCTACCTCT
 46
2495





1315260
N/A
N/A
19844
19863
AAGTAATATTTACAGGCTCC
 51
2496





1315270
N/A
N/A
68776
68795
CATGAAGTTATTCCTGCTTC
 78
2497





1315322
N/A
N/A
5997
6016
GCTCTAATCCTCCAGTGACA
 77
2498





1315346
N/A
N/A
106966
106985
CACGACAGTTCCAACATACA
120
2499





1315370
N/A
N/A
137616
137635
GTCAGAACTTTTACAGCTGT
 63
2500





1315438
N/A
N/A
17491
17510
CCTGTTTTAACATCCAATCA
 89
2501





1315461
N/A
N/A
18001
18020
AGCTTGAGTTTCTATAACAA
 54
2502





1315464
N/A
N/A
81064
81083
ACTACATCTATTCCTAAGCA
 84
2503





1315470
N/A
N/A
110318
110337
CACTTGCTTTTCTATTGTCT
 71
2504





1315522
N/A
N/A
117908
117927
TATCTCTACCATCTACTTGC
 85
2505





1315557
N/A
N/A
104538
104557
ATACATATCAATATAAGCAA
 97
2506





1315621
N/A
N/A
115130
115149
GTAGAGTACATTAACCGCTA
 25
2507





1315705
N/A
N/A
106113
106132
CATACGCTCACACATGAGCA
104
2508





106169
106188








1315807
N/A
N/A
30080
30099
GACACATCCCATCACTAGTT
 91
2509





1315881
N/A
N/A
117024
117043
CTTATGACTTTCTTGGGTTC
 31
2510





1315940
N/A
N/A
48295
48314
CTGTTTTCATTTCTCAGCAC
 48
2511





1315969
N/A
N/A
22845
22864
TTCCTATAATATATTCCAAC
 91
2512





1315973
N/A
N/A
112574
112593
GACACAATCATTACCAACAT
 79
2513





1316181
N/A
N/A
45684
45703
AAATGGGTTCTCTTACTCTA
 86
2514





1316221
N/A
N/A
46788
46807
GGCCATGGACCAATACCGCT
 87
2515





1316252
N/A
N/A
127923
127942
ATCTTAATTTTACCTTTACA
 52
2516





1316300
N/A
N/A
142742
142761
ATTGATTTCAATCCACACGG
 41
2517





1316308
N/A
N/A
86175
86194
GTCAAATTCACATAGGGTTG
 38
2518





1316321
N/A
N/A
33474
33493
CCAACAGTCCCTAATGGGAT
 97
2519





1316346
N/A
N/A
25822
25841
GCACCTCCAAACCATACATC
 29
2520





1316360
N/A
N/A
147227
147246
GTAATTTCTAAATCTGCAAC
 59
2521





1316384
N/A
N/A
15163
15182
GAACAGAATCATACACAGTA
104
2522





1316392
N/A
N/A
52277
52296
AGGCAATTTTTCATCCCATA
 13
2523





1316414
N/A
N/A
69840
69859
TAGTATATATTACCAGGTCA
 18
2524





1316554
N/A
N/A
118649
118668
GGGTGACACCTATAACCTCA
 97
2525





1316557
N/A
N/A
82897
82916
GCACTATATACAACTATTCT
 65
2526





1316577
N/A
N/A
130761
130780
TTAGTTATTATTATTCCATT
 60
2527





1316602
N/A
N/A
64047
64066
AGTCCATCTATACTATGACC
 57
2528





1316615
N/A
N/A
36873
36892
CTCATACAATTTCCCTCCCA
 89
2529





1316617
N/A
N/A
108421
108440
ACAAGGTGCACACTTTGCTC
 67
2530





1316663
N/A
N/A
3661
3680
CTTACAATATGAACAGGTTA
 39
2531





1316671
N/A
N/A
11011
11030
TGCTGTATTTTAATTGATCT
 48
2532





1316680
N/A
N/A
133368
133387
TGTCAAGACCATACTTACGG
 53
2533





1316704
N/A
N/A
126604
126623
CCAGAACCACATTTACTTTA
 29
2534





1316773
N/A
N/A
42351
42370
ACATCTTAACATCTGACTCA
 98
2535





1316835
N/A
N/A
76958
76977
GTACACACTTTCTTCTCGCA
 32
2536





1316859
N/A
N/A
10025
10044
GTTTTATGACAAACTGCCAA
 69
2537





1316927
N/A
N/A
134843
134862
TAGTTTACTTTTAAGTATCA
 79
2538





1316957
N/A
N/A
16526
16545
GACTACATTTTCACAATATA
 57
2539





1316971
N/A
N/A
99789
99808
GCCACACCACTCTACAGGTC
 59
2540





1316991
N/A
N/A
34182
34201
AGGGTCACTATTTCTGGACA
 77
2541





1316997
N/A
N/A
50117
50136
ACTAGCAGATTATATCACAA
 51
2542





1317066
N/A
N/A
52927
52946
CATGTGAGCTTTATAGTATC
 73
2543





1317070
N/A
N/A
24015
24034
AAGGAACTCATCCATTTCAT
 76
2544





1317076
N/A
N/A
80036
80055
GGATCTCACACTATGATGCC
 81
2545





1317085
N/A
N/A
45194
45213
TCATGGTAATTTAATTAAGA
110
2546





1317123
N/A
N/A
54830
54849
GATCTGTTTATAATAGGCTC
 34
2547





1317136
2962
2981
66826
66845
GGTCACATTTATAAAACAGC
 13
2548





1317144
N/A
N/A
34680
34699
CATGAAGAAATATTACACTA
 87
2549





1317152
N/A
N/A
101146
101165
CTCCAGTTTCCTCTCTAGCA
 66
2550





1317214
N/A
N/A
152615
152634
ACCCAGACCCTTGAATCCCT
 77
2551





1317237
N/A
N/A
71707
71726
GGCATTCATTTCCCACAGCT
 48
2552
















TABLE 35







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 33
 858





1314512
N/A
N/A
164356
164375
GACCAGAACTCCTAAGAGGA
 86
2553





164418
164437








1314534
N/A
N/A
13170
13189
AGTTCTACACCTCATTCATT
 64
2554





1314597
N/A
N/A
71706
71725
GCATTCATTTCCCACAGCTC
 75
2555





1314606
2961
2980
66825
66844
GTCACATTTATAAAACAGCT
 35
2556





1314741
N/A
N/A
69821
69840
ACTGAGTTAATTATAATCTA
 53
2557





1314743
N/A
N/A
42223
42242
GCTACACACCCACATCCCTA
 84
2558





1314765
N/A
N/A
10656
10675
TTTGGATGAACATTACCTCT
 60
2559





1314828
N/A
N/A
133367
133386
GTCAAGACCATACTTACGGA
 27
2560





1314866
N/A
N/A
127922
127941
TCTTAATTTTACCTTTACAT
 71
2561





1314914
N/A
N/A
17490
17509
CTGTTTTAACATCCAATCAC
 89
2562





1314971
N/A
N/A
19765
19784
ATACATGTCAATTTCTGCTC
 58
2563





1314998
N/A
N/A
110283
110302
TCCCAACAAAATCTTCACTC
104
2564





1315000
N/A
N/A
59375
59394
GCATTAACTTTACTGGCAAC
 67
2565





1315028
N/A
N/A
45679
45698
GGTTCTCTTACTCTAATCTA
 68
2566





1315043
N/A
N/A
60590
60609
GTTCTGGGTTTAACTGCAAC
 53
2567





1315054
N/A
N/A
40932
40951
ACATCCATTTCCCATTATTC
 55
2568





1315122
N/A
N/A
106965
106984
ACGACAGTTCCAACATACAT
 90
2569





1315125
N/A
N/A
68748
68767
AAGAAATTCCTTTCTCCACT
 68
2570





1315134
N/A
N/A
22843
22862
CCTATAATATATTCCAACTT
 86
2571





1315139
N/A
N/A
56123
56142
AGCACATTTTACACACAGAA
 48
2572





1315149
N/A
N/A
46787
46806
GCCATGGACCAATACCGCTC
 87
2573





1315195
N/A
N/A
16525
16544
ACTACATTTTCACAATATAC
 68
2574





1315276
N/A
N/A
130134
130153
GTTATCTATTCCTAAGCTAC
 74
2575





1315286
N/A
N/A
52887
52906
TTGTTGTTTAATTTGTGTAA
 53
2576





1315387
N/A
N/A
58079
58098
TGTGAACTTTTAACATACCA
 94
2577





1315519
N/A
N/A
5984
6003
AGTGACATCCCATCTCACTC
 93
2578





1315565
N/A
N/A
133841
133860
CTGCCGGTCATCCTTTACTC
106
2579





1315572
N/A
N/A
3562
3581
AGGAAGATATTTTAATTATT
100
2580





1315586
N/A
N/A
9989
10008
GCCGTACTATATTATATTCC
 48
2581





1315638
N/A
N/A
22240
22259
TTACTTTTCCATTCAATCTG
 86
2582





1315656
N/A
N/A
106112
106131
ATACGCTCACACATGAGCAC
 98
2583





106168
106187








1315694
N/A
N/A
130757
130776
TTATTATTATTCCATTGCTT
 36
2584





1315703
N/A
N/A
73557
73576
CCATACATTATACTTTCTTA
 39
2585





1315746
N/A
N/A
54736
54755
TAGCAGAGTTCATATAATCA
 27
2586





1315748
N/A
N/A
52266
52285
CATCCCATAATTTTTCATCC
 82
2587





1315801
N/A
N/A
81063
81082
CTACATCTATTCCTAAGCAT
 95
2588





1315820
N/A
N/A
7719
7738
ACCAAAATAATCAAATACTA
100
2589





1315828
N/A
N/A
15152
15171
TACACAGTATTTCACAAACA
 90
2590





1315830
N/A
N/A
126602
126621
AGAACCACATTTACTTTATA
 85
2591





1315919
N/A
N/A
120724
120743
TCATCTGTTTCTAAACCAGT
 87
2592





1316007
N/A
N/A
44280
44299
TTTACAATCCTTATCGACCA
 73
2593





1316026
N/A
N/A
25817
25836
TCCAAACCATACATCAGAAA
 92
2594





1316037
N/A
N/A
76957
76976
TACACACTTTCTTCTCGCAA
 38
2595





1316092
N/A
N/A
147001
147020
CTGCTTGTTCCCATATGAGA
 59
2596





1316109
N/A
N/A
72786
72805
AGCTACCCAGACATTTGGGC
 73
2597





1316352
N/A
N/A
99751
99770
GGGACATTATGAACTGCATT
 49
2598





1316380
N/A
N/A
134816
134835
TACTCCATTAATATTTTCCA
 56
2599





1316435
N/A
N/A
108398
108417
AGGATTTGCCATCATTGTTA
 13
2600





1316455
N/A
N/A
116999
117018
CCTTGTCATTTTCTTTCTCT
 54
2601





1316487
N/A
N/A
64027
64046
CCAGTACTATAAAATGTCCA
 69
2602





1316539
N/A
N/A
45193
45212
CATGGTAATTTAATTAAGAA
 86
2603





1316548
N/A
N/A
117906
117925
TCTCTACCATCTACTTGCCA
 80
2604





1316580
N/A
N/A
50115
50134
TAGCAGATTATATCACAAAC
 41
2605





1316593
N/A
N/A
34666
34685
ACACTAAATTCTTTAGATTC
 91
2606





1316644
N/A
N/A
137553
137572
ACTAAGCAAATTTATCACTC
 59
2607





1316693
N/A
N/A
112526
112545
TTGTATACACATACATGGGA
 87
2608





1316741
N/A
N/A
142723
142742
GTTGGCACTATTCTTATCCT
 42
2609





1316746
N/A
N/A
82891
82910
TATACAACTATTCTACTTCA
 77
2610





1316753
N/A
N/A
118564
118583
ACAGCAAGACTTCCATTTCT
 75
2611





1316788
N/A
N/A
18000
18019
GCTTGAGTTTCTATAACAAA
 33
2612





1316797
N/A
N/A
97366
97385
CTGTGAATCACTACTTGTCT
 93
2613





1316815
N/A
N/A
101118
101137
CCTGAGTTCACATGCCACAA
 64
2614





1316837
N/A
N/A
24006
24025
ATCCATTTCATCTATAAGTT
 57
2615





1316876
N/A
N/A
29886
29905
TTTAACTTTCATTATCATCA
 67
2616





1316914
N/A
N/A
21994
22013
CCTTATTACACCATTTCACA
 79
2617





1316915
N/A
N/A
33397
33416
GGAGACATCCTTCATTTCTC
100
2618





1316982
N/A
N/A
79921
79940
GCAGCATTTTAAACTCCTGT
 63
2619





1316983
N/A
N/A
36872
36891
TCATACAATTTCCCTCCCAT
 98
2620





1316989
N/A
N/A
34028
34047
TGGCACAGTCATCTTCCCGC
 75
2621





1317009
N/A
N/A
2225
2244
GCAAAAAACTTCAATCAACT
 69
2622





1317043
N/A
N/A
104537
104556
TACATATCAATATAAGCAAC
 97
2623





1317060
N/A
N/A
152563
152582
CCAATGTGACCTGCTAGGAA
 49
2624





1317127
N/A
N/A
86072
86091
GCAATTCTATTTTACAGACT
 65
2625





1317151
N/A
N/A
19054
19073
CAGAAGCAAAAATCTTTCAT
 79
2626





1317164
N/A
N/A
48293
48312
GTTTTCATTTCTCAGCACCT
 32
2627





1317185
N/A
N/A
140549
140568
CATATTTTATCTACCTCTCC
 81
2628





1317215
N/A
N/A
115085
115104
GTGGACACAGTCACTTGGTC
 72
2629
















TABLE 36







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 27
 858





1314498
N/A
N/A
36856
36875
CCATTCATCTTCTCTCAGGA
 80
2630





1314520
2960
2979
66824
66843
TCACATTTATAAAACAGCTT
 74
2631





1314588
N/A
N/A
73550
73569
TTATACTTTCTTAACATCCC
101
2632





1314654
N/A
N/A
19764
19783
TACATGTCAATTTCTGCTCT
 52
2633





1314679
N/A
N/A
22239
22258
TACTTTTCCATTCAATCTGA
 87
2634





1314686
N/A
N/A
2218
2237
ACTTCAATCAACTCTTCCTA
 72
2635





1314702
N/A
N/A
96631
96650
GCATGGTACCTAATTATTCC
 89
2636





1314715
N/A
N/A
126551
126570
ATGGAACCAATTTAAGGACT
 42
2637





1314749
N/A
N/A
116998
117017
CTTGTCATTTTCTTTCTCTA
 34
2638





1314782
N/A
N/A
13166
13185
CTACACCTCATTCATTCATT
 48
2639





1314829
N/A
N/A
9988
10007
CCGTACTATATTATATTCCC
 16
2640





1314843
N/A
N/A
45191
45210
TGGTAATTTAATTAAGAACA
 72
2641





1314883
N/A
N/A
52263
52282
CCCATAATTTTTCATCCCAT
 65
2642





1315082
N/A
N/A
106077
106096
CTCTGACCCCCTCAGTGACA
 93
2643





106133
106152








1315083
N/A
N/A
117878
117897
TGGTTAGTTTTCCTTTTATA
 16
2644





1315186
N/A
N/A
151463
151482
CCACTTAACCTTTCACACCC
 98
2645





1315246
N/A
N/A
106964
106983
CGACAGTTCCAACATACATT
 82
2646





1315297
N/A
N/A
130028
130047
AAGCTGCACATTCAATCAGC
 86
2647





1315299
N/A
N/A
134815
134834
ACTCCATTAATATTTTCCAG
 43
2648





1315306
N/A
N/A
34658
34677
TTCTTTAGATTCATCATCTC
 93
2649





1315398
N/A
N/A
72717
72736
GGGTGAACTCTTTATTACTA
 54
2650





1315426
N/A
N/A
45673
45692
CTTACTCTAATCTATTACTT
 94
2651





1315512
N/A
N/A
137549
137568
AGCAAATTTATCACTCAGTA
 30
2652





1315531
N/A
N/A
147000
147019
TGCTTGTTCCCATATGAGAA
 86
2653





1315632
N/A
N/A
120649
120668
GACAGCTATCTTTCTTGGCT
 80
2654





1315634
N/A
N/A
56122
56141
GCACATTTTACACACAGAAC
 39
2655





1315652
N/A
N/A
54734
54753
GCAGAGTTCATATAATCAAC
 15
2656





1315728
N/A
N/A
33389
33408
CCTTCATTTCTCTTATGATC
 96
2657





1315729
N/A
N/A
23967
23986
AGTTGTTCATAATATTACCA
 44
2658





1315770
N/A
N/A
130720
130739
ATACCCAGCATCATGTAGGC
 82
2659





1315774
N/A
N/A
115025
115044
GTAGCATTTTTTTAAGCTTT
 98
2660





1315776
N/A
N/A
22832
22851
TTCCAACTTAATGATACTGA
 52
2661





1315851
N/A
N/A
118316
118335
GCATAAATATACAATGCAGA
 81
2662





1315856
N/A
N/A
104536
104555
ACATATCAATATAAGCAACA
 94
2663





1315913
N/A
N/A
15151
15170
ACACAGTATTTCACAAACAA
 83
2664





1315928
N/A
N/A
140531
140550
CCATCCCCAATTCCTAGCTT
 90
2665





1315975
N/A
N/A
99585
99604
GCCTTAAATCATCTTTGCAT
 77
2666





1316032
N/A
N/A
59295
59314
GTGCATGGAAATATTTCCTA
 32
2667





1316036
N/A
N/A
34027
34046
GGCACAGTCATCTTCCCGCA
 76
2668





1316041
N/A
N/A
69817
69836
AGTTAATTATAATCTAGACA
 84
2669





1316089
N/A
N/A
44272
44291
CCTTATCGACCAATTTTATT
 95
2670





1316103
N/A
N/A
17489
17508
TGTTTTAACATCCAATCACT
 89
2671





1316122
N/A
N/A
57883
57902
CAGATTGTTTTCAAATGAAC
 99
2672





1316128
N/A
N/A
133317
133336
CTGCTAAATTTTCAATATAA
 81
2673





1316139
N/A
N/A
110282
110301
CCCAACAAAATCTTCACTCC
 90
2674





1316204
N/A
N/A
48191
48210
CCTGCTAAACTTTAATTCTC
 67
2675





1316233
N/A
N/A
46779
46798
CCAATACCGCTCTGCAGCCT
 94
2676





1316236
N/A
N/A
79862
79881
TTCAAGGTCACAGCTGGTTA
 62
2677





1316244
N/A
N/A
81062
81081
TACATCTATTCCTAAGCATC
103
2678





1316272
N/A
N/A
60568
60587
GGATGTTGCATTTTTCCCAC
 91
2679





1316280
N/A
N/A
108373
108392
ATAGAATTTGTAATATTTCA
 87
2680





1316351
N/A
N/A
68740
68759
CCTTTCTCCACTTCTCATCT
 66
2681





1316394
N/A
N/A
17999
18018
CTTGAGTTTCTATAACAAAA
 59
2682





1316443
N/A
N/A
40931
40950
CATCCATTTCCCATTATTCA
 81
2683





1316452
N/A
N/A
101112
101131
TTCACATGCCACAAACGGCA
 96
2684





1316499
N/A
N/A
64012
64031
GTCCAGAAAATACAAATCTT
 33
2685





1316527
N/A
N/A
19042
19061
TCTTTCATTATTTTTTAACT
 96
2686





1316532
N/A
N/A
142722
142741
TTGGCACTATTCTTATCCTC
 48
2687





1316588
N/A
N/A
71644
71663
TCCATCAGATATTTTTCCAA
 61
2688





1316599
N/A
N/A
7709
7728
TCAAATACTATCTCATGACA
 84
2689





1316661
N/A
N/A
76568
76587
TCTTCAGTCACACTAGCTGC
 99
2690





1316684
N/A
N/A
42098
42117
CCACAGTTACCCAAACAACA
 74
2691





1316696
N/A
N/A
16507
16526
ACATGAAGTTTTAAATGACT
 86
2692





1316784
N/A
N/A
10652
10671
GATGAACATTACCTCTGGTT
 70
2693





1316846
N/A
N/A
133837
133856
CGGTCATCCTTTACTCTTTA
 29
2694





1316910
N/A
N/A
5983
6002
GTGACATCCCATCTCACTCA
 82
2695





1316916
N/A
N/A
50114
50133
AGCAGATTATATCACAAACA
 37
2696





1316990
N/A
N/A
85103
85122
CGGCATTTTTCAACATGCCG
 88
2697





1317013
N/A
N/A
162972
162991
GTGTGGGTTCCACCTTCATC
 93
2698





1317049
N/A
N/A
21990
22009
ATTACACCATTICACATGCA
 68
2699





1317051
N/A
N/A
3561
3580
GGAAGATATTTTAATTATTG
106
2700





1317093
N/A
N/A
127916
127935
TTTTACCTTTACATTACCAT
 57
2701





1317114
N/A
N/A
25790
25809
AGTGCAGACATCCTCAGGGA
 70
2702





1317126
N/A
N/A
112329
112348
TCTGCTCTTCTCACTTAACC
 78
2703





1317183
N/A
N/A
82889
82908
TACAACTATTCTACTTCAGT
 71
2704





1317199
N/A
N/A
52844
52863
TTGTAAATAAATAATTACTA
 99
2705





1317202
N/A
N/A
28970
28989
GTCGATGATCTCTTTAACCG
 59
2706
















TABLE 37







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 34
 858





1314494
N/A
N/A
5982
6001
TGACATCCCATCTCACTCAC
 75
2707





1314510
N/A
N/A
46703
46722
TGCTATATCACATTATATGA
111
2708





1314524
N/A
N/A
105990
106009
TGAGCACACACACAGAGGCA
 97
2709





106099
106118








106155
106174








1314546
N/A
N/A
126550
126569
TGGAACCAATTTAAGGACTA
 59
2710





1314568
N/A
N/A
10484
10503
GACAAAGCATTTCCATTACA
 52
2711





1314593
N/A
N/A
127890
127909
ACGATATTTTTTGAAATTTA
108
2712





1314656
N/A
N/A
110281
110300
CCAACAAAATCTTCACTCCA
102
2713





1314678
N/A
N/A
45120
45139
CTAGAGTTTAGAATTTGCCA
 35
2714





1314716
N/A
N/A
63588
63607
TTGGAGTTTACTATACACTC
 49
2715





1314717
N/A
N/A
120586
120605
TGGGATGAATACCCTCCTCT
108
2716





1314736
N/A
N/A
130027
130046
AGCTGCACATTCAATCAGCA
 94
2717





1314858
N/A
N/A
60564
60583
GTTGCATTTTTCCCACACCT
 85
2718





1314895
N/A
N/A
82847
82866
CCTTAGTTTATTTAATTCAT
 79
2719





1314897
N/A
N/A
137088
137107
AGGTCTCTTTTCATGAACAC
127
2720





1314935
N/A
N/A
3558
3577
AGATATTTTAATTATTGCCC
 18
2721





1314958
N/A
N/A
99569
99588
GCATCAACCATATATATCTC
 50
2722





1314974
N/A
N/A
84856
84875
GCTATGTGAAATAATCTTTA
 79
2723





1315001
N/A
N/A
52262
52281
CCATAATTTTTCATCCCATT
 83
2724





1315037
N/A
N/A
19763
19782
ACATGTCAATTTCTGCTCTT
 62
2725





1315084
N/A
N/A
104523
104542
AGCAACATAAAATAATTCAT
101
2726





1315109
N/A
N/A
48189
48208
TGCTAAACTTTAATTCTCTT
 57
2727





1315129
N/A
N/A
22238
22257
ACTTTTCCATTCAATCTGAA
 92
2728





1315165
N/A
N/A
116994
117013
TCATTTTCTTTCTCTAGAGA
 84
2729





1315183
N/A
N/A
79817
79836
CCAGATGTATTCATAAAGCC
 82
2730





1315247
N/A
N/A
101095
101114
GCACCATTTACCTTATCTGC
103
2731





1315271
N/A
N/A
44267
44286
TCGACCAATTTTATTTAGAT
 84
2732





1315287
N/A
N/A
21988
22007
TACACCATTTCACATGCAGC
 54
2733





1315309
N/A
N/A
142721
142740
TGGCACTATTCTTATCCTCA
 33
2734





1315334
N/A
N/A
45669
45688
CTCTAATCTATTACTTGCTT
 84
2735





1315347
N/A
N/A
9987
10006
CGTACTATATTATATTCCCA
 17
2736





1315350
N/A
N/A
40929
40948
TCCATTTCCCATTATTCAAA
 61
2737





1315354
N/A
N/A
134798
134817
CAGAAATTTCATTTATACTC
 96
2738





1315372
N/A
N/A
34657
34676
TCTTTAGATTCATCATCTCC
106
2739





1315406
3283
3302
N/A
N/A
GAGGCACTCCACAGTGCCAA
118
2740





1315423
N/A
N/A
56102
56121
ACAAATGTACTCATCTGTCA
 64
2741





1315471
N/A
N/A
81061
81080
ACATCTATTCCTAAGCATCT
 99
2742





1315499
N/A
N/A
23965
23984
TTGTTCATAATATTACCATA
 44
2743





1315501
N/A
N/A
133790
133809
TAGGAAGGTTCTATTATGGC
 19
2744





1315584
N/A
N/A
72713
72732
GAACTCTTTATTACTATGGA
 36
2745





1315627
N/A
N/A
133292
133311
TATCAGGGTTTCTCTTCCCA
 64
2746





1315738
N/A
N/A
28780
28799
CTGAAAGTCCTTAAATGAGC
 87
2747





1315816
N/A
N/A
68737
68756
TTCTCCACTTCTCATCTCCC
 78
2748





1315855
N/A
N/A
19039
19058
TTCATTATTTTTTAACTGAA
102
2749





1315885
N/A
N/A
69805
69824
TCTAGACATTTTAAACTTCT
 34
2750





1315932
N/A
N/A
75570
75589
CTGGTCTATCTTAAATCCAT
 95
2751





1315951
N/A
N/A
96506
96525
ATGTAACTCAACTAACCTCA
111
2752





1316042
N/A
N/A
112322
112341
TTCTCACTTAACCCAGTGCA
102
2753





1316058
N/A
N/A
151461
151480
ACTTAACCTTTCACACCCCC
 95
2754





1316101
N/A
N/A
146784
146803
AACTGGGATCTATTTTCTCA
 88
2755





1316113
N/A
N/A
15149
15168
ACAGTATTTCACAAACAACA
 90
2756





1316163
N/A
N/A
42077
42096
GAGAAACTGTCAACTGACCT
 99
2757





1316198
N/A
N/A
16506
16525
CATGAAGTTTTAAATGACTT
 97
2758





1316203
N/A
N/A
59273
59292
AAGCTCCAATTTTAATTGTA
 85
2759





1316330
N/A
N/A
108367
108386
TTTGTAATATTTCACAATCA
 82
2760





1316339
N/A
N/A
118298
118317
GACCACAGAATTACAACACT
 72
2761





1316342
N/A
N/A
13139
13158
TGTTTCTCGACTACTATGAA
 49
2762





1316368
N/A
N/A
17488
17507
GTTTTAACATCCAATCACTA
 91
2763





1316409
N/A
N/A
7678
7697
TATGAAATTCAAACTTCCTT
 69
2764





1316473
N/A
N/A
162971
162990
TGTGGGTTCCACCTTCATCC
101
2765





1316482
N/A
N/A
32882
32901
GAATCTCTATCTAAACGGCA
 75
2766





1316507
N/A
N/A
115000
115019
CTGTACACCATTACACAAAT
 64
2767





1316608
N/A
N/A
33981
34000
GCCGAAAACAAATCTGCTCT
 99
2768





1316627
N/A
N/A
2206
2225
TCTTCCTAATATTTAAGATA
 98
2769





1316639
N/A
N/A
117877
117896
GGTTAGTTTTCCTTTTATAT
 14
2770





1316660
N/A
N/A
50083
50102
GTTAAGTTTTATCAGAACAT
 63
2771





1316706
N/A
N/A
130685
130704
GGCATTTGATAAATGAGTCA
 92
2772





1316715
N/A
N/A
22814
22833
GAGGTCAGAAAACATACTCT
 97
2773





1316820
N/A
N/A
25694
25713
CACACGGTTCTTACTTTGAT
 96
2774





1316828
N/A
N/A
106963
106982
GACAGTTCCAACATACATTC
106
2775





1316831
N/A
N/A
54715
54734
CTATTCCAATTTTTTACCTC
 74
2776





1316870
N/A
N/A
17963
17982
GGTGGTTTAAACAATAAGCA
 83
2777





1316888
N/A
N/A
36777
36796
TGCAAAGGAAATTCCAGGCT
 85
2778





1316918
N/A
N/A
140495
140514
GCAGCACAAAATAAAAACAT
 68
2779





1316924
N/A
N/A
66757
66776
GATGAAACTCACCTGTGATA
109
2780





1316958
N/A
N/A
73440
73459
GAGGCTACTTTAAAATACTC
 93
2781





1317068
N/A
N/A
52828
52847
ACTACTAGAATTATTCAGAT
 64
2782





1317169
N/A
N/A
57835
57854
CCATCATTTCCTCCCTCCCC
 84
2783
















TABLE 38







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 36
 858





1314496
N/A
N/A
60563
60582
TTGCATTTTTCCCACACCTC
 75
2784





1314511
4387
4406
N/A
N/A
GAATAGCATTCTTATCTGCA
 27
2785





1314540
N/A
N/A
117872
117891
GTTTTCCTTTTATATTCATC
 27
2786





1314655
N/A
N/A
17887
17906
ACAGTGTTTTTCTTAACGAT
105
2787





1314722
N/A
N/A
28751
28770
TGGACAAACATTTATTTCAA
 52
2788





1314725
N/A
N/A
19732
19751
GCTATTGTCATACAATTCAC
 51
2789





1314729
N/A
N/A
3557
3576
GATATTTTAATTATTGCCCT
 33
2790





1314737
N/A
N/A
44266
44285
CGACCAATTTTATTTAGATG
 67
2791





1314750
N/A
N/A
45089
45108
TGCCACATCATTTATTTACT
 57
2792





1314771
N/A
N/A
21987
22006
ACACCATTTCACATGCAGCA
 41
2793





1314787
N/A
N/A
52817
52836
TATTCAGATTTTCCTCTCTA
 75
2794





1314792
N/A
N/A
33954
33973
TGCCTTTTCAATTTGCATCT
 84
2795





1314814
N/A
N/A
34656
34675
CTTTAGATTCATCATCTCCC
 78
2796





1314949
N/A
N/A
130026
130045
GCTGCACATTCAATCAGCAC
 91
2797





1315045
N/A
N/A
134790
134809
TCATTTATACTCAAACACTG
 91
2798





1315103
N/A
N/A
56092
56111
TCATCTGTCATTTATTTCAA
 64
2799





1315118
N/A
N/A
106079
106098
CACTCTGACCCCCTCAGTGA
 93
2800





106135
106154








1315136
N/A
N/A
72712
72731
AACTCTTTATTACTATGGAA
 64
2801





1315187
N/A
N/A
57728
57747
ACCTAGTTATTTCCTTCAAC
 64
2802





1315349
N/A
N/A
46702
46721
GCTATATCACATTATATGAA
 63
2803





1315530
N/A
N/A
22813
22832
AGGTCAGAAAACATACTCTG
 63
2804





1315537
N/A
N/A
126509
126528
GCATGACAAGCATATCCCAC
 26
2805





1315683
N/A
N/A
23559
23578
TCACTGTTTTTCCTATCAGC
 74
2806





1315699
N/A
N/A
120346
120365
GATGAATTATTTCAACTCTT
 49
2807





1315716
N/A
N/A
19038
19057
TCATTATTTTTTAACTGAAT
100
2808





1315762
N/A
N/A
15059
15078
GGCATTAAAAATAAGCAGAT
 76
2809





1315768
N/A
N/A
146737
146756
AAAATGTATTCACATAGGTT
109
2810





1315825
N/A
N/A
130654
130673
TCTCACAGTCCAACTTAGAA
 74
2811





1315925
N/A
N/A
50053
50072
ACAAAGTTAAATATGGCTGA
101
2812





1315945
N/A
N/A
108325
108344
TCAAATGTATATTAATCTTT
117
2813





1315950
N/A
N/A
69804
69823
CTAGACATTTTAAACTTCTG
 14
2814





1315961
N/A
N/A
66744
66763
TGTGATAGACCACCCTCCTC
 96
2815





1315976
N/A
N/A
118297
118316
ACCACAGAATTACAACACTA
 79
2816





1316013
N/A
N/A
63188
63207
GGTAACTCAACTTCCAGGAA
 36
2817





1316053
3221
3240
71459
71478
CACAAAGCTTCACAGCATCC
 63
2818





1316097
N/A
N/A
84837
84856
AAGTTTTTTTTAAAATCCTT
123
2819





1316146
N/A
N/A
114996
115015
ACACCATTACACAAATACAA
 66
2820





1316160
N/A
N/A
79816
79835
CAGATGTATTCATAAAGCCT
 61
2821





1316165
N/A
N/A
2191
2210
AGATAATTTCATTAATCACC
 91
2822





1316192
N/A
N/A
99562
99581
CCATATATATCTCCTAGAGT
 63
2823





1316249
N/A
N/A
68736
68755
TCTCCACTTCTCATCTCCCA
 78
2824





1316322
N/A
N/A
160915
160934
CCACGCACCATTTCTACCTG
 99
2825





1316359
N/A
N/A
127864
127883
AGGTTAAAAATCCATTGATC
 39
2826





1316362
N/A
N/A
81060
81079
CATCTATTCCTAAGCATCTA
 93
2827





1316400
N/A
N/A
82783
82802
GCTGAGGCTTTTCAACAGGT
 23
2828





1316424
N/A
N/A
32823
32842
AGACCCAGTTATATTCTTTA
 80
2829





1316440
N/A
N/A
42037
42056
CGAGGCACAGTCTCAAGCCT
 71
2830





1316449
N/A
N/A
140095
140114
GCTCCATTACATTCAGTCCT
 44
2831





1316485
N/A
N/A
75566
75585
TCTATCTTAAATCCATTGTA
 69
2832





1316491
N/A
N/A
73436
73455
CTACTTTAAAATACTCAGCA
 59
2833





1316517
N/A
N/A
96461
96480
GAACACAAAAATATATAGCA
 96
2834





1316525
N/A
N/A
45655
45674
TTGCTTAAAATTTATTCTGC
 94
2835





1316549
N/A
N/A
36069
36088
GGTACAGTCACCAACTTCAT
 67
2836





1316592
N/A
N/A
133291
133310
ATCAGGGTTTCTCTTCCCAA
 72
2837





1316619
N/A
N/A
25570
25589
CTGGAGAATTTCTAAGCAAA
104
2838





1316621
N/A
N/A
54712
54731
TTCCAATTTTTTACCTCAGT
 20
2839





1316672
N/A
N/A
48188
48207
GCTAAACTTTAATTCTCTTA
 25
2840





1316733
N/A
N/A
22226
22245
AATCTGAAAAATCGCTGCCT
 75
2841





1316735
N/A
N/A
40928
40947
CCATTTCCCATTATTCAAAA
 59
2842





1316751
N/A
N/A
104489
104508
AGCAAGCACACATCAAGCTA
107
2843





1316766
N/A
N/A
133788
133807
GGAAGGTTCTATTATGGCAC
 25
2844





1316783
N/A
N/A
116993
117012
CATTTTCTTTCTCTAGAGAC
 78
2845





1316825
N/A
N/A
7660
7679
TTGTCATTAATAAAATTCTA
104
2846





1316826
N/A
N/A
10483
10502
ACAAAGCATTTCCATTACAA
 57
2847





1316829
N/A
N/A
16503
16522
GAAGTTTTAAATGACTTCCT
 78
2848





1316847
N/A
N/A
106962
106981
ACAGTTCCAACATACATTCC
121
2849





1316867
N/A
N/A
142717
142736
ACTATTCTTATCCTCACCAC
 83
2850





1316906
N/A
N/A
17485
17504
TTAACATCCAATCACTATTT
 85
2851





1316936
N/A
N/A
13061
13080
CACGAGTTCACCAATGGCTG
 42
2852





1316961
N/A
N/A
137081
137100
TTTTCATGAACACCTGCCGT
101
2853





1316969
N/A
N/A
110180
110199
TCTGAATGCAACATGCACCT
 92
2854





1317014
1497
1516
51878
51897
AGAGTCATCCTCCAAGGCTT
 73
2855





1317016
N/A
N/A
59269
59288
TCCAATTTTAATTGTAGCAA
 78
2856





1317017
N/A
N/A
9986
10005
GTACTATATTATATTCCCAC
 19
2857





1317150
N/A
N/A
151420
151439
TCATGTCTTTCTGCTGGGCA
 86
2858





1317203
N/A
N/A
5976
5995
CCCATCTCACTCACATAAAT
 85
2859





1317217
N/A
N/A
112229
112248
TCCATTTATTTCCTTCCTTC
 63
2860
















TABLE 39







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 31
 858





1314480
N/A
N/A
57724
57743
AGTTATTTCCTTCAACTGTG
 94
2861





1314505
N/A
N/A
23557
23576
ACTGTTTTTCCTATCAGCTT
 91
2862





1314517
N/A
N/A
133767
133786
TCTGCAGTAAACCCACCTAT
 74
2863





1314559
N/A
N/A
33940
33959
GCATCTAGAAACCATCTCCC
 79
2864





1314603
N/A
N/A
114949
114968
GTATCATCAATTTTAGCCAG
 26
2865





1314609
N/A
N/A
75525
75544
GAAGTTGATTTTATTGCTTC
 88
2866





1314699
N/A
N/A
60561
60580
GCATTTTTCCCACACCTCTC
 92
2867





1314721
N/A
N/A
22797
22816
TCTGAATAATTTGAATGCTT
 57
2868





1314818
N/A
N/A
16464
16483
CTGCCATTTATATAACCTCA
 48
2869





1314925
N/A
N/A
56088
56107
CTGTCATTTATTTCAAGGCA
 76
2870





1314965
N/A
N/A
45088
45107
GCCACATCATTTATTTACTT
 67
2871





1315005
N/A
N/A
116695
116714
CCTCCAAATTTAACACAGGA
 85
2872





1315008
N/A
N/A
106078
106097
ACTCTGACCCCCTCAGTGAC
117
2873





106134
106153








1315049
N/A
N/A
106961
106980
CAGTTCCAACATACATTCCT
 92
2874





1315053
N/A
N/A
46701
46720
CTATATCACATTATATGAAC
 92
2875





1315071
N/A
N/A
111916
111935
CAGAACATTTTTAATCATGC
 65
2876





1315102
N/A
N/A
104488
104507
GCAAGCACACATCAAGCTAA
115
2877





1315163
N/A
N/A
40921
40940
CCATTATTCAAAACTATGCT
 94
2878





1315206
N/A
N/A
45654
45673
TGCTTAAAATTTATTCTGCA
 73
2879





1315219
N/A
N/A
130024
130043
TGCACATTCAATCAGCACCT
 63
2880





1315236
N/A
N/A
137043
137062
GCATTTGTCCTCCCAGGTGC
102
2881





1315275
N/A
N/A
52806
52825
TCCTCTCTAAATATTTAAGT
 96
2882





1315317
N/A
N/A
126438
126457
AACTGCTATTTTGAATGCCT
 13
2883





1315365
N/A
N/A
110117
110136
TGTTGTATCACACAATTTCC
 90
2884





1315367
2633
2652
N/A
N/A
ACACAGTTCCTCACAGCTGT
100
2885





1315408
N/A
N/A
130589
130608
GCAGAAGTAAACATTCATTC
 23
2886





1315412
N/A
N/A
69803
69822
TAGACATTTTAAACTTCTGA
 29
2887





1315419
1487
1506
51868
51887
TCCAAGGCTTCTTCTTCTCC
 60
2888





1315421
N/A
N/A
44183
44202
GTTTAATATTTTCAGGTCTA
 37
2889





1315536
N/A
N/A
108320
108339
TGTATATTAATCTTTGGCAA
 25
2890





1315563
N/A
N/A
101094
101113
CACCATTTACCTTATCTGCA
107
2891





1315592
N/A
N/A
96457
96476
ACAAAAATATATAGCATCCA
 86
2892





1315600
N/A
N/A
21986
22005
CACCATTTCACATGCAGCAT
 46
2893





1315606
N/A
N/A
22191
22210
CTTTTTGACATAGTTAGGTT
 69
2894





1315647
N/A
N/A
14985
15004
GCAGTTACACTCATACAGAC
129
2895





1315653
N/A
N/A
19026
19045
AACTGAATTTTTTAACACAT
 82
2896





1315777
N/A
N/A
28750
28769
GGACAAACATTTATTTCAAC
 33
2897





1315792
N/A
N/A
32819
32838
CCAGTTATATTCTTTAAGGT
 88
2898





1315794
N/A
N/A
3516
3535
TCATGTCAATGTATTACTTA
 29
2899





1315887
N/A
N/A
42028
42047
GTCTCAAGCCTACAAGACTC
112
2900





1315903
N/A
N/A
36062
36081
TCACCAACTTCATCTGTCCT
 94
2901





1315908
N/A
N/A
84823
84842
ATCCTTTAAATTTCATGTGC
 50
2902





1315917
N/A
N/A
19731
19750
CTATTGTCATACAATTCACT
 76
2903





1315958
N/A
N/A
160912
160931
CGCACCATTTCTACCTGGAT
104
2904





1315967
N/A
N/A
17482
17501
ACATCCAATCACTATTTTAA
 84
2905





1316162
N/A
N/A
127448
127467
ACAGTCACAGAATTTACCTA
 30
2906





1316283
N/A
N/A
120223
120242
CACACACAACTTACTTGCAA
 65
2907





1316302
N/A
N/A
118229
118248
CCAACACATTCTTTCTCTTA
 71
2908





1316432
N/A
N/A
17886
17905
CAGTGTTTTTCTTAACGATA
100
2909





1316434
N/A
N/A
66632
66651
TTGTCTCCAATCTCAGGGTC
 70
2910





1316437
N/A
N/A
134780
134799
TCAAACACTGCAACAGGCAA
 90
2911





1316472
N/A
N/A
139710
139729
TATAAAGTATTTCATCCTGC
101
2912





1316504
N/A
N/A
34632
34651
TCATTCCAAAACCCCATGAC
105
2913





1316575
N/A
N/A
10480
10499
AAGCATTTCCATTACAAGTA
 41
2914





1316635
N/A
N/A
68733
68752
CCACTTCTCATCTCCCACGG
 59
2915





1316648
N/A
N/A
117871
117890
TTTTCCTTTTATATTCATCA
 48
2916





1316745
N/A
N/A
9984
10003
ACTATATTATATTCCCACCA
 33
2917





1316775
N/A
N/A
49694
49713
ACAACACATTCCCTAAGGCA
 30
2918





1316779
N/A
N/A
25218
25237
GCAATTCTCATTTTTCTTTT
 38
2919





1316792
N/A
N/A
72711
72730
ACTCTTTATTACTATGGAAA
 63
2920





1316807
N/A
N/A
2190
2209
GATAATTTCATTAATCACCA
 51
2921





1316844
N/A
N/A
81053
81072
TCCTAAGCATCTACACCACT
 88
2922





1316866
N/A
N/A
54638
54657
CAAGCTCTCCATTAATGATC
 63
2923





1316908
N/A
N/A
150725
150744
TGGTTGAGTTCTTAACATAA
 27
2924





1316932
N/A
N/A
79800
79819
GCCTCAACTATCTCCAATAC
103
2925





1316967
N/A
N/A
142716
142735
CTATTCTTATCCTCACCACA
 82
2926





1317007
N/A
N/A
73356
73375
GGGACAAGCCATCACTGGCA
117
2927





1317025
N/A
N/A
71392
71411
GTTTATTGAATTATATCTCC
 87
2928





1317031
N/A
N/A
82782
82801
CTGAGGCTTTTCAACAGGTC
 20
2929





1317033
N/A
N/A
99492
99511
TTATTCTTTTACAAAGTATT
 95
2930





1317034
N/A
N/A
63187
63206
GTAACTCAACTTCCAGGAAT
 89
2931





1317050
N/A
N/A
13000
13019
AAGCAGTTCATTTCCCCCAT
 29
2932





1317080
N/A
N/A
5973
5992
ATCTCACTCACATAAATGCC
 92
2933





1317159
6194
6213
133255
133274
GCCAGAAGCATTTCTACCCG
 85
2934





1317192
N/A
N/A
7636
7655
AACACAGACACTCATACATA
 77
2935





1317194
1259
1278
47572
47591
GCTCCGGTCACAACATTGTG
 64
2936





1317207
N/A
N/A
146723
146742
TAGGTTTGTATTATTATCAT
 58
2937
















TABLE 40







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 34
 858





1314561
N/A
N/A
36060
36079
ACCAACTTCATCTGTCCTCC
 77
2938





1314575
N/A
N/A
56087
56106
TGTCATTTATTTCAAGGCAC
 67
2939





1314610
N/A
N/A
68731
68750
ACTTCTCATCTCCCACGGCA
 61
2940





1314638
N/A
N/A
79798
79817
CTCAACTATCTCCAATACAC
 85
2941





1314675
N/A
N/A
22178
22197
TTAGGTTGAAATCTACCATC
 94
2942





1314718
N/A
N/A
44174
44193
TTTCAGGTCTAACAATGGCA
 55
2943





1314762
2234
2253
N/A
N/A
AGCACATTTTTTCCCCCTGT
  8
2944





1314781
N/A
N/A
130023
130042
GCACATTCAATCAGCACCTT
 48
2945





1314847
N/A
N/A
71296
71315
CACCATGGTACAACTTCCTA
 87
2946





1314860
N/A
N/A
134771
134790
GCAACAGGCAATACACAGTA
 49
2947





1314871
N/A
N/A
136978
136997
CAGGAGGTTTCTCCCGTCCT
 84
2948





1314875
N/A
N/A
19025
19044
ACTGAATTTTTTAACACATT
 84
2949





1314885
N/A
N/A
45084
45103
CATCATTTATTTACTTTGGA
 68
2950





1314890
N/A
N/A
75524
75543
AAGTTGATTTTATTGCTTCA
 72
2951





1315033
N/A
N/A
9955
9974
GACCTAGTTTTTCTAAATCC
 60
2952





1315061
N/A
N/A
45653
45672
GCTTAAAATTTATTCTGCAC
 84
2953





1315067
N/A
N/A
22784
22803
AATGCTTTTAATTTAGAGAC
 83
2954





1315164
N/A
N/A
40891
40910
ACTTGATTCCAATCATTGTT
 88
2955





1315191
N/A
N/A
99480
99499
AAAGTATTTCCTGCTTGCTC
 49
2956





1315196
N/A
N/A
12774
12793
ACGATGTTGCCCAATTGCTC
 41
2957





1315203
N/A
N/A
146719
146738
TTTGTATTATTATCATGCTT
 86
2958





1315233
N/A
N/A
106067
106086
CTCAGTGACACATACGCTCA
 99
2959





106123
106142








106179
106198








1315300
N/A
N/A
73248
73267
ACTCAGTACCAGTACCTGCA
 96
2960





1315329
N/A
N/A
130583
130602
GTAAACATTCATTCTAGATT
 61
2961





1315338
N/A
N/A
7632
7651
CAGACACTCATACATATTGC
 59
2962





1315369
N/A
N/A
52805
52824
CCTCTCTAAATATTTAAGTC
 94
2963





1315373
4328
4347
101035
101054
GTAGACACTTTCTGGAGGAC
 38
2964





1315422
N/A
N/A
46699
46718
ATATCACATTATATGAACAT
 90
2965





1315427
N/A
N/A
17478
17497
CCAATCACTATTTTAATGTC
 67
2966





1315463
N/A
N/A
117867
117886
CCTTTTATATTCATCAGAAC
 81
2967





1315475
N/A
N/A
111915
111934
AGAACATTTTTAATCATGCA
 89
2968





1315483
1486
1505
51867
51886
CCAAGGCTTCTTCTTCTCCT
 46
2969





1315484
N/A
N/A
127445
127464
GTCACAGAATTTACCTACAT
 42
2970





1315488
N/A
N/A
34613
34632
CTAGTTTGAATATCTCCTTA
 65
2971





1315526
N/A
N/A
42018
42037
TACAAGACTCACCATAGTCA
 75
2972





1315554
N/A
N/A
25180
25199
CTTCAGATACTTCAATCCTA
 72
2973





1315598
N/A
N/A
19727
19746
TGTCATACAATTCACTTCTA
 63
2974





1315612
N/A
N/A
106960
106979
AGTTCCAACATACATTCCTC
 84
2975





1315712
N/A
N/A
108305
108324
GGCAAACTTCAAACACAGCC
 64
2976





1315749
N/A
N/A
49605
49624
TCATGTCTTTACAACTGCAT
 30
2977





1315758
N/A
N/A
104460
104479
CGTGATCTACTCTAACCCCA
 92
2978





1315791
N/A
N/A
33929
33948
CCATCTCCCAATTCAACTCT
 81
2979





1315793
N/A
N/A
120198
120217
GGGCAGATTAAATAAGGTCA
 73
2980





1315860
N/A
N/A
116347
116366
CCATCTTAACCATTTTTGGC
 72
2981





1315905
N/A
N/A
96357
96376
GAGGAGTATCAATCAACCAA
 75
2982





1315939
N/A
N/A
150478
150497
GCCAGTCTTCTCTCATTCTA
 76
2983





1316006
N/A
N/A
114843
114862
TCCTTCGACAACACAGGGCA
 91
2984





1316086
N/A
N/A
82772
82791
TCAACAGGTCAATCTTCCTC
 58
2985





1316108
1256
1275
47569
47588
CCGGTCACAACATTGTGGTC
 87
2986





1316127
N/A
N/A
66581
66600
TGCTGTACTTTCTTTTTTTC
 54
2987





1316174
N/A
N/A
17875
17894
TTAACGATATTTATAACTGC
101
2988





1316247
6190
6209
133251
133270
GAAGCATTTCTACCCGGCGA
 71
2989





1316301
N/A
N/A
21885
21904
TTTCACAGTTTTAGAGGCCA
 54
2990





1316385
N/A
N/A
69792
69811
AACTTCTGATACATTACCAA
 46
2991





1316408
N/A
N/A
2170
2189
CGTAAGTTCACCACTTTACT
 87
2992





1316419
N/A
N/A
14982
15001
GTTACACTCATACAGACAGA
 93
2993





1316438
N/A
N/A
133762
133781
AGTAAACCCACCTATAAGGC
 86
2994





1316471
N/A
N/A
5972
5991
TCTCACTCACATAAATGCCA
 85
2995





1316477
N/A
N/A
81050
81069
TAAGCATCTACACCACTTCC
 79
2996





1316537
1722
1741
53737
53756
CAAGATATCCTCCTCATCCC
 73
2997





1316544
N/A
N/A
3513
3532
TGTCAATGTATTACTTATGC
 18
2998





1316668
N/A
N/A
16461
16480
CCATTTATATAACCTCATTA
 75
2999





1316673
2617
2636
59189
59208
CTGTACAAGCTAACTTGCAA
 78
3000





1316674
N/A
N/A
72620
72639
CCAATGGTATCCTTTAACAC
 86
3001





1316849
N/A
N/A
60528
60547
AAGAATACTTTATCTCAGTA
 74
3002





1316850
N/A
N/A
142693
142712
GCACAGGATCCACAGCCTGA
 97
3003





1316892
N/A
N/A
139709
139728
ATAAAGTATTTCATCCTGCA
 77
3004





1316894
N/A
N/A
23556
23575
CTGTTTTTCCTATCAGCTTT
 101
3005





1316945
N/A
N/A
63067
63086
CCATAACTAAAATTACTGTT
 71
3006





1317047
N/A
N/A
126404
126423
TGTTTGTCCCAATAATATGC
 61
3007





1317048
N/A
N/A
28748
28767
ACAAACATTTATTTCAACAT
110
3008





1317075
N/A
N/A
110116
110135
GTTGTATCACACAATTTCCA
 60
3009





1317092
N/A
N/A
160873
160892
CCAAACGCAACTCCTGGACC
 82
3010





1317116
N/A
N/A
84821
84840
CCTTTAAATTTCATGTGCTT
 69
3011





1317156
N/A
N/A
32818
32837
CAGTTATATTCTTTAAGGTC
 72
3012





1317186
N/A
N/A
118226
118245
ACACATTCTTTCTCTTACTC
 64
3013





1317223
N/A
N/A
10454
10473
TGTGTTGTCCTTTTATAACC
 46
3014
















TABLE 41







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 42
 858





1314543
2592
2611
59164
59183
AGAAGACTCATCCTTCAGTG
 58
3015





1314558
N/A
N/A
16051
16070
CCAACATTCCATGAATTCCA
 59
3016





1314563
N/A
N/A
142638
142657
TGGGTGTTTTCATATTCCTT
 86
3017





1314602
N/A
N/A
126360
126379
GCAGCAGAAATTTCACAAGC
 47
3018





1314645
N/A
N/A
57687
57706
TCACCATTTTTTCCCCCTGT
 63
3019





1314705
N/A
N/A
19024
19043
CTGAATTTTTTAACACATTG
 74
3020





1314727
N/A
N/A
19726
19745
GTCATACAATTCACTTCTAC
 45
3021





1314788
N/A
N/A
127444
127463
TCACAGAATTTACCTACATT
 78
3022





1314827
N/A
N/A
108304
108323
GCAAACTTCAAACACAGCCT
 45
3023





1314861
N/A
N/A
106959
106978
GTTCCAACATACATTCCTCT
104
3024





1314891
N/A
N/A
130010
130029
GCACCTTTATTTCAGAACTC
 40
3025





1314892
N/A
N/A
41867
41886
CAGTGCAGTTCACATTCAAT
 66
3026





1314913
N/A
N/A
72618
72637
AATGGTATCCTTTAACACGC
 71
3027





1314920
N/A
N/A
5957
5976
TGCCAATATCTTTATTCCAT
 41
3028





1314967
N/A
N/A
62837
62856
GCATTACTTTTTACAATGGA
  8
3029





1314984
N/A
N/A
9954
9973
ACCTAGTTTTTCTAAATCCT
 51
3030





1315022
N/A
N/A
17873
17892
AACGATATTTATAACTGCTC
 93
3031





1315158
N/A
N/A
133761
133780
GTAAACCCACCTATAAGGCA
 94
3032





1315172
N/A
N/A
17477
17496
CAATCACTATTTTAATGTCA
 81
3033





1315184
N/A
N/A
118224
118243
ACATTCTTTCTCTTACTCTA
 85
3034





1315218
N/A
N/A
106065
106084
CAGTGACACATACGCTCACA
103
3035





106121
106140








106177
106196








1315231
N/A
N/A
111858
111877
AGTGTGTTCAACCATTACTT
 88
3036





1315240
N/A
N/A
101020
101039
AGGACATCAAACCATCTGCC
 87
3037





1315252
N/A
N/A
22177
22196
TAGGTTGAAATCTACCATCA
101
3038





1315268
N/A
N/A
104340
104359
CAGCAGCTACGATCTTCCTA
 81
3039





1315331
N/A
N/A
20135
20154
CACCACATTCCCTCTGGAGT
 95
3040





1315340
N/A
N/A
3512
3531
GTCAATGTATTACTTATGCA
 13
3041





1315362
1557
1576
53572
53591
ACTGATCTCATCCTTCACTG
 49
3042





1315366
N/A
N/A
56037
56056
TTACTGATCACTCATTCCCA
 70
3043





1315375
N/A
N/A
51836
51855
GCCTAGTAAATAATGTACCA
 94
3044





1315458
N/A
N/A
117849
117868
ACCGAAGACATTTTCATTCT
113
3045





1315459
N/A
N/A
84110
84129
AGACACATACTTCATATCTA
 92
3046





1315532
N/A
N/A
46697
46716
ATCACATTATATGAACATAA
 84
3047





1315579
N/A
N/A
32764
32783
GCTTCAGAAATATAACACAT
 78
3048





1315626
N/A
N/A
75478
75497
TGGCAGAACATTCTACAACC
 47
3049





1315633
N/A
N/A
110115
110134
TTGTATCACACAATTTCCAT
 78
3050





1315676
N/A
N/A
68707
68726
TTTGCATTCCCTTCATGGCA
 69
3051





1315786
N/A
N/A
40890
40909
CTTGATTCCAATCATTGTTC
 86
3052





1315844
N/A
N/A
7631
7650
AGACACTCATACATATTGCT
 83
3053





1315854
N/A
N/A
114786
114805
GTCACAGCCACTTAGCAGAA
 95
3054





1315859
N/A
N/A
116260
116279
GGCATGAACACATCTCACTA
 71
3055





1315884
N/A
N/A
45617
45636
CTTGGATCACAAATTTCCTT
 99
3056





1315900
N/A
N/A
96356
96375
AGGAGTATCAATCAACCAAT
 87
3057





1316022
N/A
N/A
130507
130526
CAAGTGTCATCTACACAGGA
 81
3058





1316040
N/A
N/A
79794
79813
ACTATCTCCAATACACAACA
 84
3059





1316062
N/A
N/A
65968
65987
GGGTAACATTTTCCTACAAA
 17
3060





1316085
3350
3369
73156
73175
AGGGTCAGAATCATTGTGGC
 53
3061





1316131
N/A
N/A
14860
14879
GGCTGTACAACATTACGAAT
 63
3062





1316167
N/A
N/A
12677
12696
GCCTCACTTCCCCCATTATA
 95
3063





1316168
N/A
N/A
45038
45057
AAGTCTCACATCCATACCCT
103
3064





1316178
N/A
N/A
71283
71302
CTTCCTACTTTAGACACCTC
 76
3065





1316189
N/A
N/A
34599
34618
TCCTTAGTATTAACAAGAAA
111
3066





1316211
N/A
N/A
132766
132785
GATGAGAGATTCATTTTCAA
102
3067





1316213
N/A
N/A
36019
36038
TCCAGTTTCAACCCAGAGCA
103
3068





1316291
N/A
N/A
60517
60536
ATCTCAGTAAATACAAGCTT
105
3069





1316332
N/A
N/A
49604
49623
CATGTCTTTACAACTGCATT
 60
3070





1316349
N/A
N/A
28160
28179
CAGGAAGCCTTTCCTGCCTC
 96
3071





1316382
N/A
N/A
22783
22802
ATGCTTTTAATTTAGAGACT
 92
3072





1316410
N/A
N/A
23474
23493
GTTTTCTATTTTACTGACTT
 65
3073





1316454
N/A
N/A
25176
25195
AGATACTTCAATCCTAGACA
 63
3074





1316470
N/A
N/A
139683
139702
AGGCACATAATATAATCAGC
 75
3075





1316475
N/A
N/A
52804
52823
CTCTCTAAATATTTAAGTCT
100
3076





1316486
N/A
N/A
33924
33943
TCCCAATTCAACTCTTCACC
 88
3077





1316495
N/A
N/A
44172
44191
TCAGGTCTAACAATGGCACT
103
3078





1316529
N/A
N/A
81049
81068
AAGCATCTACACCACTTCCC
 88
3079





1316641
N/A
N/A
99445
99464
AACGACAGCATTCTTGCCAC
 88
3080





1316643
N/A
N/A
134700
134719
TCAAATGCACAAATTCCACT
 96
3081





1316722
N/A
N/A
10448
10467
GTCCTTTTATAACCACATTC
 44
3082





1316740
N/A
N/A
120197
120216
GGCAGATTAAATAAGGTCAA
 86
3083





1316786
N/A
N/A
160857
160876
GACCACCTCAACTCTCCTTC
 80
3084





1316895
N/A
N/A
136929
136948
CCATGGCTGCACCATACCCA
 94
3085





1316907
N/A
N/A
146718
146737
TTGTATTATTATCATGCTTA
 51
3086





1316948
7827
7846
150346
150365
TCTCTTTGAAACCATTGCTT
 68
3087





1317011
N/A
N/A
2164
2183
TTCACCACTTTACTTGGCAA
 63
3088





1317073
N/A
N/A
47525
47544
CAGTTCATAAACCTAGAAAC
101
3089





1317102
N/A
N/A
69788
69807
TCTGATACATTACCAATGCA
 48
3090





1317134
N/A
N/A
82771
82790
CAACAGGTCAATCTTCCTCC
 72
3091
















TABLE 42







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop
Sequence
(%
ID


Number
Site
Site
Site
Site
(5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 44
 858





1314481
N/A
N/A
46683
46702
ACATAATGAATTTATTCTTT
 85
3092





1314515
N/A
N/A
79789
79808
CTCCAATACACAACACATGA
 94
3093





1314634
N/A
N/A
23197
23216
GCCAGTCTCAAACAATCCAC
 78
3094





1314647
N/A
N/A
110110
110129
TCACACAATTTCCATTGCGG
 47
3095





1314708
N/A
N/A
142633
142652
GTTTTCATATTCCTTAGGTA
 16
3096





1314714
N/A
N/A
136758
136777
GTAGAGGAAATCTCGCTGCA
 64
3097





1314760
N/A
N/A
52755
52774
TAGATAGGATTATACAACCA
 63
3098





1314799
N/A
N/A
14805
14824
ACAGTCAATTTTATGTGCAT
 61
3099





1314839
N/A
N/A
17476
17495
AATCACTATTTTAATGTCAC
 69
3100





1314853
N/A
N/A
34542
34561
ACAGTTTATTCCAAATCATT
 65
3101





1314857
N/A
N/A
117847
117866
CGAAGACATTTTCATTCTGT
 83
3102





1314864
N/A
N/A
19010
19029
ACATTGTTAATATATTTTCC
 52
3103





1314907
N/A
N/A
62836
62855
CATTACTTTTTACAATGGAC
 17
3104





1314918
2233
2252
N/A
N/A
GCACATTTTTTCCCCCTGTT
  8
3105





1314926
N/A
N/A
22176
22195
AGGTTGAAATCTACCATCAA
 77
3106





1314977
N/A
N/A
32695
32714
TTAGTGATTATACCTCTGCA
 67
3107





1314996
N/A
N/A
15972
15991
GAGATCTTATTTCCTGGGTC
 43
3108





1315093
N/A
N/A
45031
45050
ACATCCATACCCTTTTTTCC
 98
3109





1315146
N/A
N/A
27915
27934
ACCTAGTTTTCACCATACAC
 70
3110





1315156
N/A
N/A
116253
116272
ACACATCTCACTAGAGACTT
 50
3111





1315162
N/A
N/A
106957
106976
TCCAACATACATTCCTCTTA
 69
3112





1315242
N/A
N/A
146707
146726
TCATGCTTAAATCTTTTCTG
 79
3113





1315290
N/A
N/A
105978
105997
CAGAGGCACACTCTGACCCC
 97
3114





106033
106052








106087
106106








106143
106162








1315308
N/A
N/A
20134
20153
ACCACATTCCCTCTGGAGTA
 81
3115





1315389
N/A
N/A
7629
7648
ACACTCATACATATTGCTTA
 62
3116





1315410
N/A
N/A
133729
133748
GTCCTGTGAATTTATTCCCG
 60
3117





1315467
N/A
N/A
56033
56052
TGATCACTCATTCCCACTAC
 86
3118





1315514
N/A
N/A
99153
99172
ACAACACTTTTAAGAATCTC
 99
3119





1315521
N/A
N/A
111717
111736
CCACATCTTACAACAAGGGA
 60
3120





1315551
N/A
N/A
130464
130483
TCAACCCCGTTTACAGGCAT
 73
3121





1315564
3349
3368
73155
73174
GGGTCAGAATCATTGTGGCC
 92
3122





1315568
N/A
N/A
75477
75496
GGCAGAACATTCTACAACCA
 51
3123





1315678
N/A
N/A
65967
65986
GGTAACATTTTCCTACAAAA
 22
3124





1315682
N/A
N/A
139682
139701
GGCACATAATATAATCAGCA
 69
3125





1315684
N/A
N/A
108287
108306
CCTTGACTAAACTATTCTGC
 83
3126





1315709
N/A
N/A
17872
17891
ACGATATTTATAACTGCTCT
 56
3127





1315795
N/A
N/A
10442
10461
TTATAACCACATTCACCTCC
 70
3128





1315799
N/A
N/A
114688
114707
GCAAGCACTTACGAGTGCCT
 89
3129





1315812
N/A
N/A
49039
49058
TCGCAGTTCAACATTTTAAT
 33
3130





1315850
N/A
N/A
100969
100988
AATATCTTTAAATAATCTCC
 90
3131





1315865
N/A
N/A
126359
126378
CAGCAGAAATTTCACAAGCC
 52
3132





1315879
N/A
N/A
19673
19692
GCGAACAATTTAATTAATCT
 33
3133





1315912
N/A
N/A
25119
25138
AACCTACAATATTCTTGGAA
 82
3134





1315981
N/A
N/A
82403
82422
TCAAGGATACAAAATTTCAT
 68
3135





1316015
N/A
N/A
134696
134715
ATGCACAAATTCCACTATCA
 63
3136





1316039
N/A
N/A
95286
95305
GCCTAAAATTTTCCAAACTT
 79
3137





1316051
N/A
N/A
5955
5974
CCAATATCTTTATTCCATCT
 42
3138





1316070
N/A
N/A
160850
160869
TCAACTCTCCTTCCCTGAGT
100
3139





1316147
N/A
N/A
150214
150233
ACCAGAACTTTCCCTCCGCT
 88
3140





1316210
N/A
N/A
41865
41884
GTGCAGTTCACATTCAATCA
 55
3141





1316235
N/A
N/A
68706
68725
TTGCATTCCCTTCATGGCAC
 47
3142





1316275
N/A
N/A
118171
118190
GACTGTTGAATACAATCACC
 79
3143





1316407
N/A
N/A
127443
127462
CACAGAATTTACCTACATTT
 62
3144





1316411
N/A
N/A
69445
69464
CTGGCTTATTTTAATTGTTG
 87
3145





1316441
N/A
N/A
53405
53424
CAGTGCATCCTTCAAGCATC
 74
3146





1316446
N/A
N/A
132618
132637
GAAACTCGATTTACCAAGGC
 56
3147





1316501
N/A
N/A
72616
72635
TGGTATCCTTTAACACGCCA
 74
3148





1316712
N/A
N/A
33845
33864
GATGGTAGTCTAAATTACGA
 61
3149





1316730
N/A
N/A
3511
3530
TCAATGTATTACTTATGCAA
 50
3150





1316762
N/A
N/A
12593
12612
CCAGCATTTAAACCCAGGTC
 31
3151





1316790
N/A
N/A
59112
59131
GAAAATGTATTTCCTAACCA
 83
3152





1316798
N/A
N/A
22749
22768
GCATCTGCTCTATCTTGGCA
 73
3153





1316821
N/A
N/A
84108
84127
ACACATACTTCATATCTAAC
 93
3154





1316822
N/A
N/A
60516
60535
TCTCAGTAAATACAAGCTTA
 72
3155





1316902
N/A
N/A
43973
43992
CTGATTTTTTTCTTTAAGAC
 78
3156





1316974
N/A
N/A
119915
119934
TGGACAACACTTCAACAGTA
 74
3157





1316981
N/A
N/A
45615
45634
TGGATCACAAATTTCCTTTA
 71
3158





1316985
N/A
N/A
2149
2168
GGCAACCACAACTCATTCAA
 39
3159





1317004
N/A
N/A
51827
51846
ATAATGTACCAACATTCCTT
 73
3160





1317012
N/A
N/A
47485
47504
GTCAGAGTTTATAAAATGCA
 67
3161





1317022
N/A
N/A
40889
40908
TTGATTCCAATCATTGTTCA
 68
3162





1317064
N/A
N/A
104336
104355
AGCTACGATCTTCCTAGCTC
 80
3163





1317095
N/A
N/A
130006
130025
CTTTATTTCAGAACTCACAC
 83
3164





1317155
N/A
N/A
9953
9972
CCTAGTTTTTCTAAATCCTC
 65
3165





1317196
N/A
N/A
81048
81067
AGCATCTACACCACTTCCCT
 81
3166





1317229
N/A
N/A
71084
71103
ATCCTGTTTTTCCATCCCAA
 47
3167





1317232
N/A
N/A
35996
36015
AACACAGCTTTCTCATCAAA
 85
3168
















TABLE 43







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop
Sequence
(%
ID


Number
Site
Site
Site
Site
(5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 25
 858





1314489
N/A
N/A
22601
22620
TGTTCTACAAATCATTGAGA
 74
3169





1314538
N/A
N/A
119789
119808
AGAACACACCACCCTTATCC
 90
3170





1314591
N/A
N/A
3163
3182
AAGGTAATCATATATTACCT
 99
3171





1314600
N/A
N/A
23196
23215
CCAGTCTCAAACAATCCACC
 89
3172





1314652
N/A
N/A
52754
52773
AGATAGGATTATACAACCAA
 50
3173





1314720
N/A
N/A
118167
118186
GTTGAATACAATCACCACAT
 52
3174





1314732
N/A
N/A
46679
46698
AATGAATTTATTCTTTTTCC
 87
3175





1314766
N/A
N/A
160838
160857
CCCTGAGTCCTCCATGCCCA
 67
3176





1314816
N/A
N/A
45613
45632
GATCACAAATTTCCTTTATA
 74
3177





1314836
N/A
N/A
17860
17879
ACTGCTCTTTACACAGGCTA
 77
3178





1314889
N/A
N/A
47484
47503
TCAGAGTTTATAAAATGCAT
 95
3179





1314921
N/A
N/A
106956
106975
CCAACATACATTCCTCTTAC
 91
3180





1314928
N/A
N/A
56032
56051
GATCACTCATTCCCACTACA
 37
3181





1314932
N/A
N/A
79767
79786
GCATATAGAACATCGAGACT
 74
3182





1314942
N/A
N/A
5948
5967
CTTTATTCCATCTACAAGGC
 44
3183





1314957
N/A
N/A
75476
75495
GCAGAACATTCTACAACCAT
 39
3184





1314973
N/A
N/A
15971
15990
AGATCTTATTTCCTGGGTCA
 56
3185





1314985
N/A
N/A
32693
32712
AGTGATTATACCTCTGCAGC
 63
3186





1314988
N/A
N/A
17461
17480
GTCACATACATTAAGTCTCA
 43
3187





1315031
N/A
N/A
83974
83993
GCTGACATAAACTTTCCCTA
 58
3188





1315060
N/A
N/A
108286
108305
CTTGACTAAACTATTCTGCA
 80
3189





1315077
N/A
N/A
82236
82255
GGTTAATTAGCCATTCCACA
 28
3190





1315117
N/A
N/A
117846
117865
GAAGACATTTTCATTCTGTT
 63
3191





1315140
N/A
N/A
60469
60488
TGGTTCTTTCTTCCTTCCAT
 58
3192





1315147
N/A
N/A
129960
129979
GCTTTTGAAATTCTCCATCT
 23
3193





1315181
N/A
N/A
114647
114666
TCCAAACAATTTATGAGGGA
 39
3194





1315226
N/A
N/A
19671
19690
GAACAATTTAATTAATCTCT
 59
3195





1315235
N/A
N/A
139638
139657
ACGCTGACTTTCCCACTTCC
 63
3196





1315279
N/A
N/A
20055
20074
GCTTATAGCTTCATCACTCC
 66
3197





1315341
N/A
N/A
68690
68709
GCACATGTCAATTTCTATCC
 14
3198





1315378
N/A
N/A
2148
2167
GCAACCACAACTCATTCAAA
 68
3199





1315388
N/A
N/A
81047
81066
GCATCTACACCACTTCCCTT
 65
3200





1315396
3348
3367
73154
73173
GGTCAGAATCATTGTGGCCA
 71
3201





1315450
N/A
N/A
72563
72582
GCAACCTCAAATAAGCAGGA
 44
3202





1315490
N/A
N/A
116182
116201
ACCACATGCACACCACTATC
101
3203





1315491
N/A
N/A
130455
130474
TTTACAGGCATTTCAAACTT
 90
3204





1315502
N/A
N/A
41863
41882
GCAGTTCACATTCAATCAAC
 52
3205





1315548
N/A
N/A
45025
45044
ATACCCTTTTTTCCCCTTCA
 80
3206





1315595
N/A
N/A
9952
9971
CTAGTTTTTCTAAATCCTCA
 53
3207





1315610
N/A
N/A
51816
51835
ACATTCCTTTTAGTTTGCTA
 97
3208





1315662
N/A
N/A
49035
49054
AGTTCAACATTTTAATTTCA
 53
3209





1315677
N/A
N/A
133727
133746
CCTGTGAATTTATTCCCGTA
 66
3210





1315680
N/A
N/A
104335
104354
GCTACGATCTTCCTAGCTCT
 88
3211





1315695
N/A
N/A
105919
105938
CACTCTGACCCCTCAGTGAC
 96
3212





105970
105989








106025
106044








1315722
N/A
N/A
35939
35958
CCATGACTATTTACTTAGGC
 30
3213





1315773
N/A
N/A
25118
25137
ACCTACAATATTCTTGGAAC
 77
3214





1315784
N/A
N/A
142507
142526
TGGGTCATTCTCTAATTACA
 37
3215





1315785
N/A
N/A
70585
70604
AGCAAATTAACATTACTTTT
 56
3216





1315823
N/A
N/A
40806
40825
AGTAAACTAGTAACTGGCAT
 43
3217





1315888
N/A
N/A
65920
65939
ACTCAGTAATACTTTTAGAA
 78
3218





1315893
N/A
N/A
53390
53409
GCATCTCTCACACTGCCTCC
 42
3219





1315938
N/A
N/A
127442
127461
ACAGAATTTACCTACATTTA
 70
3220





1315974
N/A
N/A
69408
69427
TGAATTTTTTTATTTTGGGC
 29
3221





1316014
N/A
N/A
12571
12590
CTGGCTTTAAATCTCCTCTG
 54
3222





1316029
N/A
N/A
22173
22192
TTGAAATCTACCATCAAGCT
 81
3223





1316049
N/A
N/A
14077
14096
TCTGACTGACTATAAAGGCT
 66
3224





1316050
N/A
N/A
111602
111621
TGCTCTGTCATCCATGCAGC
 98
3225





1316082
N/A
N/A
62709
62728
CTGCTCTACATCCTTTGAAT
 65
3226





1316161
N/A
N/A
27667
27686
CCAAACTTAAGCATAAGGGA
 77
3227





1316259
N/A
N/A
59086
59105
CAAGCAACAAACATCATCAT
106
3228





1316279
N/A
N/A
126357
126376
GCAGAAATTTCACAAGCCCT
 39
3229





1316293
N/A
N/A
19009
19028
CATTGTTAATATATTTTCCA
 67
3230





1316313
N/A
N/A
150170
150189
ACCAAATGAAACTCACTTCC
 87
3231





1316490
4017
4036
98625
98644
TCCTAGGATCTCTTCAACAC
 72
3232





1316503
N/A
N/A
110109
110128
CACACAATTTCCATTGCGGC
 47
3233





1316569
N/A
N/A
34541
34560
CAGTTTATTCCAAATCATTC
 69
3234





1316574
N/A
N/A
57535
57554
TCAACAATACATTCATGCAT
 88
3235





1316656
N/A
N/A
33842
33861
GGTAGTCTAAATTACGACAT
 58
3236





1316782
N/A
N/A
10440
10459
ATAACCACATTCACCTCCCT
 76
3237





1316801
N/A
N/A
132598
132617
CGTCACCTCCAACCACGCAC
 93
3238





1316805
N/A
N/A
100968
100987
ATATCTTTAAATAATCTCCT
 91
3239





1316812
N/A
N/A
94658
94677
CCGTCGCCACATCAAGCTCA
 68
3240





1316951
N/A
N/A
134695
134714
TGCACAAATTCCACTATCAA
 83
3241





1316960
N/A
N/A
7528
7547
CTGACCATTTACACAAAGTT
 60
3242





1317097
N/A
N/A
43595
43614
AATGTATTATTACCATGGCT
 54
3243





1317132
N/A
N/A
136720
136739
GACTAAAGATCAACTTCCAA
 90
3244





1317160
7482
7501
146574
146593
GATGAACTCCTTAAAGACTT
 75
3245
















TABLE 44







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 31
 858





1314569
N/A
N/A
23113
23132
ACTCTGGATTCCATTTGCTT
 68
3246





1314579
N/A
N/A
100949
100968
TCTGCACTCAGATATACTCC
 97
3247





1314682
N/A
N/A
20048
20067
GCTTCATCACTCCAATTTTC
 66
3248





1314700
N/A
N/A
52753
52772
GATAGGATTATACAACCAAA
 39
3249





1314759
N/A
N/A
47448
47467
TTGTTGTTTTTAATAGGACT
 64
3250





1314845
N/A
N/A
108248
108267
TGGACATTCACTTCAATTCT
 21
3251





1314912
N/A
N/A
106955
106974
CAACATACATTCCTCTTACC
100
3252





1314916
N/A
N/A
70545
70564
AACAAAAGTTATACTTGCTC
 25
3253





1315120
N/A
N/A
34540
34559
AGTTTATTCCAAATCATTCA
 70
3254





1315128
N/A
N/A
5894
5913
CTCTTGGACCTTACTTCTTA
 72
3255





1315197
N/A
N/A
59085
59104
AAGCAACAAACATCATCATC
 76
3256





1315230
N/A
N/A
12555
12574
TCTGTATTTCACCAATACTC
 84
3257





1315243
N/A
N/A
110108
110127
ACACAATTTCCATTGCGGCA
 47
3258





1315274
N/A
N/A
68688
68707
ACATGTCAATTTCTATCCCC
 50
3259





1315333
N/A
N/A
19670
19689
AACAATTTAATTAATCTCTT
 91
3260





1315425
N/A
N/A
53331
53350
GGTGATATTCTCAAATGCTG
 20
3261





1315478
N/A
N/A
133725
133744
TGTGAATTTATTCCCGTACA
 58
3262





1315498
3321
3340
73127
73146
GGTACAGCTCTTCCTAGACT
 28
3263





1315520
N/A
N/A
105929
105948
CACACAGGCACACTCTGACC
 99
3264





106232
106251








1315596
N/A
N/A
130451
130470
CAGGCATTTCAAACTTACGA
 57
3265





1315603
N/A
N/A
9949
9968
GTTTTTCTAAATCCTCACCA
 87
3266





1315665
N/A
N/A
60440
60459
TGTCATGGTTTCAACTCTCA
 47
3267





1315666
N/A
N/A
83970
83989
ACATAAACTTTCCCTAGCTG
 97
3268





1315734
N/A
N/A
104194
104213
TGGGAACACTTTCCTTCTGC
 73
3269





1315897
N/A
N/A
69362
69381
ACATAGTCATTTACATTCCT
 32
3270





1315963
N/A
N/A
62700
62719
ATCCTTTGAATTCTTCCCTC
 46
3271





1315984
N/A
N/A
81881
81900
GTACACATATTTCAAACATC
 36
3272





1316009
N/A
N/A
119664
119683
CTATCATTCATTAACAAGCC
 69
3273





1316072
N/A
N/A
142147
142166
CCAAAGAATCTTCCTCCCAA
 70
3274





1316105
N/A
N/A
125991
126010
TCTTTGCTTTCATCTCGGTC
 91
3275





1316135
7752
7771
149840
149859
GTCGAGAGCTTTCAGAGGCT
 75
3276





1316137
N/A
N/A
10439
10458
TAACCACATTCACCTCCCTC
 85
3277





1316188
N/A
N/A
116179
116198
ACATGCACACCACTATCCCC
 93
3278





1316194
N/A
N/A
51147
51166
TTGGGAATTTCTAATTTCTG
 62
3279





1316232
N/A
N/A
15877
15896
GCCAAGTATTTAAAGTCATT
 30
3280





1316245
N/A
N/A
118156
118175
TCACCACATCATAATTTGTC
 78
3281





1316260
N/A
N/A
14066
14085
ATAAAGGCTTTTTCTAGCTT
 83
3282





1316268
N/A
N/A
22172
22191
TGAAATCTACCATCAAGCTC
 70
3283





1316277
N/A
N/A
56030
56049
TCACTCATTCCCACTACATT
 69
3284





1316284
N/A
N/A
46678
46697
ATGAATTTATTCTTTTTCCC
 77
3285





1316343
N/A
N/A
33829
33848
ACGACATACAACATACCCCA
 83
3286





1316355
7474
7493
146566
146585
CCTTAAAGACTTCCTTTTCC
 81
3287





1316406
N/A
N/A
25082
25101
GCAGTCTATCTCTCCTGCCC
 65
3288





1316412
N/A
N/A
139636
139655
GCTGACTTTCCCACTTCCCC
 50
3289





1316420
N/A
N/A
111482
111501
CCTTCATTTCTGCCAACTTA
 66
3290





1316421
N/A
N/A
7494
7513
GGTGGAAGACAATATTGTTA
 28
3291





1316447
N/A
N/A
98619
98638
GATCTCTTCAACACACTGTA
 65
3292





1316458
N/A
N/A
3162
3181
AGGTAATCATATATTACCTT
 90
3293





1316493
N/A
N/A
17448
17467
AGTCTCACCATATTAGTGTT
 59
3294





1316502
N/A
N/A
19005
19024
GTTAATATATTTTCCAGTCA
 34
3295





1316508
N/A
N/A
35938
35957
CATGACTATTTACTTAGGCA
 33
3296





1316526
N/A
N/A
129865
129884
TCACCACTCTAAACATGTTG
 83
3297





1316642
N/A
N/A
114576
114595
GAGAAGACTTTTATTACTGA
 58
3298





1316667
N/A
N/A
134685
134704
CCACTATCAAATATCCCAGT
 69
3299





1316670
N/A
N/A
49033
49052
TTCAACATTTTAATTTCAAT
 69
3300





1316717
N/A
N/A
94648
94667
ATCAAGCTCACCTCTCCAGC
 75
3301





1316734
N/A
N/A
22599
22618
TTCTACAAATCATTGAGAGC
 90
3302





1316736
N/A
N/A
127413
127432
GTAGTTTGCCCTCAGAGGGC
101
3303





1316763
N/A
N/A
32691
32710
TGATTATACCTCTGCAGCCA
 83
3304





1316777
N/A
N/A
75473
75492
GAACATTCTACAACCATGGA
 63
3305





1316781
N/A
N/A
45602
45621
TCCTTTATAAATCTTGCTGA
 81
3306





1316793
N/A
N/A
41862
41881
CAGTTCACATTCAATCAACC
 67
3307





1316794
N/A
N/A
40143
40162
GCCACAGGACTCCCTCCCAA
 83
3308





1316921
N/A
N/A
17823
17842
TGCTGTCAATACTTTCCCCA
 52
3309





1316930
N/A
N/A
111914
111933
GAACATTTTTAATCATGCAA
 42
3310





1316934
N/A
N/A
57518
57537
CATTAGTTCATTCAACAGAT
 74
3311





1316939
N/A
N/A
81041
81060
ACACCACTTCCCTTACTGAA
 68
3312





1316995
N/A
N/A
132366
132385
CTCCAATTACTCTTTTTCCA
 34
3313





1317029
N/A
N/A
79758
79777
ACATCGAGACTCCCAATGCT
 76
3314





1317039
N/A
N/A
117845
117864
AAGACATTTTCATTCTGTTC
 76
3315





1317077
N/A
N/A
160816
160835
GCAAGAGCCATAGAACAGCC
 71
3316





1317096
N/A
N/A
43583
43602
CCATGGCTACACCCTTTTTA
 74
3317





1317103
N/A
N/A
136631
136650
CTTGACTTCCATTCTGTCTT
 88
3318





1317109
N/A
N/A
65894
65913
AACTATTTTATCATATTGGT
 61
3319





1317165
N/A
N/A
26786
26805
GGAGCTAGAATCCCATGGCT
100
3320





1317170
N/A
N/A
72552
72571
TAAGCAGGACTACCCAGGGC
 59
3321





1317221
N/A
N/A
45023
45042
ACCCTTTTTTCCCCTTCACC
 79
3322
















TABLE 45







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ








ID
ID
SEQ
SEQ






No: 1
No: 1
ID No:
ID No:

HTT
SEQ


Compound
Start
Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 42
 858





1231500
4275
4294
99393
99412
CGCCTGCACCATGTTCCTCA
 89
3323





1231544
6011
6030
132941
132960
CGAGACTGAATTGCCTGGAT
 37
3324





1315753
8661
8680
161607
161626
ATAGTTCTCAATGAGGTAAA
 78
3325





1315817
2795
2814
62219
62238
TCTGCTTTTGCCTCCAAAAA
 10†
3326





1315833
4858
4877
106913
106932
GTAACATTGACACCACCACC
 45
3327





1316023
4609
4628
N/A
N/A
TTGCCTCTGATTCCCTGAAC
 35
3328





1316059
4733
4752
104720
104739
GCCTTCCTTCCACTGGCCAT
 89
3329





1316117
4813
4832
106868
106887
CTGCATCAGCTTTATTTGTT
 45
3330





1316152
4605
4624
N/A
N/A
CTCTGATTCCCTGAACTGGC
 66
3331





1316206
 171
 190
1156
1175
CTTGAGGGACTCGAAGGCCT
 64
3332





1316266
N/A
N/A
1446
1465
GCAGGGTTACCGCCATCCCC
 87
3333





1316341
7724
7743
149812
149831
GGCTGCTGCTCCAAGCAGCT
 94
3334





1316545
5808
5827
130391
130410
TTCTCTATTGCACATTCCAA
 36
3335





1316899
4713
4732
104700
104719
GATGCCATCACAGAGCTGAA
 56
3336





1316926
4384
4403
N/A
N/A
TAGCATTCTTATCTGCACGG
 20
3337





1316928
 127
 146
1112
1131
TGGCGGTCTCCCGCCCGGCA
101
3338





1316972
4826
4845
106881
106900
TCAAGCTCTTTTCCTGCATC
 26
1232





1317019
 107
 126
1092
1111
CGGCAGTCCCCGGAGGCCTC
 92
3339





1317101
N/A
N/A
1437
1456
CCGCCATCCCCGCCGTAGCC
 85
3340





1317179
 389
 408
1368
1387
TGCAGCGGCTCCTCAGCCAC
 91
3341





1318565
4820
4839
106875
106894
TCTTTTCCTGCATCAGCTTT
 57
3342





1318568
 967
 986
41677
41696
GGCAGATGCTCACTGCTGAT
 84
3343





1318569
4810
4829
106865
106884
CATCAGCTTTATTTGTTCCT
 26
3344





1318579
  12
  31
997
1016
CGGCCGTCCATCTTGGACCC
 80
3345





1318584
3554
3573
74416
74435
AGCTGCTCCACCATGGGCAC
 98
3346





1318585
N/A
N/A
115063
115082
TCTGTGTATCACCTTCCTCA
 51
3347





1318588
N/A
N/A
1630
1649
GACAGGCCCCAACAAGGCTC
 94
3348





1318592
2121
2140
N/A
N/A
AGGCTTGTTTTCTTGATCAC
 32
3349





1318595
N/A
N/A
1498
1517
GGGTCACTCTGTCTCTGCGG
 86
3350





1318596
N/A
N/A
1442
1461
GGTTACCGCCATCCCCGCCG
 78
3351





1318600
3213
3232
N/A
N/A
TTCACAGCATCCAAATGTGA
 85
3352





1318601
5230
5249
114044
114063
AGAGCTCCTGAATACGAGAA
 47
3353





1318602
 161
 180
1146
1165
TCGAAGGCCTTCATCAGCTT
 97
3354





1318609
 702
 721
31684
31703
AAACCTCCACAGGGCAGCAC
 66
3355





1318610
3218
3237
71456
71475
AAAGCTTCACAGCATCCAAA
 55
3356





1318614
N/A
N/A
1609
1628
GCCTCCCCTCGCGAGAGGAC
 98
3357





1318615
4701
4720
104688
104707
GAGCTGAATGATTTTAGGAA
 21
3358





1318621
4933
4952
108690
108709
CTTCATTCTCCTTGTGGCAC
 40
3359





1318622
4593
4612
103670
103689
GAACTGGCCCACTTCAATGT
 53
3360





1318627
N/A
N/A
101088
101107
TTACCTTATCTGCACGGTTC
 72
3361





1318632
4827
4846
106882
106901
TTCAAGCTCTTTTCCTGCAT
 33
3362





1318638
4043
4062
98651
98670
TCTCGACTAAAGCAGGATTT
 34
3363





1318640
4562
4581
103639
103658
TTCAATACAAAGCCAATAAA
 84
3364





1318642
4513
4532
101366
101385
TAACCCGTAACTGAACCAGC
 52
3365





1318645
5529
5548
126045
126064
GGCAGCTGCTGTGATTCTCC
 79
3366





1318648
4565
4584
103642
103661
TGTTTCAATACAAAGCCAAT
 66
3367





1318653
5804
5823
130387
130406
CTATTGCACATTCCAAGTTT
 80
3368





1318656
 386
 405
1365
1384
AGCGGCTCCTCAGCCACAGC
 98
3369





1318660
7721
7740
149809
149828
TGCTGCTCCAAGCAGCTTAC
 93
3370





1318663
6770
6789
N/A
N/A
GCAGCATCCCCAAACAGATC
 76
3371





1318666
6767
6786
N/A
N/A
GCATCCCCAAACAGATCATT
 85
3372





1318670
7392
7411
N/A
N/A
CCATCCAAGCTTCCACACCA
 79
3373





1318672
7387
7406
N/A
N/A
CAAGCTTCCACACCAGTGGG
 85
3374





1318674
6777
6796
N/A
N/A
ATACAGTGCAGCATCCCCAA
 89
3375





1318677
6774
6793
N/A
N/A
CAGTGCAGCATCCCCAAACA
 71
3376





1318678
7833
7852
150352
150371
ATTCTCTCTCTTTGAAACCA
 35
3377





1318680
9767
9786
166516
166535
CCAGGACTGCAGACACTCCC
 75
3378





1318681
N/A
N/A
141020
141039
ACAAATGCACAGATGAAAAC
 80
3379





1318684
7829
7848
150348
150367
TCTCTCTTTGAAACCATTGC
 41
3380





1318686
6153
6172
133214
133233
CATGCGAGCCAGCACACGGA
 56
3381





1318691
4832
4851
106887
106906
TGGGTTTCAAGCTCTTTTCC
 46
3382





1318696
4864
4883
106919
106938
GTCTCAGTAACATTGACACC
 96
3383





1318697
7180
7199
141490
141509
TGTTTGGATCTACTTCCTCC
 69
3384





1318703
4855
4874
106910
106929
ACATTGACACCACCACCTCT
 73
3385





1318705
4952
4971
108709
108728
GACAGTCGCTTCCACTTGTC
 70
3386





1318706
N/A
N/A
115060
115079
GTGTATCACCTTCCTCACTG
 78
3387





1318708
N/A
N/A
104599
104618
TGATTGCCTCTGATTCCCTA
 23
3388





1318710
 157
 176
1142
1161
AGGCCTTCATCAGCTTTTCC
 92
3389





1318715
4622
4641
104609
104628
ATGTTTGGAATGATTGCCTC
 28
3390





1318724
5507
5526
N/A
N/A
AACATTCCAGACTTGAAGAT
 79
3391





1318725
 706
 725
31688
31707
CAGCAAACCTCCACAGGGCA
 46
3392





1318727
6788
6807
138876
138895
GGCAGGGACTGATACAGTGC
 66
3393





1318731
4569
4588
103646
103665
AAACTGTTTCAATACAAAGC
 51
3394





1318733
4506
4525
101359
101378
TAACTGAACCAGCTGCGCCA
 80
3395





1318734
4873
4892
106928
106947
ACTGGATGAGTCTCAGTAAC
 74
3396





1318740
2790
2809
62214
62233
TTTTGCCTCCAAAAAGCTCA
 27
3397





1318746
4738
4757
104725
104744
TCACAGCCTTCCTTCCACTG
 76
3398
















TABLE 46







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 43
 858





1231501
4277
4296
99395
99414
TCCGCCTGCACCATGTTCCT
 82
3399





1231516
4604
4623
N/A
N/A
TCTGATTCCCTGAACTGGCC
 77
3400





1315878
5806
5825
130389
130408
CTCTATTGCACATTCCAAGT
 29
3401





1315892
N/A
N/A
1441
1460
GTTACCGCCATCCCCGCCGT
 91
3402





1315898
4608
4627
N/A
N/A
TGCCTCTGATTCCCTGAACT
 55
3403





1316129
N/A
N/A
115065
115084
TCTCTGTGTATCACCTTCCT
 67
3404





1316143
5801
5820
130384
130403
TTGCACATTCCAAGTTTGGC
 34
3405





1316282
6769
6788
N/A
N/A
CAGCATCCCCAAACAGATCA
 84
3406





1316297
N/A
N/A
1629
1648
ACAGGCCCCAACAAGGCTCT
 84
3407





1316325
2123
2142
N/A
N/A
CAAGGCTTGTTTTCTTGATC
 57
3408





1316430
6152
6171
133213
133232
ATGCGAGCCAGCACACGGAA
 76
3409





1316552
2829
2848
62253
62272
CCCTGTATAATGATGAGCCC
17†
3410





1317030
4822
4841
106877
106896
GCTCTTTTCCTGCATCAGCT
 57
3411





1317131
4511
4530
101364
101383
ACCCGTAACTGAACCAGCTG
 70
3412





1317175
4564
4583
103641
103660
GTTTCAATACAAAGCCAATA
 36
3413





1318567
N/A
N/A
1444
1463
AGGGTTACCGCCATCCCCGC
 84
3414





1318570
4735
4754
104722
104741
CAGCCTTCCTTCCACTGGCC
104
3415





1318574
N/A
N/A
1436
1455
CGCCATCCCCGCCGTAGCCT
 83
3416





1318575
N/A
N/A
1466
1485
GTGTCGCCGGCCCGCAGGCT
 80
3417





1318576
 966
 985
41676
41695
GCAGATGCTCACTGCTGATC
 76
3418





1318577
4812
4831
106867
106886
TGCATCAGCTTTATTTGTTC
 62
3419





1318578
  11
  30
996
1015
GGCCGTCCATCTTGGACCCG
 93
3420





1318580
N/A
N/A
115062
115081
CTGTGTATCACCTTCCTCAC
 62
3421





1318582
3556
3575
74418
74437
AGAGCTGCTCCACCATGGGC
 83
3422





1318587
N/A
N/A
1503
1522
TTGCTGGGTCACTCTGTCTC
 64
3423





1318593
N/A
N/A
1632
1651
AGGACAGGCCCCAACAAGGC
 73
3424





1318598
 160
 179
1145
1164
CGAAGGCCTTCATCAGCTTT
 82
3425





1318599
5233
5252
114047
114066
AGGAGAGCTCCTGAATACGA
 45
3426





1318603
5229
5248
114043
114062
GAGCTCCTGAATACGAGAAA
 64
3427





1318604
4615
4634
104602
104621
GAATGATTGCCTCTGATTCC
 48
3428





1318607
 165
 184
1150
1169
GGACTCGAAGGCCTTCATCA
 81
3429





1318613
 704
 723
31686
31705
GCAAACCTCCACAGGGCAGC
 83
3430





1318617
3217
3236
N/A
N/A
AAGCTTCACAGCATCCAAAT
 82
3431





1318623
4932
4951
108689
108708
TTCATTCTCCTTGTGGCACT
 41
3432





1318624
4716
4735
104703
104722
CATGATGCCATCACAGAGCT
 57
3433





1318625
4592
4611
103669
103688
AACTGGCCCACTTCAATGTA
 73
3434





1318626
4712
4731
104699
104718
ATGCCATCACAGAGCTGAAT
 71
3435





1318630
4867
4886
106922
106941
TGAGTCTCAGTAACATTGAC
 62
3436





1318631
 129
 148
1114
1133
CATGGCGGTCTCCCGCCCGG
 55
3437





1318633
 388
 407
1367
1386
GCAGCGGCTCCTCAGCCACA
 86
3438





1318636
4819
4838
106874
106893
CTTTTCCTGCATCAGCTTTA
 48
3439





1318637
 126
 145
1111
1130
GGCGGTCTCCCGCCCGGCAC
 89
3440





1318641
4613
4632
104600
104619
ATGATTGCCTCTGATTCCCT
 30
3441





1318643
5525
5544
126041
126060
GCTGCTGTGATTCTCCGGAA
 46
3442





1318649
6786
6805
138874
138893
CAGGGACTGATACAGTGCAG
 72
3443





1318654
8664
8683
161610
161629
AGGATAGTTCTCAATGAGGT
 41
3444





1318655
4567
4586
103644
103663
ACTGTTTCAATACAAAGCCA
 59
3445





1318661
6772
6791
N/A
N/A
GTGCAGCATCCCCAAACAGA
 84
3446





1318665
6766
6785
N/A
N/A
CATCCCCAAACAGATCATTC
 96
3447





1318667
9789
9808
166538
166557
GAAGGCCTCAGGCTCAGCCC
 90
3448





1318668
7723
7742
149811
149830
GCTGCTGCTCCAAGCAGCTT
 88
3449





1318671
7390
7409
N/A
N/A
ATCCAAGCTTCCACACCAGT
 87
3450





1318673
6776
6795
N/A
N/A
TACAGTGCAGCATCCCCAAA
 72
3451





1318675
4863
4882
106918
106937
TCTCAGTAACATTGACACCA
 43
3452





1318682
N/A
N/A
141016
141035
ATGCACAGATGAAAACAATT
 82
3453





1318685
7832
7851
150351
150370
TTCTCTCTCTTTGAAACCAT
 37
3454





1318688
7184
7203
141494
141513
TGTGTGTTTGGATCTACTTC
 59
3455





1318695
4829
4848
106884
106903
GTTTCAAGCTCTTTTCCTGC
 26
3456





1318699
2793
2812
62217
62236
TGCTTTTGCCTCCAAAAAGC
 43†
3457





1318701
4857
4876
106912
106931
TAACATTGACACCACCACCT
 38
3458





1318713
3552
3571
74414
74433
CTGCTCCACCATGGGCACCA
 99
3459





1318717
 102
 121
1087
1106
GTCCCCGGAGGCCTCGGGCC
 92
3460





1318718
 988
1007
41698
41717
ATTGTGTCCTTCTTGAGTGC
 57
3461





1318719
 385
 404
1364
1383
GCGGCTCCTCAGCCACAGCC
107
3462





1318720
N/A
N/A
101091
101110
CATTTACCTTATCTGCACGG
 89
3463





1318721
4389
4408
N/A
N/A
ATGAATAGCATTCTTATCTG
 54
3464





1318723
4698
4717
104685
104704
CTGAATGATTTTAGGAATTC
 52
3465





1318726
4047
4066
98655
98674
TGGTTCTCGACTAAAGCAGG
 27
3466





1318729
7624
7643
149712
149731
TCTGGGTCCTCTCTGTGTCT
 62
3467





1318732
4559
4578
103636
103655
AATACAAAGCCAATAAACAC
 79
3468





1318737
4950
4969
108707
108726
CAGTCGCTTCCACTTGTCTT
 66
3469





1318738
4853
4872
106908
106927
ATTGACACCACCACCTCTTT
 99
3470





1318739
7178
7197
141488
141507
TTTGGATCTACTTCCTCCTC
 87
3471





1318742
5813
5832
130396
130415
ACTATTTCTCTATTGCACAT
 34
3472





1318743
7836
7855
150355
150374
AATATTCTCTCTCTTTGAAA
 98
3473





1318744
7826
7845
150345
150364
CTCTTTGAAACCATTGCTTG
 63
3474





1318747
4809
4828
106864
106883
ATCAGCTTTATTTGTTCCTC
 33
3475
















TABLE 47







Reduction of HTT RNA by 5-10-5 MOE gapmers with mixed PO/PS internucleoside


linkages in A431 cells















SEQ
SEQ
SEQ
SEQ






ID No:
ID No:
ID No:
ID No:

HTT
SEQ


Compound
1 Start
1 Stop
2 Start
2 Stop

(%
ID


Number
Site
Site
Site
Site
Sequence (5′ to 3′)
UTC)
NO

















 388241
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 42
 858





 627246
4862
4881
106917
106936
CTCAGTAACATTGACACCAC
 67
 858





1231517
4607
4626
N/A
N/A
GCCTCTGATTCCCTGAACTG
 57
3476





1231536
5812
5831
130395
130414
CTATTTCTCTATTGCACATT
 45
3477





1315904
 968
 987
41678
41697
TGGCAGATGCTCACTGCTGA
 89
3478





1316055
N/A
N/A
1443
1462
GGGTTACCGCCATCCCCGCC
 94
3479





1316138
N/A
N/A
1502
1521
TGCTGGGTCACTCTGTCTCT
 77
3480





1316364
6775
6794
N/A
N/A
ACAGTGCAGCATCCCCAAAC
 71
3481





1316386
7389
7408
N/A
N/A
TCCAAGCTTCCACACCAGTG
 80
3482





1316513
7831
7850
150350
150369
TCTCTCTCTTTGAAACCATT
 39
3483





1316596
 162
 181
1147
1166
CTCGAAGGCCTTCATCAGCT
 98
3484





1316624
5231
5250
114045
114064
GAGAGCTCCTGAATACGAGA
 54
3485





1317002
 390
 409
1369
1388
GTGCAGCGGCTCCTCAGCCA
 80
3486





1317142
4610
4629
N/A
N/A
ATTGCCTCTGATTCCCTGAA
 25
3487





1318566
4821
4840
106876
106895
CTCTTTTCCTGCATCAGCTT
 47
3488





1318571
4734
4753
104721
104740
AGCCTTCCTTCCACTGGCCA
 89
3489





1318572
 965
 984
41675
41694
CAGATGCTCACTGCTGATCC
 60
3490





1318573
4811
4830
106866
106885
GCATCAGCTTTATTTGTTCC
 39
3491





1318581
N/A
N/A
1440
1459
TTACCGCCATCCCCGCCGTA
102
3492





1318583
3555
3574
74417
74436
GAGCTGCTCCACCATGGGCA
 92
3493





1318586
N/A
N/A
115064
115083
CTCTGTGTATCACCTTCCTC
 47
3494





1318589
N/A
N/A
1631
1650
GGACAGGCCCCAACAAGGCT
 87
3495





1318590
 159
 178
1144
1163
GAAGGCCTTCATCAGCTTTT
 91
3496





1318591
4276
4295
99394
99413
CCGCCTGCACCATGTTCCTC
 78
3497





1318594
2122
2141
N/A
N/A
AAGGCTTGTTTTCTTGATCA
 36
3498





1318597
N/A
N/A
1447
1466
TGCAGGGTTACCGCCATCCC
 91
3499





1318605
4614
4633
104601
104620
AATGATTGCCTCTGATTCCC
 26
3500





1318606
 109
 128
1094
1113
CACGGCAGTCCCCGGAGGCC
 91
3501





1318608
3214
3233
N/A
N/A
CTTCACAGCATCCAAATGTG
 91
3502





1318611
4603
4622
N/A
N/A
CTGATTCCCTGAACTGGCCC
 58
3503





1318612
4706
4725
104693
104712
TCACAGAGCTGAATGATTTT
 58
3504





1318616
 703
 722
31685
31704
CAAACCTCCACAGGGCAGCA
 68
3505





1318618
4934
4953
108691
108710
TCTTCATTCTCCTTGTGGCA
 52
3506





1318619
4715
4734
104702
104721
ATGATGCCATCACAGAGCTG
 54
3507





1318620
4383
4402
N/A
N/A
AGCATTCTTATCTGCACGGT
 24
3508





1318628
 387
 406
1366
1385
CAGCGGCTCCTCAGCCACAG
 97
3509





1318629
4386
4405
N/A
N/A
AATAGCATTCTTATCTGCAC
 43
3510





1318634
4818
4837
106873
106892
TTTTCCTGCATCAGCTTTAT
 75
3511





1318635
 128
 147
1113
1132
ATGGCGGTCTCCCGCCCGGC
 87
3512





1318639
4563
4582
103640
103659
TTTCAATACAAAGCCAATAA
 75
3513





1318644
4045
4064
98653
98672
GTTCTCGACTAAAGCAGGAT
 41
3514





1318646
4508
4527
101361
101380
CGTAACTGAACCAGCTGCGC
 65
3515





1318647
5524
5543
126040
126059
CTGCTGTGATTCTCCGGAAC
 46
3516





1318650
6785
6804
138873
138892
AGGGACTGATACAGTGCAGC
 58
3517





1318651
8663
8682
161609
161628
GGATAGTTCTCAATGAGGTA
 49
3518





1318652
5805
5824
130388
130407
TCTATTGCACATTCCAAGTT
 48
3519





1318657
4566
4585
103643
103662
CTGTTTCAATACAAAGCCAA
 43
3520





1318658
7722
7741
149810
149829
CTGCTGCTCCAAGCAGCTTA
 97
3521





1318659
9788
9807
166537
166556
AAGGCCTCAGGCTCAGCCCC
 97
3522





1318662
6771
6790
N/A
N/A
TGCAGCATCCCCAAACAGAT
 74
3523





1318664
6768
6787
N/A
N/A
AGCATCCCCAAACAGATCAT
110
3524





1318669
6151
6170
133212
133231
TGCGAGCCAGCACACGGAAA
 73
3525





1318676
7725
7744
149813
149832
GGGCTGCTGCTCCAAGCAGC
 70
3526





1318679
N/A
N/A
141021
141040
TACAAATGCACAGATGAAAA
 78
3527





1318683
N/A
N/A
141015
141034
TGCACAGATGAAAACAATTA
 91
3528





1318687
7834
7853
150353
150372
TATTCTCTCTCTTTGAAACC
 69
3529





1318689
7181
7200
141491
141510
GTGTTTGGATCTACTTCCTC
 53
3530





1318690
4828
4847
106883
106902
TTTCAAGCTCTTTTCCTGCA
 42
3531





1318692
2792
2811
62216
62235
GCTTTTGCCTCCAAAAAGCT
 61†
3532





1318693
4865
4884
106920
106939
AGTCTCAGTAACATTGACAC
 76
3533





1318694
4922
4941
108679
108698
TTGTGGCACTGCTGCAGGAC
 69
3534





1318698
4676
4695
104663
104682
ATGATCTGTTTTGAATGATA
 26
3535





1318700
4953
4972
108710
108729
AGACAGTCGCTTCCACTTGT
 55
3536





1318702
4856
4875
106911
106930
AACATTGACACCACCACCTC
 79
3537





1318704
2798
2817
62222
62241
TTTTCTGCTTTTGCCTCCAA
 22†
3538





1318707
  14
  33
999
1018
AGCGGCCGTCCATCTTGGAC
 96
3539





1318709
N/A
N/A
1624
1643
CCCCAACAAGGCTCTGCCTC
 78
3540





1318711
5693
5712
126209
126228
ACTTCTGCCCACCAGCGGTA
 83
3541





1318712
N/A
N/A
115061
115080
TGTGTATCACCTTCCTCACT
 73
3542





1318714
   4
  23
989
1008
CATCTTGGACCCGTCCCGGC
 92
3543





1318716
3220
3239
71458
71477
ACAAAGCTTCACAGCATCCA
 60
3544





1318722
4590
4609
103667
103686
CTGGCCCACTTCAATGTATT
 89
3545





1318728
7614
7633
N/A
N/A
CTCTGTGTCTTCTTCTGGTG
 86
3546





1318730
 384
 403
1363
1382
CGGCTCCTCAGCCACAGCCG
 86
3547





1318735
4516
4535
101369
101388
AATTAACCCGTAACTGAACC
 58
3548





1318736
6764
6783
N/A
N/A
TCCCCAAACAGATCATTCAA
 88
3549





1318741
4836
4855
106891
106910
TTTTTGGGTTTCAAGCTCTT
 48
3550





1318745
4808
4827
106863
106882
TCAGCTTTATTTGTTCCTCT
 25
3551









Example 4: Dose-Dependent Inhibition of Human HTT in HepG2 Cells by Modified Oligonucleotides Modified oligonucleotides selected from the examples above were tested at various doses in HepG2 cells. Cultured HepG2 cells at a density of 20,000 cells per well were treated by electroporation with various concentrations of modified oligonucleotide as specified in the tables below. After a treatment period of approximately 24 hours, total RNA was isolated from the cells and HTT RNA levels were measured by quantitative real-time RTPCR. Human HTT primer-probe set RTS2617 (described herein above) was used to measure RNA levels as described above. HTT RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of HTT RNA is presented in the tables below as percent HTT RNA, relative to the amount of HTT RNA in untreated control cells (% UTC).


The half maximal inhibitory concentration (IC50) of each modified oligonucleotide was calculated using a linear regression on a log/linear plot of the data in Excel and is also presented in the tables below.









TABLE 48







Dose-dependent reduction of human HTT RNA


in HepG2 cells by modified oligonucleotides









Compound
HTT RNA (% UTC)
IC50













No.
62 nM
185 nM
556 nM
1667 nM
5000 nM
(μM)
















387916
100
94
90
58
34
2.87


646210
83
80
70
50
29
1.47


646211
85
70
51
34
12
0.57


646214
103
99
77
57
29
2.10


646215
92
94
74
68
36
3.48


646218
105
81
54
33
16
0.82


646219
86
88
68
48
21
1.23


646221
104
86
69
42
33
1.48


646222
102
97
71
46
32
1.71


646259
94
85
77
55
27
1.80


646264
96
88
76
47
41
2.27


646265
98
103
71
43
21
1.32


646284
93
89
69
57
35
2.20


646311
94
100
61
47
26
1.38


646344
92
69
57
30
14
0.64
















TABLE 49







Dose-dependent reduction of human HTT RNA


in HepG2 cells by modified oligonucleotides









Compound
HTT RNA (% UTC)
IC50













No.
62 nM
185 nM
556 nM
1667 nM
5000 nM
(μM)
















387916
103
98
89
42
28
1.82


646287
112
106
100
80
56
>5


646301
99
76
37
28
13
0.57


646313
97
93
63
52
22
1.32


646342
114
98
74
52
26
1.72


646356
92
87
62
46
29
1.33


646364
98
93
74
40
18
1.18


646366
91
90
72
60
23
1.72


646370
94
102
72
38
20
1.23


646376
94
83
54
26
12
0.67


646384
97
97
81
50
43
2.99


646398
104
99
90
52
32
2.41


646401
95
81
69
36
14
0.89


646411
95
81
56
32
13
0.74


646412
105
84
52
25
12
0.71









Example 5: Dose-Dependent Inhibition of Human HTT in A431 Cells by Modified Oligonucleotides

Modified oligonucleotides selected from the examples above were tested at various doses in A431 cells. Cultured A431 cells at a density of 10,000 cells per well were treated by free uptake with various concentrations of modified oligonucleotide as specified in the tables below. After a treatment period of approximately 48 hours, total RNA was isolated from the cells and HTT RNA levels were measured by quantitative real-time RTPCR. Human HTT primer-probe set RTS36485 (described herein above) was used to measure RNA levels as described above. HTT RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of HTT RNA is presented in the tables below as percent HTT RNA, relative to the amount of HTT RNA in untreated control cells (% UTC).


The half maximal inhibitory concentration (IC50) of each modified oligonucleotide was calculated using a linear regression on a log/linear plot of the data in Excel and is also presented in the tables below.









TABLE 50







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides









Compound
HTT RNA (% UTC)
IC50












No.
234 nM
938 nM
3750 nM
15000 nM
(μM)















387916
38
16
7
3
<0.23


953845
102
83
59
58
>15


953941
94
87
61
54
>15


953957
127
117
115
116
>15


953966
78
64
54
49
9.37


954021
78
57
43
32
2.36


954022
100
87
75
65
>15


954030
74
55
41
39
2.42


954047
66
32
17
13
0.44


954085
113
105
92
81
>15


954101
92
84
71
57
>15


954118
88
73
62
49
13.74


954205
93
79
45
47
6.83


954238
72
66
44
31
2.52


954294
88
89
69
60
>15


954317
99
89
61
47
11.37


954365
76
52
39
33
1.89


954366
92
74
54
48
8.77


954374
89
65
44
39
3.99
















TABLE 51







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
234 nM
938 nM
3750 nM
15000 nM
(μM)















387916
37
14
6
3
<0.23


953799
109
119
107
119
>15


953871
112
101
83
74
>15


953896
74
59
50
38
3.45


953905
111
87
61
33
6.44


953991
104
90
79
65
>15


953993
102
83
84
72
>15


954023
87
60
49
38
4.05


954033
94
80
58
58
>15


954129
108
117
100
111
>15


954135
121
110
117
107
>15


954272
87
73
56
41
6.78


954288
102
90
73
62
>15


954304
86
63
45
21
2.39


954313
104
94
76
58
>15


954335
88
65
52
33
3.86


954343
90
63
44
36
3.62


954391
83
76
57
48
11.41


954392
88
84
74
73
>15
















TABLE 52







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
234 nM
938 nM
3750 nM
15000 nM
(μM)















387916
41
16
7
2
<0.23


953906
71
74
65
49
>15


953921
66
93
78
62
>15


953954
75
62
52
36
3.76


953978
102
98
89
81
>15


954027
77
63
35
24
1.81


954042
80
43
35
21
1.28


954058
102
87
75
56
>15


954066
99
63
51
31
3.77


954081
96
95
66
47
13.91


954123
88
67
49
39
4.63


954185
106
102
110
114
>15


954194
91
84
60
46
10.83


954266
69
64
51
44
5.69


954273
87
81
61
51
>15


954274
79
66
52
49
8.19


954290
82
51
44
34
2.39


954329
86
91
82
78
>15


954353
97
116
88
85
>15
















TABLE 53







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
234 nM
938 nM
3750 nM
15000 nM
(μM)















387916
39
14
5
2
<0.23


388817
100
93
81
82
>15


953827
87
87
65
69
>15


953979
86
89
72
65
>15


953980
94
81
77
56
>15


954028
77
100
72
54
>15


954035
100
88
74
59
>15


954043
78
61
40
28
2.14


954044
68
49
32
27
1.03


954068
72
58
36
17
1.36


954204
110
93
77
57
>15


954219
113
106
126
101
>15


954299
95
79
75
101
>15


954339
75
82
66
53
>15


954364
65
45
41
28
1.00


954372
87
71
78
65
>15


954395
102
106
78
91
>15


954411
77
66
52
63
>15


954412
104
98
77
68
>15









Modified oligonucleotides selected from the examples above were tested at various doses in A431 cells. Cultured A431 cells at a density of 10,000 cells per well were treated by free uptake with various concentrations of modified oligonucleotide as specified in the tables below. After a treatment period of approximately 48 hours, total RNA was isolated from the cells and HTT RNA levels were measured by quantitative real-time RTPCR. Human HTT primer-probe set RTS36478 (described herein above) was used to measure RNA levels as described above. HTT RNA levels were normalized to total RNA content, as measured by RIBOGREEN®. Reduction of HTT RNA is presented in the tables below as percent HTT RNA, relative to the amount of HTT RNA in untreated control cells (% UTC).


The half maximal inhibitory concentration (IC50) of each modified oligonucleotide was calculated using a linear regression on a log/linear plot of the data in Excel and is also presented in the tables below. N.D. in the tables below refers to instances where the value was Not Defined.









TABLE 54







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
85
61
39
24
0.59


1314541
60
38
22
12
0.11


1314544
71
41
26
14
0.20


1314723
57
37
19
10
0.09


1314943
73
44
27
17
0.24


1315039
67
45
28
16
0.20


1315041
70
47
33
19
0.26


1315074
32
15
9
9
<0.06


1315123
71
42
30
15
0.23


1315615
78
63
41
29
0.63


1315692
56
31
20
11
0.07


1315698
71
47
29
18
0.25


1315847
73
53
34
21
0.35


1316080
99
71
49
29
1.02


1316096
81
55
39
25
0.50


1316234
79
55
36
18
0.41


1316312
47
26
16
10
<0.06


1316500
84
60
38
21
0.53


1316679
81
55
34
18
0.41
















TABLE 55







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
90
64
40
24
0.67


1314789
63
42
23
11
0.15


1314848
78
50
28
16
0.31


1315014
69
43
25
16
0.20


1315137
66
45
24
11
0.18


1315143
68
37
17
9
0.15


1315207
88
66
38
21
0.61


1315294
65
40
23
13
0.15


1315566
73
41
26
19
0.24


1315702
57
32
20
12
0.08


1315752
74
49
32
16
0.30


1315874
87
63
34
17
0.50


1316169
69
51
27
14
0.25


1316218
73
54
36
18
0.35


1316589
72
46
28
16
0.25


1316616
85
64
42
20
0.59


1316620
76
59
37
25
0.47


1316972
81
55
33
20
0.41


1317178
75
53
33
22
0.35
















TABLE 56







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
72
63
40
25
0.50


1314696
84
54
30
31
0.43


1314810
42
25
14
10
<0.06


1314894
96
85
77
35
2.75


1314930
75
51
38
23
0.38


1314999
55
35
21
13
0.08


1315027
77
50
30
20
0.33


1315155
65
44
36
24
0.22


1315174
74
46
32
15
0.27


1315556
64
42
38
24
0.21


1315578
62
39
22
11
0.13


1315808
100
75
57
40
1.71


1316170
74
54
33
21
0.36


1316535
71
52
44
34
0.51


1316563
46
26
15
9
<0.06


1316725
73
50
31
17
0.29


1316768
112
61
43
30
0.91


1316803
78
58
37
30
0.54


1316893
101
86
81
58
>4
















TABLE 57







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
100
64
45
26
0.83


1314562
90
67
67
34
1.62


1314685
72
47
26
23
0.26


1314813
64
41
25
15
0.15


1314888
81
66
41
20
0.58


1315056
64
43
29
13
0.17


1315482
90
47
27
15
0.37


1315558
96
104
85
77
>4


1315781
96
65
45
27
0.82


1315803
79
62
43
26
0.59


1316274
74
56
40
26
0.47


1316324
85
62
45
31
0.77


1316938
95
73
62
58
>4


1317061
82
48
38
19
0.40


1317115
75
53
37
23
0.39


1317128
79
59
31
16
0.40


1317163
87
65
47
25
0.76


1317190
106
95
88
79
>4


1317205
75
47
27
13
0.27
















TABLE 58







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
86
49
33
18
0.40


1314548
80
58
28
11
0.36


1314650
59
31
23
11
0.09


1314744
61
42
25
15
0.14


1314824
68
49
31
18
0.25


1314964
79
57
35
20
0.43


1314982
87
47
29
20
0.39


1315234
74
52
29
18
0.31


1315321
46
23
13
9
<0.06


1315447
69
43
30
23
0.23


1315636
77
48
31
16
0.31


1315877
72
45
23
10
0.22


1315886
93
72
64
63
>4


1315921
38
16
8
4
<0.06


1316310
75
50
31
16
0.31


1316551
84
43
28
14
0.31


1316772
93
63
37
21
0.61


1317204
72
48
29
15
0.26


1317227
73
44
27
15
0.24
















TABLE 59







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
77
65
42
23
0.56


1314487
54
35
18
10
0.07


1314570
71
47
36
20
0.29


1314596
78
61
33
22
0.45


1314899
79
54
30
20
0.38


1314904
60
35
24
15
0.11


1315562
69
50
30
21
0.26


1315672
55
34
18
11
0.08


1315733
76
48
32
23
0.33


1315747
67
45
35
19
0.24


1315754
70
45
29
14
0.23


1315964
44
24
16
8
<0.06


1316061
70
49
31
26
0.29


1316098
72
49
32
19
0.28


1316154
66
47
30
15
0.22


1316254
89
52
33
23
0.48


1316604
47
28
14
19
<0.06


1316716
65
45
27
20
0.19


1316965
78
55
32
18
0.38
















TABLE 60







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
85
107
51
26
1.30


1314791
106
66
46
34
1.07


1314822
77
79
41
22
0.76


1314849
42
24
12
8
<0.06


1315621
105
60
38
20
0.66


1315723
67
46
29
N.D.
0.20


1315867
52
36
22
12
0.07


1315881
90
55
46
29
0.74


1315883
70
55
N.D.
19
0.34


1315911
87
62
46
28
0.75


1316106
72
53
36
22
0.35


1316346
140
59
38
21
0.85


1316392
63
42
18
7
0.14


1316414
68
39
17
6
0.16


1316704
79
60
37
19
0.46


1316835
85
59
44
29
0.68


1317084
66
52
37
22
0.29


1317090
48
32
24
12
<0.06


1317136
76
39
20
8
0.21
















TABLE 61







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
78
58
41
18
0.46


1314606
80
60
36
22
0.48


1314678
81
60
41
39
0.83


1314828
72
49
29
19
0.28


1314829
58
29
16
9
0.07


1314935
59
44
26
16
0.14


1315083
48
28
16
11
<0.06


1315309
75
60
36
22
0.44


1315347
56
36
20
10
0.09


1315501
59
36
26
13
0.11


1315512
79
44
33
17
0.31


1315652
61
32
20
8
0.10


1315746
71
43
26
20
0.23


1315885
88
69
45
24
0.76


1316435
47
23
13
8
<0.06


1316639
38
23
14
9
<0.06


1316788
79
49
38
20
0.38


1316846
74
57
29
22
0.36


1317164
72
52
39
17
0.34
















TABLE 62







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
91
64
31
20
0.54


1314511
86
41
23
17
0.30


1314540
75
42
27
13
0.24


1314603
73
47
33
23
0.33


1315317
48
26
14
7
<0.06


1315408
62
41
26
14
0.14


1315499
95
77
69
52
>4


1315536
73
43
26
14
0.23


1315537
85
52
28
16
0.38


1315584
75
60
35
18
0.40


1315794
75
37
23
13
0.20


1315950
55
32
14
6
0.07


1316400
66
39
21
12
0.15


1316621
69
39
26
8
0.19


1316672
77
51
28
12
0.30


1316766
65
34
24
17
0.13


1316908
70
46
24
19
0.22


1317017
63
33
17
9
0.11


1317031
63
30
20
10
0.10
















TABLE 63







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
83
58
44
24
0.59


1314708
52
31
18
15
<0.06


1314762
45
20
9
6
<0.06


1314827
81
58
41
24
0.55


1314891
74
57
35
22
0.40


1314907
71
34
18
8
0.16


1314918
45
22
12
6
<0.06


1314920
88
64
43
25
0.68


1314967
33
14
6
4
<0.06


1315340
53
22
14
6
<0.06


1315412
80
53
36
22
0.42


1315678
90
44
24
11
0.33


1315749
71
49
31
18
0.28


1316062
57
30
14
8
0.07


1316162
97
80
58
34
1.54


1316544
57
35
19
10
0.09


1316722
90
73
49
27
0.94


1316775
81
60
41
21
0.52


1317050
77
49
34
23
0.35
















TABLE 64







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
83
61
38
23
0.56


1314845
61
44
25
13
0.15


1314916
90
81
31
16
0.63


1314928
85
68
53
34
1.11


1315077
68
44
18
20
0.18


1315147
74
45
31
15
0.26


1315341
54
27
16
9
<0.06


1315425
64
42
28
17
0.16


1315498
81
53
38
23
0.46


1315722
86
58
39
22
0.54


1315812
70
52
32
23
0.30


1315879
81
61
47
26
0.66


1315897
98
66
40
23
0.73


1315974
65
44
33
27
0.20


1316232
83
52
35
21
0.42


1316421
85
66
49
27
0.81


1316508
99
64
41
26
0.76


1316762
73
60
37
27
0.46


1316926
55
31
21
22
<0.06
















TABLE 65







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
90
56
37
21
0.53


1315878
67
42
27
15
0.18


1316143
64
48
31
21
0.21


1316972
69
47
32
19
0.25


1317142
73
38
26
15
0.21


1318569
72
49
31
19
0.29


1318594
70
52
42
31
0.43


1318605
80
46
29
19
0.32


1318615
61
39
21
13
0.12


1318620
61
35
28
15
0.12


1318641
75
50
39
21
0.37


1318695
68
39
23
15
0.17


1318698
83
47
24
16
0.31


1318708
57
30
19
13
0.07


1318715
79
51
33
19
0.36


1318726
66
41
27
17
0.17


1318742
63
38
25
15
0.13


1318745
66
41
26
16
0.17


1318747
64
41
32
17
0.17
















TABLE 66







Dose-dependent reduction of human HTT RNA


in A431 cells by modified oligonucleotides










HTT RNA (% UTC)
IC50












Compound No.
63 nM
250 nM
1000 nM
4000 nM
(μM)















388241
66
58
43
32
0.50


1314755
95
61
39
27
0.70


1314833
56
53
47
22
0.25


1314867
71
50
25
17
0.25


1314905
38
22
15
6
<0.06


1315119
73
51
24
20
0.27


1315141
74
46
28
22
0.28


1315214
48
22
16
9
<0.06


1315282
125
120
112
76
>4


1315343
66
37
25
9
0.15


1315405
56
44
22
17
0.11


1315604
65
42
38
27
0.22


1315813
77
67
38
13
0.46


1316229
100
72
49
29
1.03


1316506
68
35
20
10
0.15


1316802
70
40
24
13
0.18


1316984
74
63
59
33
1.08









Example 6: Design of Modified Oligonucleotides Complementary to Human HTT Nucleic Acid

Modified oligonucleotides complementary to a human HTT nucleic acid were designed, as described in the tables below. “Start site” indicates the 5′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. “Stop site” indicates the 3′-most nucleoside to which the modified oligonucleotide is complementary in the target nucleic acid sequence. Each modified oligonucleotide listed in the tables below is 100% complementary to SEQ ID NO: 1 (described herein above), to SEQ ID NO: 2 (described herein above), or to both. ‘N/A’ indicates that the modified oligonucleotide is not 100% complementary to that particular target nucleic acid sequence.


The modified oligonucleotides in the table below are 17 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeddddddddkkeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, each “e” represents a 2′-MOE sugar moiety, and each “k” represents a cEt sugar moiety. The modified oligonucleotides have an internucleoside linkage motif of (from 5′ to 3′): soosssssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 67







Modified oligonucleotides with a mixed MOE/cEt sugar motif and mixed PO/PS


internucleoside linkages complementary to human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.
















1419386
ACAGCTTTTATTTCCAT
N/A
N/A
126800
126816
3552





1419387
ACTCATTTCCACCTTCA
5430
5446
115308
115324
3553





1419388
AGAGGTCATCTTCGGTC
N/A
N/A
118733
118749
3554





1419389
AGCTTTTATTTCCATAC
N/A
N/A
126798
126814
3555





1419390
ATCTTGTTTTACCACCC
N/A
N/A
35334
35350
3556





1419391
ATTACTTTTTACAATGG
N/A
N/A
62838
62854
3557





1419392
CACAGCTTTTATTTCCA
N/A
N/A
126801
126817
3558





1419393
CACTCATTTCCACCTTC
5431
5447
115309
115325
3559





1419394
CAGCTTTTATTTCCATA
N/A
N/A
126799
126815
3560





1419395
CATCTTGTTTTACCACC
N/A
N/A
35335
35351
3561





1419396
CATTACTTTTTACAATG
N/A
N/A
62839
62855
3562





1419397
CATTTCCACCTTCAGCT
5427
5443
115305
115321
3563





1419398
CTAGAGGTCATCTTCGG
N/A
N/A
118735
118751
3564





1419399
CTCATTTCCACCTTCAG
5429
5445
115307
115323
3565





1419400
CTTTGATTTTTACCAGT
N/A
N/A
60027
60043
3566





1419401
GAGGTCATCTTCGGTCA
N/A
N/A
118732
118748
3567





1419402
GCATCTTGTTTTACCAC
N/A
N/A
35336
35352
3568





1419403
GCATTACTTTTTACAAT
N/A
N/A
62840
62856
3569





1419404
GCTGCTCACTCATTTCC
5437
5453
115315
115331
3570





1419405
GCTTTGATTTTTACCAG
N/A
N/A
60028
60044
3571





1419406
GCTTTTATTTCCATACA
N/A
N/A
126797
126813
3572





1419407
GGTCACAGCTTTTATTT
N/A
N/A
126804
126820
3573





1419408
GGTTAGTTTTCCTTTTA
N/A
N/A
117880
117896
3574





1419409
GTCACAGCTTTTATTTC
N/A
N/A
126803
126819
3575





1419410
GTTAGTTTTCCTTTTAT
N/A
N/A
117879
117895
3576





1419412
TAGAGGTCATCTTCGGT
N/A
N/A
118734
118750
3577





1419413
TAGTTTTCCTTTTATAT
N/A
N/A
117877
117893
3578





1419414
TCACAGCTTTTATTTCC
N/A
N/A
126802
126818
3579





1419415
TCACTCATTTCCACCTT
5432
5448
115310
115326
3580





1419416
TCATTTCCACCTTCAGC
5428
5444
115306
115322
3581





1419417
TCTTGTTTTACCACCCA
N/A
N/A
35333
35349
3582





1419418
TGCTGCTCACTCATTTC
5438
5454
115316
115332
3583





1419419
TGGTCACAGCTTTTATT
N/A
N/A
126805
126821
3584





1419420
TGTTGCTGCTCACTCAT
5441
5457
115319
115335
3585





1419421
TTACTTTTTACAATGGA
N/A
N/A
62837
62853
3586





1419422
TTAGTTTTCCTTTTATA
N/A
N/A
117878
117894
3587





1419423
TTGATTTTTACCAGTTA
N/A
N/A
60025
60041
3588





1419424
TTGCTGCTCACTCATTT
5439
5455
115317
115333
3589





1419425
TTTGATTTTTACCAGTT
N/A
N/A
60026
60042
3590









The modified oligonucleotide in the table below is a 5-10-5 MOE gapmer. The gapmer is 20 nucleosides in length, wherein the sugar motif for the gapmer is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmer has an internucleoside linkage motif of (from 5′ to 3′): sooosssssssssssooos; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 68







5-10-5 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





444652
TTTCTCTATTGCACATTCCA
5809
5828
130392
130411
3591









The modified oligonucleotides in the table below are 5-10-5 MOE gapmers. The gapmers are 20 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmers have an internucleoside linkage motif of (from 5′ to 3′): sooosssssssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 69







5-10-5 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





1391291
ACACAGCCTGCTAGAGGTCA
N/A
N/A
118742
118761
3592





1391292
CTGCTCACTCATTTCCACCT
5433
5452
115311
115330
3593





1391293
CTCACTCATTTCCACCTTCA
5430
5449
115308
115327
3594





1391294
ACAGCCTGCTAGAGGTCATC
N/A
N/A
118740
118759
3595





1391295
CTTTGATTTTTACCAGTTAA
N/A
N/A
 60024
 60043
3596





1391296
TCATTTCCACCTTCAGCTGT
5425
5444
115303
115322
3597





1391297
TTGGGGGTGGTCACAGCTTT
N/A
N/A
126809
126828
3598





1391298
TTTTGCTTTGATTTTTACCA
N/A
N/A
 60029
 60048
3599





1391299
CCACCTTCAGCTGTTTTGTA
5419
5438
115297
115316
3600





1391301
TGCTGCTCACTCATTTCCAC
5435
5454
115313
115332
3601





1391302
GTTTTTTGCTTTGATTTTTA
N/A
N/A
 60032
 60051
3602





1391303
TTTGCTTTGATTTTTACCAG
N/A
N/A
 60028
 60047
3603





1391304
TTCCACCTTCAGCTGTTTTG
5421
5440
115299
115318
3604





1391305
TTTTTGCTTTGATTTTTACC
N/A
N/A
 60030
 60049
3605





1391306
GCCTGCTAGAGGTCATCTTC
N/A
N/A
118737
118756
3606





1391307
TTGTAGGTTTTTTGCTTTGA
N/A
N/A
 60038
 60057
3607





1391308
TGGTCACAGCTTTTATTTCC
N/A
N/A
126802
126821
3608





1391309
TGTTTTACCACCCATGCTGG
N/A
N/A
 35327
 35346
3609





1391310
GTGCATTACTTTTTACAATG
N/A
N/A
 62839
 62858
3610





1391311
GGGGTGGTCACAGCTTTTAT
N/A
N/A
126806
126825
3611





1391312
TAGAGGTCATCTTCGGTCAT
N/A
N/A
118731
118750
3612





1391313
GTTGGGGGTGGTCACAGCTT
N/A
N/A
126810
126829
3613





1391314
TATGTTGCTGCTCACTCATT
5440
5459
115318
115337
3614





1391315
TGCTTTGATTTTTACCAGTT
N/A
N/A
 60026
 60045
3615





1391316
ATTTCCACCTTCAGCTGTTT
5423
5442
115301
115320
3616





1391318
GAGGTCATCTTCGGTCATGT
N/A
N/A
118729
118748
3617





1391319
TCTTGTTTTACCACCCATGC
N/A
N/A
 35330
 35349
3618





1391320
CACAGCTTTTATTTCCATAC
N/A
N/A
126798
126817
3619





1391321
TACTTTTTACAATGGACAGT
N/A
N/A
 62833
 62852
3620





1391322
AGGTCATCTTCGGTCATGTG
N/A
N/A
118728
118747
3621





1391323
ATTACTTTTTACAATGGACA
N/A
N/A
 62835
 62854
3622





1391324
TGCATTACTTTTTACAATGG
N/A
N/A
 62838
 62857
3623





1391325
GGCATCTTGTTTTACCACCC
N/A
N/A
 35334
 35353
3624





1391326
TTGCTTTGATTTTTACCAGT
N/A
N/A
 60027
 60046
3625





1391327
ATCTTGTTTTACCACCCATG
N/A
N/A
 35331
 35350
3626





1391328
TTACTTTTTACAATGGACAG
N/A
N/A
 62834
 62853
3627





1391329
TGGGGGTGGTCACAGCTTTT
N/A
N/A
126808
126827
3628





1391330
CTGCTAGAGGTCATCTTCGG
N/A
N/A
118735
118754
3629





1391332
GCTGCTCACTCATTTCCACC
5434
5453
115312
115331
3630





1391333
GTTGCTGCTCACTCATTTCC
5437
5456
115315
115334
3631





1391334
AGCCTGCTAGAGGTCATCTT
N/A
N/A
118738
118757
3632





1391335
TGGCATCTTGTTTTACCACC
N/A
N/A
 35335
 35354
3633





1391336
AAGTGCATTACTTTTTACAA
N/A
N/A
 62841
 62860
3634





1391337
GGTGGTCACAGCTTTTATTT
N/A
N/A
126804
126823
3635





1391338
ATGGCATCTTGTTTTACCAC
N/A
N/A
 35336
 35355
3636





1391339
CTCATTTCCACCTTCAGCTG
5426
5445
115304
115323
3637





1391340
TGTAGGTTTTTTGCTTTGAT
N/A
N/A
 60037
 60056
3638





1391341
GTTTTACCACCCATGCTGGA
N/A
N/A
 35326
 35345
3639





1391342
CCTGCTAGAGGTCATCTTCG
N/A
N/A
118736
118755
3640





1391343
TAGGTTTTTTGCTTTGATTT
N/A
N/A
 60035
 60054
3641





1391344
TTTTTTGCTTTGATTTTTAC
N/A
N/A
 60031
 60050
3642





1391345
CAGCCTGCTAGAGGTCATCT
N/A
N/A
118739
118758
3643





1391346
GGGGGTGGTCACAGCTTTTA
N/A
N/A
126807
126826
3644





1391347
GTAGGTTTTTTGCTTTGATT
N/A
N/A
 60036
 60055
3645





1391348
ACAGCTTTTATTTCCATACA
N/A
N/A
126797
126816
3646





1391349
CACAGCCTGCTAGAGGTCAT
N/A
N/A
118741
118760
3647





1391351
GCTCACTCATTTCCACCTTC
5431
5450
115309
115328
3648





1391352
GTGGTCACAGCTTTTATTTC
N/A
N/A
126803
126822
3649





1391353
TGTTGCTGCTCACTCATTTC
5438
5457
115316
115335
3650





1391355
TTGTTTTACCACCCATGCTG
N/A
N/A
 35328
 35347
3651





1391356
ATGTTGCTGCTCACTCATTT
5439
5458
115317
115336
3652





1391357
TTTCCACCTTCAGCTGTTTT
5422
5441
115300
115319
3653





1391358
AGAGGTCATCTTCGGTCATG
N/A
N/A
118730
118749
3654





1391359
GGTTTTTTGCTTTGATTTTT
N/A
N/A
 60033
 60052
3655





1391360
AGGTTTTTTGCTTTGATTTT
N/A
N/A
 60034
 60053
3656





1391361
GCTAGAGGTCATCTTCGGTC
N/A
N/A
118733
118752
3657





1391362
GGTCATCTTCGGTCATGTGA
N/A
N/A
118727
118746
3658





1391363
TGCTAGAGGTCATCTTCGGT
N/A
N/A
118734
118753
3659





1391364
TCACTCATTTCCACCTTCAG
5429
5448
115307
115326
3660





1391365
CATTTCCACCTTCAGCTGTT
5424
5443
115302
115321
3661





1391366
TCCACCTTCAGCTGTTTTGT
5420
5439
115298
115317
3662





1391367
GGGTGGTCACAGCTTTTATT
N/A
N/A
126805
126824
3663





1391368
AGTGCATTACTTTTTACAAT
N/A
N/A
 62840
 62859
3664





1394315
GTTAGTTTTCCTTTTATATT
N/A
N/A
117876
117895
3665





1394316
ACTTGGTTAGTTTTCCTTTT
N/A
N/A
117881
117900
3666





1394317
TCCTTTTATATTCATCAGAA
N/A
N/A
117868
117887
3667





1394318
TTCCTTTTATATTCATCAGA
N/A
N/A
117869
117888
3668





1394320
TTAGTTTTCCTTTTATATTC
N/A
N/A
117875
117894
3669





1394321
TAACTTGGTTAGTTTTCCTT
N/A
N/A
117883
117902
3670





1394323
AACTTGGTTAGTTTTCCTTT
N/A
N/A
117882
117901
3671





1394325
TTGGTTAGTTTTCCTTTTAT
N/A
N/A
117879
117898
3672





1394326
TAGTTTTCCTTTTATATTCA
N/A
N/A
117874
117893
3673





1394331
CTTGGTTAGTTTTCCTTTTA
N/A
N/A
117880
117899
3674





1394335
AGTTTTCCTTTTATATTCAT
N/A
N/A
117873
117892
3675





1394336
TTTCCTTTTATATTCATCAG
N/A
N/A
117870
117889
3676





1456397
ATATTTTCTCAACTTTAAAC
N/A
N/A
119644
119663
3677





1456398
CATATTTTCTCAACTTTAAA
N/A
N/A
119645
119664
3678





1456399
CCATATTTTCTCAACTTTAA
N/A
N/A
119646
119665
3679





1456400
AGCCATATTTTCTCAACTTT
N/A
N/A
119648
119667
3680





1456401
CAAGCCATATTTTCTCAACT
N/A
N/A
119650
119669
3681





1456402
ACAAGCCATATTTTCTCAAC
N/A
N/A
119651
119670
3682









The modified oligonucleotides in the table below are 5-10-5 MOE gapmers. The gapmers are 20 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmers have an internucleoside linkage motif of (from 5′ to 3′): sossssssssssssssoss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 70







5-10-5 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





1394439
GGTTAGTTTTCCTTTTATAT
N/A
N/A
117877
117896
2770





1394440
GCATTACTTTTTACAATGGA
N/A
N/A
 62837
 62856
3029





1394441
ACTCATTTCCACCTTCAGCT
5427
5446
115305
115324
2471





1394442
GCATCTTGTTTTACCACCCA
N/A
N/A
 35333
 35352
1208





1394443
GCTTTGATTTTTACCAGTTA
N/A
N/A
 60025
 60044
1502





1394444
GTCACAGCTTTTATTTCCAT
N/A
N/A
126800
126819
1652





1394445
CTAGAGGTCATCTTCGGTCA
N/A
N/A
118732
118751
2412









The modified oligonucleotides in the table below are 5-10-5 MOE gapmers. The gapmers are 20 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmers have an internucleoside linkage motif of (from 5′ to 3′): ssoosssssssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 71







5-10-5 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





1394446
CTAGAGGTCATCTTCGGTCA
N/A
N/A
118732
118751
2412





1394447
GGTTAGTTTTCCTTTTATAT
N/A
N/A
117877
117896
2770





1394448
GCTTTGATTTTTACCAGTTA
N/A
N/A
 60025
 60044
1502





1394449
ACTCATTTCCACCTTCAGCT
5427
5446
115305
115324
2471





1394450
GTCACAGCTTTTATTTCCAT
N/A
N/A
126800
126819
1652





1394451
GCATTACTTTTTACAATGGA
N/A
N/A
 62837
 62856
3029





1394452
GCATCTTGTTTTACCACCCA
N/A
N/A
 35333
 35352
1208









The modified oligonucleotides in the table below are 5-8-5 MOE gapmers. The gapmers are 18 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmers have an internucleoside linkage motif of (from 5′ to 3′): sooosssssssssooss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 72







5-8-5 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





1394418
TCACAGCTTTTATTTCCA
N/A
N/A
126801
126818
3683





1394419
TCATTTCCACCTTCAGCT
5427
5444
115305
115322
3684





1394420
ATCTTGTTTTACCACCCA
N/A
N/A
 35333
 35350
3685





1394421
GGTTAGTTTTCCTTTTAT
N/A
N/A
117879
117896
3686





1394422
GCATTACTTTTTACAATG
N/A
N/A
 62839
 62856
3687





1394423
GTCACAGCTTTTATTTCC
N/A
N/A
126802
126819
3688





1394424
CTCATTTCCACCTTCAGC
5428
5445
115306
115323
3689





1394425
CACAGCTTTTATTTCCAT
N/A
N/A
126800
126817
3690





1394427
CATCTTGTTTTACCACCC
N/A
N/A
 35334
 35351
3691





1394428
ATTACTTTTTACAATGGA
N/A
N/A
 62837
 62854
3692





1394429
AGAGGTCATCTTCGGTCA
N/A
N/A
118732
118749
3693





1394430
TTAGTTTTCCTTTTATAT
N/A
N/A
117877
117894
3694





1394431
TAGAGGTCATCTTCGGTC
N/A
N/A
118733
118750
3695





1394432
TTTGATTTTTACCAGTTA
N/A
N/A
 60025
 60042
3696





1394433
CATTACTTTTTACAATGG
N/A
N/A
 62838
 62855
3697





1394434
GTTAGTTTTCCTTTTATA
N/A
N/A
117878
117895
3698





1394437
GCATCTTGTTTTACCACC
N/A
N/A
 35335
 35352
3699





1419360
GGTCACAGCTTTTATTTC
N/A
N/A
126803
126820
3700





1419361
ACAGCTTTTATTTCCATA
N/A
N/A
126799
126816
3701





1419362
CAGCTTTTATTTCCATAC
N/A
N/A
126798
126815
3702





1419365
TGGTCACAGCTTTTATTT
N/A
N/A
126804
126821
3703





1419370
AGCTTTTATTTCCATACA
N/A
N/A
126797
126814
3704





1456411
CCATATTTTCTCAACTTT
N/A
N/A
119648
119665
3705





1456412
GCCATATTTTCTCAACTT
N/A
N/A
119649
119666
3706





1456413
CATATTTTCTCAACTTTA
N/A
N/A
119647
119664
3707









The modified oligonucleotides in the table below are 5-8-5 MOE gapmers. The gapmers are 18 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeddddddddeeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmers have an internucleoside linkage motif of (from 5′ to 3′): sossssssssssssoss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 73







5-8-5 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





1419374
GGTCACAGCTTTTATTTC
N/A
N/A
126803
126820
3700





1419375
ACAGCTTTTATTTCCATA
N/A
N/A
126799
126816
3701





1419376
CAGCTTTTATTTCCATAC
N/A
N/A
126798
126815
3702





1419379
TGGTCACAGCTTTTATTT
N/A
N/A
126804
126821
3703





1419380
CACAGCTTTTATTTCCAT
N/A
N/A
126800
126817
3690





1419383
GTCACAGCTTTTATTTCC
N/A
N/A
126802
126819
3688





1419384
AGCTTTTATTTCCATACA
N/A
N/A
126797
126814
3704









The modified oligonucleotides in the table below are 6-10-4 MOE gapmers. The gapmers are 20 nucleosides in length, wherein the sugar motif for the gapmers is (from 5′ to 3′): eeeeeeddddddddddeeee; wherein each “d” represents a 2′-β-D-deoxyribosyl sugar moiety, and each “e” represents a 2′-MOE sugar moiety. The gapmers have an internucleoside linkage motif of (from 5′ to 3′): sooooossssssssssoss; wherein each “s” represents a phosphorothioate internucleoside linkage, and each “o” represents a phosphodiester internucleoside linkage. Each cytosine residue is a 5-methylcytosine.









TABLE 74







6-10-4 MOE gapmers with mixed PO/PS internucleoside linkages complementary to


human HTT















SEQ
SEQ
SEQ ID
SEQ ID





ID No:
ID No:
No: 2
No: 2



Compound

1 Start
1 Stop
Start
Stop
SEQ


Number
Sequence (5′ to 3′)
Site
Site
Site
Site
ID NO.





1394343
ACTCATTTCCACCTTCAGCT
5427
5446
115305
115324
2471





1394344
GCATCTTGTTTTACCACCCA
N/A
N/A
 35333
 35352
1208





1394345
GTCACAGCTTTTATTTCCAT
N/A
N/A
126800
126819
1652





1394346
GCATTACTTTTTACAATGGA
N/A
N/A
 62837
 62856
3029





1394347
GCTTTGATTTTTACCAGTTA
N/A
N/A
 60025
 60044
1502





1394348
CTAGAGGTCATCTTCGGTCA
N/A
N/A
118732
118751
2412





1394349
GGTTAGTTTTCCTTTTATAT
N/A
N/A
117877
117896
2770





1394357
GGCATCTTGTTTTACCACCC
N/A
N/A
 35334
 35353
3624





1394358
TCTTGTTTTACCACCCATGC
N/A
N/A
 35330
 35349
3618





1394359
TGGCATCTTGTTTTACCACC
N/A
N/A
 35335
 35354
3633





1394360
ATCTTGTTTTACCACCCATG
N/A
N/A
 35331
 35350
3626





1394361
ATGGCATCTTGTTTTACCAC
N/A
N/A
 35336
 35355
3636





1394367
GGGTGGTCACAGCTTTTATT
N/A
N/A
126805
126824
3663





1394368
GGTGGTCACAGCTTTTATTT
N/A
N/A
126804
126823
3635





1394369
TTTGCTTTGATTTTTACCAG
N/A
N/A
 60028
 60047
3603





1394370
TAGAGGTCATCTTCGGTCAT
N/A
N/A
118731
118750
3612





1394371
CACAGCTTTTATTTCCATAC
N/A
N/A
126798
126817
3619





1394372
CTGCTAGAGGTCATCTTCGG
N/A
N/A
118735
118754
3629





1394373
GCTCACTCATTTCCACCTTC
5431
5450
115309
115328
3648





1394374
GAGGTCATCTTCGGTCATGT
N/A
N/A
118729
118748
3617





1394375
TGCATTACTTTTTACAATGG
N/A
N/A
 62838
 62857
3623





1394376
GCTAGAGGTCATCTTCGGTC
N/A
N/A
118733
118752
3657





1394377
CTCATTTCCACCTTCAGCTG
5426
5445
115304
115323
3637





1394378
ACAGCTTTTATTTCCATACA
N/A
N/A
126797
126816
3646





1394379
TGGTCACAGCTTTTATTTCC
N/A
N/A
126802
126821
3608





1394380
TGCTAGAGGTCATCTTCGGT
N/A
N/A
118734
118753
3659





1394381
AGTGCATTACTTTTTACAAT
N/A
N/A
 62840
 62859
3664





1394382
CTCACTCATTTCCACCTTCA
5430
5449
115308
115327
3594





1394383
AGAGGTCATCTTCGGTCATG
N/A
N/A
118730
118749
3654





1394384
ATTACTTTTTACAATGGACA
N/A
N/A
 62835
 62854
3622





1394385
TACTTTTTACAATGGACAGT
N/A
N/A
 62833
 62852
3620





1394386
TCATTTCCACCTTCAGCTGT
5425
5444
115303
115322
3597





1394387
GTGGTCACAGCTTTTATTTC
N/A
N/A
126803
126822
3649





1394388
TTTTTGCTTTGATTTTTACC
N/A
N/A
 60030
 60049
3605





1394389
TTTTGCTTTGATTTTTACCA
N/A
N/A
 60029
 60048
3599





1394390
TGCTTTGATTTTTACCAGTT
N/A
N/A
 60026
 60045
3615





1394391
CTTTGATTTTTACCAGTTAA
N/A
N/A
 60024
 60043
3596





1394392
TCACTCATTTCCACCTTCAG
5429
5448
115307
115326
3660





1394393
GTGCATTACTTTTTACAATG
N/A
N/A
 62839
 62858
3610





1394394
CATTTCCACCTTCAGCTGTT
5424
5443
115302
115321
3661





1394395
TTACTTTTTACAATGGACAG
N/A
N/A
 62834
 62853
3627





1394396
TTGCTTTGATTTTTACCAGT
N/A
N/A
 60027
 60046
3625





1394397
ACTTGGTTAGTTTTCCTTTT
N/A
N/A
117881
117900
3666





1394398
GTTAGTTTTCCTTTTATATT
N/A
N/A
117876
117895
3665





1394399
TAGTTTTCCTTTTATATTCA
N/A
N/A
117874
117893
3673





1394400
TTAGTTTTCCTTTTATATTC
N/A
N/A
117875
117894
3669





1394401
CTTGGTTAGTTTTCCTTTTA
N/A
N/A
117880
117899
3674





1394402
TTGGTTAGTTTTCCTTTTAT
N/A
N/A
117879
117898
3672





1456403
ATATTTTCTCAACTTTAAAC
N/A
N/A
119644
119663
3677





1456404
CATATTTTCTCAACTTTAAA
N/A
N/A
119645
119664
3678





1456405
CCATATTTTCTCAACTTTAA
N/A
N/A
119646
119665
3679





1456406
GCCATATTTTCTCAACTTTA
N/A
N/A
119647
119666
 940





1456407
AGCCATATTTTCTCAACTTT
N/A
N/A
119648
119667
3680





1456408
AAGCCATATTTTCTCAACTT
N/A
N/A
119649
119668
 919





1456409
CAAGCCATATTTTCTCAACT
N/A
N/A
119650
119669
3681





1456410
ACAAGCCATATTTTCTCAAC
N/A
N/A
119651
119670
3682









Example 7: Tolerability of Modified Oligonucleotides Complementary to Human HTT in Wild-Type Mice, 3 Hour Study

Modified oligonucleotides described above were tested in wild-type female C57/Bl6 mice to assess the tolerability of the oligonucleotides. Wild-type female C57/Bl6 mice each received a single ICV dose of modified oligonucleotide at 700 μg. Each treatment group consisted of 4 mice. A group of 4 mice received PBS as a negative control for each experiment. Each experiment is identified in separate tables below. At 3 hours post-injection, mice were evaluated according to seven different criteria. The criteria are (1) the mouse was bright, alert, and responsive; (2) the mouse was standing or hunched without stimuli; (3) the mouse showed any movement without stimuli; (4) the mouse demonstrated forward movement after it was lifted; (5) the mouse demonstrated any movement after it was lifted; (6) the mouse responded to tail pinching; (7) regular breathing. For each of the 7 criteria, a mouse was given a sub-score of 0 if it met the criteria and 1 if it did not (the functional observational battery score or FOB). After all 7 criteria were evaluated, the scores were summed for each mouse and averaged within each treatment group. The results are presented in the tables below.









TABLE 75







Tolerability scores in mice (n = 4) at 700 μg dose










Compound No.
3 hr. FOB







PBS
0.00



1314967
1.00



1314979
2.00



1315343
1.00



1315578
1.00



1316218
1.50



1316639
1.00



1317084
0.00

















TABLE 76







Tolerability scores in mice (n = 4) at 700 μg dose










Compound No.
3 hr. FOB







PBS
0.00



1314723
0.00



1315073
0.00



1315119
4.50



1315147
6.75



1315214
0.00



1315813
0.00



1391301
0.00



1391310
1.25



1391320
0.00



1394347
0.50



1394371
0.00



1394375
6.50



1394378
0.00



1394401
4.25



1394402
0.00



1394418
0.00



1394421
1.00



1394440
5.25



1394444
1.25



1419386
0.00

















TABLE 77







Tolerability scores in mice (n = 4) at 700 μg dose










Compound No.
3 hr. FOB







PBS
0.00



1314833
3.00



1391348
1.00



1394393
3.00










Example 8: Tolerability of Modified Oligonucleotides Complementary to Human HTT in Rats, 3-Hour Study

Modified oligonucleotides described above were tested in rats to assess the tolerability of the oligonucleotides. Sprague Dawley rats each received a single intrathecal (IT) dose of 3 mg of modified oligonucleotide listed in the tables below. Each treatment group consisted of 3-4 rats. A group of 3-4 rats received PBS as a negative control. Each experiment is identified in separate tables below. At 3 hours post-injection, movement in 7 different parts of the body were evaluated for each rat. The 7 body parts are (1) the rat's tail; (2) the rat's posterior posture; (3) the rat's hind limbs; (4) the rat's hind paws; (5) the rat's forepaws; (6) the rat's anterior posture; (7) the rat's head. For each of the 7 different body parts, each rat was given a sub-score of 0 if the body part was moving or 1 if the body part was paralyzed (the functional observational battery score or FOB). After each of the 7 body parts were evaluated, the sub-scores were summed for each rat and then averaged for each group. For example, if a rat's tail, head, and all other evaluated body parts were moving 3 hours after the 3 mg IT dose, it would get a summed score of 0. If another rat was not moving its tail 3 hours after the 3 mg IT dose but all other evaluated body parts were moving, it would receive a score of 1. Results are presented as the average score for each treatment group.









TABLE 78







Tolerability scores in rats (n = 4) at 3 mg dose










Compound No.
3 hr. FOB







PBS
0.25



388241
2.75



1315343
0.50



1315578
0.50



1316218
1.50



1316639
2.25



1317084
0.25

















TABLE 79







Tolerability scores in rats (n = 4) at 3 mg dose










Compound No.
3 hr. FOB







PBS
0.00



1314979
2.50



1391333
2.00



1391353
4.00



1394371
0.00



1394378
0.00



1394379
2.00



1394392
2.00

















TABLE 80







Tolerability scores in rats (n = 4) at 3 mg dose










Compound No.
3 hr. FOB














PBS
0.25



1314967
2.25



1315073
1.00



1315214
3.00‡



1315813
1.50‡



1316392
0.50



1318641
3.00



1391293
0.25



1391320
0.00



1394375
3.25



1394401
2.50



1394402
1.75



1394439
4.00



1394440
3.50







‡indicates that fewer than 4 samples were available













TABLE 81







Tolerability scores in rats (n = 3) at 3 mg dose










Compound No.
3 hr. FOB














PBS
0.00



1314833
0.33



1316061
0.67



1316846
0.33



1391301
2.33



1391310
0.67



1391348
0.00



1391351
3.00



1391364
2.00



1394336
0.33



1394346
1.33



1394347
3.00‡



1394348
2.67



1394393
2.67



1394443
2.67



1394444
5.00



1394445
3.00



1394446
1.67



1394450
1.33







‡indicates that fewer than 3 samples were available













TABLE 82







Tolerability scores in rats (n = 3) at 3 mg dose










Compound No.
3 hr. FOB














PBS
0.00



1314723
0.00



1315077
1.33



1315119
1.00



1315147
0.00



1315321
2.00



1315833
3.00‡



1315921
3.33



1318605
4.00



1391314
4.00



1391356
4.00



1394418
0.00



1394421
1.67



1394441
0.00



1419386
0.00



1419392
0.33







‡indicates that fewer than 3 samples were available













TABLE 83







Tolerability scores in rats (n = 3) at 3 mg dose










Compound No.
3 hr. FOB







PBS
0.00



1419387
0.00



1419404
0.00



1419415
0.33



1419420
2.67

















TABLE 84







Tolerability scores in rats (n = 3) at 3 mg dose










Compound No.
3 hr. FOB







PBS
0.00



1316689
1.00



1456397
0.33



1456398
0.00



1456399
0.33



1456400
1.00



1456401
0.00



1456402
0.00



1456403
0.00



1456404
0.00



1456405
0.00



1456406
0.67



1456407
1.00



1456408
1.00



1456409
0.00



1456410
0.00



1456411
1.33



1456412
2.00



1456413
3.33










Example 9: Activity of Modified Oligonucleotides Complementary to Human HTT in Transgenic Mice

Transgenic mice expressing human HTT (The Jackson Laboratory, Stock No: 008197) were used to test activity of modified oligonucleotides described above.


Treatment

Transgenic mice were divided into groups of 3-4 mice each. Each mouse received a single ICV bolus of 200-300 μg of modified oligonucleotide as indicated in the tables below. A group of 3-4 mice received PBS as a negative control.


RNA Analysis

Two weeks post treatment, mice were sacrificed, and RNA was extracted from cortical brain tissue and spinal cord for RTPCR analysis to measure amount of HTT RNA using human primer probe set RTS2617 (described herein above). Results are presented as percent human HTT relative to PBS control, normalized to mouse cyclophilin A. Mouse cyclophilin A RNA was amplified using mouse prime probe set m_cyclo24 (forward sequence TCGCCGCTTGCTGCA, designated herein as SEQ ID NO: 20; reverse sequence ATCGGCCGTGATGTCGA, designated herein as SEQ ID NO: 21; probe sequence CCATGGTCAACCCCACCGTGTTC, designated herein as SEQ ID NO: 22).


Each experiment is identified in separate tables below. N.D. in the tables below refers to instances where the value was Not Defined.









TABLE 85







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex





PBS
100 
100 


1314810
47
52


1314849
54
52


1314935
24
43


1314999
32
44


1315234
64
72


1315340
57
57


1315621
44
46


1315781
61
75


1316535
69
34


1316768
50
36


1316788
60
31


1317090
20
25


1317204
 49‡
 73‡


1317227
41
42





‡indicates that fewer than 4 samples were available













TABLE 86







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex





PBS
100 
100 


1314540
62
44


1314541
51
22


1314544
73
40


1314606
78
34


1314708
74
40


1314723
35
19


1314891
74
31


1314967
35
 5


1314979
 46‡
 8‡


1315041
54
25


1315089
49
20


1315143
49
42


1315321
53
18


1315343
32
 9


1315405
75
35


1315578
46
10


1315652
67
28


1315698
 47‡
 44‡


1315702
 48‡
 21‡


1315797
65
29


1315877
42
25


1316169
44
25


1316218
27
 9


1316235
64
34


1316392
34
14


1316435
83
33


1316762
81
50


1316766
91
57


1316803
53
22


1316846
39
16


1317084
29
11


1317136
48
29


1317229
32
20





‡indicates that fewer than 4 samples were available













TABLE 87







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex





PBS
100 
100 


1314685
60
23


1314789
59
39


1314813
125 
74


1314824
87
51


1314845
51
28


1314848
57
25


1314916
75
37


1314943
64
52


1315119
39
19


1315294
 92‡
 68‡


1315309
36
31


1315408
72
45


1315584
84
45


1315672
54
21


1315722
60
45


1315974
78
45


1316062
54
43


1316154
59
74


1316185
134 
94


1316254
97
42


1316310
 66‡
 20‡


1316324
68
54


1316414
57
28


1316604
96
69


1316614
63
34


1316716
74
65


1316775
48
45


1316858
61
88


1316936
39
54


1317017
28
33


1317031
36
27


1317128
63
58


1317205
57
39


1318725
99
86





‡indicates that fewer than 4 samples were available













TABLE 88







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


388241
44
20


1314635
56
68


1314647
66
68


1314833
29
16


1315027
41
48


1315039
35
47


1315214
26
12


1315501
68
61


1315813
29
14


1315833
51
19


1316545
56
30


1316620
48
35


1316722
45
29


1317164
41
20


1318569
38
28


1318621
54
42


1318675
42
27
















TABLE 89







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1314696
22
44


1314904
30
38


1315141
59
84


1315878
67
36


1315964
53
65


1316117
43
61


1316143
78
53


1316449
31
35


1316972
34
21


1318566
92
46


1318573
42
31


1318690
50
30


1318691
86
87


1318695
41
44


1318745
53
45


1318747
40
28
















TABLE 90







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1314526
121
159


1314549
74
56


1314870
107
107


1314905
54
100


1314966
59
79


1315056
46
51


1315074
28
43


1315083
60
35


1315137
68
122


1315341
20
39


1315425
83
165


1315817
49
63


1315867
32
49


1316312
33
46


1316563
42
41


1316621
33
40


1316802
30
23
















TABLE 91







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


388241
56
44


1314603
52
31


1314762
53
42


1314829
20
20


1314918
27
31


1314955
52
54


1315077
20
19


1315347
27
22


1315544
115
77


1315692
78
50


1315747
66
44


1315883
47
50


1315921
27
19


1315950
47
35


1316506
63
50


1316544
32
41


1316551
35
21


1316552
80
58


1316639
14
10


1316725
34
25


1317175
63
N.D.


1318657
88
N.D.


1318685
52
N.D.
















TABLE 92







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1314511
70
65


1315178
53
27


1315556
57
41


1316023
59
32


1316926
50
38


1317142
51
21


1318592
86
56


1318594
104
61


1318605
41
19


1318620
57
27


1318629
62
52


1318632
44
30


1318641
33
14


1318701
67
25


1318741
93
49
















TABLE 93







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1318708
24
66


1314771
49
49


1314828
67
47


1314920
34
27


1315482
45
38


1316232
48
49


1316400
26
28


1317236
34
35


1318652
64
47


1314487
50
61


1314650
51
37


1314678
47
24


1314815
53
49


1314996
48
48


1315014
29
32


1315123
35
27


1315147
28
18
















TABLE 94







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100 
100


388241
73
56


1315373
81
105


1315537
45
53


1315723
41
87


1315749
25
49


1315800
78
65


1315808
48
75


1315865
42
69


1315911
46
64


1316051
56
71


1316096
51
92


1316679
43
74


1316745
44
44


1317163
 40‡
102


1318586
39
42


1318623
86
63


1318715
90
77


1318742
83
67





‡indicates that fewer than 4 samples were available













TABLE 95







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1314592
29
40


1316811
40
61


1391295
45
62


1391298
51
37


1391303
46
50


1391305
47
46


1391309
70
92


1391315
44
43


1391319
37
44


1391325
28
33


1391326
54
59


1391327
37
36


1391335
32
29


1391338
45
55


1391341
61
119


1391355
74
70


1394344
21
21


1394347
17
17


1394357
29
23


1394358
50
53


1394359
18
30


1394360
40
38


1394361
29
38


1394369
32
43


1394388
40
31
















TABLE 96







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1314907
31
27


1391293
36
14


1391296
51
31


1391299
42
45


1391304
47
49


1391310
26
17


1391316
56
35


1391321
52
51


1391323
64
43


1391324
39
37


1391336
52
54


1391339
48
23


1391351
18
17


1391357
72
50


1391364
32
15


1391365
57
24


1391366
95
31


1391368
50
27


1394346
16
10


1394375
35
11


1394381
39
133


1394384
74
47


1394385
54
96
















TABLE 97







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1391292
25
32


1391301
38
16


1391306
87
70


1391312
54
39


1391314
89
19


1391318
65
73


1391322
66
69


1391330
75
90


1391332
27
23


1391333
15
3


1391334
84
97


1391342
58
52


1391353
14
5


1391356
20
19


1391358
65
71


1391361
57
54


1391362
46
48


1391363
81
96


1394343
50
46


1394373
23
23


1394377
56
45


1394382
45
20


1394386
66
42
















TABLE 98







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1315073
25
11


1316061
27
18


1391291
81
112


1391294
86
87


1391328
56
36


1391345
82
83


1391349
60
77


1394348
31
23


1394390
36
24


1394391
39
24


1394392
27
10


1394393
31
18


1394394
58
40


1394395
132
55


1394396
51
24


1394440
39
13


1394441
55
19


1394442
30
24


1394443
42
25


1394448
83
37


1394449
32
24


1394451
33
26


1394452
29
22
















TABLE 99







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1315670
40
39


1391308
28
31


1391320
23
14


1391337
74
67


1391348
30
16


1391352
70
48


1391367
73
32


1394345
17
25


1394367
78
42


1394368
54
26


1394370
56
28


1394371
26
10


1394372
81
34


1394374
92
36


1394376
54
31


1394378
28
10


1394379
27
6


1394380
62
23


1394383
66
30


1394387
61
23


1394444
61
15


1394445
74
29


1394446
74
26
















TABLE 100







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1394315
51
29


1394316
47
21


1394317
56
45


1394318
41
23


1394320
86
78


1394321
68
74


1394323
58
96


1394325
76
58


1394326
49
54


1394331
50
44


1394335
86
41


1394336
48
14


1394349
25
37


1394397
36
27


1394398
56
77


1394399
46
55


1394400
43
50


1394401
33
14


1394402
22
8


1394439
20
10


1394447
34
41


1394450
38
25
















TABLE 101







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1314899
66
43


1315156
76
38


1315412
78
47


1315754
49
31


1315794
75
54


1316106
67
44


1316193
68
29


1316421
79
57


1316500
68
59


1316984
74
57
















TABLE 102







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1394429
82
80


1394430
67
78


1394431
67
59


1394432
90
77


1394433
78
77


1394434
82
80


1394437
34
34


1316648
44
21
















TABLE 103







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100 
100


1316776
47
27


1391297
137 
82


1391302
112 
64


1391307
64
31


1391311
86
45


1391313
123 
84


1391329
126 
64


1391340
85
24


1391343
65
48


1391344
123 
51


1391346
145 
52


1391347
 81‡
72


1391359
83
40


1391360
124 
58


1394389
58
23


1394418
49
19


1394419
86
37


1394420
96
50


1394421
43
17


1394422
180 
64


1394423
40
25


1394424
59
37


1394425
32
22


1394427
25
37


1394428
72
80





‡indicates that fewer than 4 samples were available













TABLE 104







Reduction of human HTT RNA in transgenic mice (n = 3)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex





PBS
100
100 


388241
 86§
 36§


1419360
 39‡
 24‡


1419361
 90
61


1419362
108
39


1419365
 136‡
 58‡


1419370
 67
57


1419374
164
84


1419375
115
41


1419376
 82
23


1419379
100
52


1419380
102
39


1419383
128
34


1419384
133
56


1419386
 29
12


1419389
 82
39


1419392
 84
10


1419394
133
29


1419406
 73
56


1419407
157
136 


1419409
182
132 


1419414
135
47


1419419
134
71





‡indicates that fewer than 3 samples were available


§indicates that 4 samples were available













TABLE 105







Reduction of human HTT RNA in transgenic mice (n = 3)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1419387
32
18


1419390
75
49


1419391
90
81


1419395
69
90


1419396
109
97


1419397
47
30


1419399
72
22


1419400
70
68


1419402
57
57


1419403
82
75


1419405
59
52


1419416
56
25


1419417
56
56


1419421
103
96


1419423
97
89


1419425
83
94
















TABLE 106







Reduction of human HTT RNA in transgenic mice (n = 3)


treated with 200 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex












PBS
100
100


1419388
50
44


1419393
45
25


1419398
93
67


1419401
62
75


1419404
15
12


1419408
120
54


1419410
127
47


1419412
75
47


1419413
132
51


1419415
28
17


1419418
52
28


1419420
12
6


1419422
124
73


1419424
41
50
















TABLE 107







Reduction of human HTT RNA in transgenic mice (n = 4)


treated with 300 μg of modified oligonucleotide










HTT RNA (% control)










Compound ID
Spinal Cord
Cortex





PBS
100 
100 


1316689
45
27


1456397
107 
90


1456398
101 
107 


1456399
 61‡
 18‡


1456400
42
12


1456401
49
23


1456402
62
31


1456403
79
60


1456404
 58‡
 51‡


1456405
47
14


1456406
20
6


1456407
29
13


1456408
32
18


1456409
 42‡
 17‡


1456410
 42‡
 28‡


1456411
58
25


1456412
40
22


1456413
67
47





‡indicates that fewer than 4 samples were available






Example 10: Potency of Modified Oligonucleotides Complementary to Human HTT RNA in Transgenic Mice

Modified oligonucleotides described above were tested in human HTT transgenic mice (described herein above).


Treatment

Human HTT transgenic mice were divided into groups of 4 mice each. Each mouse received a single ICV bolus of modified oligonucleotide at the doses indicated in tables below. A group of 3-4 mice received PBS as a negative control.


RNA Analysis

Two weeks post treatment, mice were sacrificed, and RNA was extracted from the spinal cord and cortex for quantitative real-time RTPCR analysis of RNA expression of HTT using primer probe set RTS2617 (described herein above). Results are presented as percent human HTT RNA relative to PBS control, adjusted to mouse cyclophilin A (described herein above).


Dose response and tissue concentration response data were analyzed using Microsoft Excel (v14.4) and GraphPad Prism software (v 8.2.0, San Diego, CA). ED50 values were calculated from log transformed dose and individual animal HTT RNA levels using the built in GraphPad formula “log(agonist) vs. response—Find ECanything”, with the following constraints: bottom >0, top=100, and F=50 for ED50.


Each experiment is identified in separate tables below. As shown in the tables below, treatment with modified oligonucleotides resulted in dose-responsive reduction of HTT RNA in comparison to the PBS control. N.D. in the tables below refers to instances where the value was Not Defined.









TABLE 108







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)















PBS
N/A
100
N/A
100
N/A


388241
10
85
185.4
62
31.1



30
85

56



100
55

30



300
44

26


444652
10
89
277.5
133
186.1



30
95

71



100
56

54



300
53

48
















TABLE 109







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


1314967
3
82
45.5
118 
108.5



10
61

95



30
61

87



100
36

52



300
31

20


1314979
3
147 
73.6
82
119.2



10
133 

73



30
98

78



100
97

51



300
103 

35


1315343
3
163 
124.7
95
49.1



10
102 

67



30
80

65



100
49

37



300
35

19


1315578
3
113 
156.7
110 
70.6



10
58

103 



30
96

69



100
69

28



300
26

34


1316218
3
68
106.0
130 
34.3



10
111‡

99



30
71

42



100
33

25



300
 26‡

 22‡


1394379
3
111 
73.6
121 
37.9



10
84

97



30
56

55



100
54

20



300
18

 5





‡indicates that fewer than 4 samples were available













TABLE 110







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


388241
3
60
16.9
75
44.4



10
61

87



30
50

51



100
 24‡

 34‡



300
28

24


444652
3
57
41.1
75
47.5



10
82

77



30
47

41



100
40

52



300
34

27


627246
3
61
13.1
77
74.3



10
42

69



30
50

57



100
46

43



300
30

41





‡indicates that fewer than 4 samples were available













TABLE 111







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


627246
3
75
N.D.
84
166.9



10
68

89



30
 81‡

 81‡



100
61

52



300
42

46



700
35

26


1314723
3
90
44.6
69
12.2



10
80

56



30
55

38



100
27

16



300
28

 6



700
13

 4


1315073
3
108 
177.1
87
36.1



10
186 

67



30
123 

62



100
45

31



300
34

 9



700
31

 8





‡indicates that fewer than 4 samples were available













TABLE 112







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


388241
3
141 
438.0
109 
107.8



10
87

83



30
84

82



100
70

47



300
58

28



700
 45‡

 18‡


1316218
3
102 
157.9
63
30.7



10
118 

83



30
52

52



100
44

30



300
48

17



700
34

13


1391320
3
231 
352.6
82
40.2



10
177 

82



30
136 

55



100
99

31



300
43

17



700
36

 6


1394347
3
69
1475.0
79
19.1



10
97

64



30
62

39



100
42

20



300
60

16



700
 65‡

 15‡





‡indicates that fewer than 4 samples were available













TABLE 113







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


1315813
3
83
63.3
85
38.4



10
71

76



30
67

50



100
44

 28‡



300
28

28



700
18

 9


1391301
3
70
14.0
40
2.2



10
45

42



30
43

37



100
33

12



300
28

12



700
 16‡

 8‡


1394371
3
63
24.5
50
6.7



10
74

62



30
49

27



100
26

16



300
26

13



700
15

 6


1394375
3
68
34.2
107 
40.5



10
65

73



30
44

59



100
34

18



300
44

26



700
29

12


1394378
3
73
12.8
96
26.7



10
42

66



30
38

37



100
35

36



300
25

13



700
14

 6


1394401
3
91
24.5
134 
64.8



10
45

105 



30
45

47



100
28

42



300
36

23



700
17

11





‡indicates that fewer than 4 samples were available













TABLE 114







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)















PBS
N/A
100
N/A
100
N/A


1315214
3
136
111.4
40
2.4



10
107

35



30
75

18



100
49

20



300
30

9



700
N.D.

N.D.


1394401
3
103
182.9
85
40.8



10
94

65



30
86

56



100
57

48



300
39

11



700
28

12


1394402
3
72
55.4
61
8.4



10
85

39



30
60

51



100
31

23



300
31

9



700
25

7


1394440
3
86
43.8
74
18.5



10
70

62



30
58

44



100
36

23



300
23

16



700
15

9


1394444
3
145
244.3
37
N.D.



10
145

43



30
78

38



100
55

27



300
42

15



700
41

9
















TABLE 115







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


1315578
3
114 
111.4
116 
70.0



10
85

80



30
 76‡

 72‡



100
56

40



300
49

19



700
39

10





‡indicates that fewer than 4 samples were available













TABLE 116







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


1314833
3
55
2.3
56
4.1



10
26

39



30
 33‡

 26‡



100
17

18



300
18

17



700
16

 9


1315921
3
77
17.2
116 
46.8



10
41

57



30
49

67



100
35

22



300
24

33



700
 13‡

 9‡


1394346
3
57
2.5
51
4.7



10
21

35



30
24

56



100
20

15



300
12

11



700
11

 8


1394393
3
84
21.4
125 
55.0



10
50

65



30
44

52



100
30

44



300
25

25



700
 18‡

 11‡





‡indicates that fewer than 4 samples were available













TABLE 117







Reduction of human HTT RNA in transgenic mice










Spinal Cord
Cortex













Dose
HTT RNA
ED50
HTT RNA
ED50


Compound ID
(μg)
(% control)
(μg)
(% control)
(μg)





PBS
N/A
100 
N/A
100 
N/A


1315077
3
120 
116.5
293 
136.6



10
67

100 



30
60

104 



100
42

53



300
36

21



700
43

26


1315119
3
43
N.D.
149 
358.3



10
31

177 



30
29

173 



100
22

131 



300
33

58



700
19

 21‡


1391348
3
95
359.2
264 
507.1



10
88

122 



30
88

119 



100
 61‡

111‡



300
53

67



700
42

38


1394418
3
127 
143.0
62
42.7



10
76

65



30
82

57



100
73

29



300
17

55



700
 16‡

 22‡





‡indicates that fewer than 4 samples were available






Example 11: Activity of Modified Oligonucleotides Complementary to Human HTT RNA in Transgenic Mice, Multiple Doses

Modified oligonucleotides described above were tested in human HTT transgenic mice (described herein above).


Human HTT transgenic mice were divided into groups of 4 mice each. Each mouse received a single ICV bolus of modified oligonucleotide at the various doses indicated in the table below. A group of 4 mice received PBS as a negative control.


Two weeks post treatment, mice were sacrificed, and RNA was extracted from cortical brain tissue and spinal cord for quantitative real-time RT-PCR analysis to measure the amount of HTT RNA using human primer probe set RTS2617 (described herein above) which detects total HTT RNA levels. HTT RNA levels were normalized to mouse cyclophilin A. Mouse cyclophilin A was amplified using primer probe set m_cyclo24 (described herein above). Results are presented as percent human HTT RNA relative to the amount of HTT RNA in PBS treated animals, (% control). ED50s were calculated in Prism using nonlinear fit with variable slope (four parameter), top constrained to 100% (or 1), bottom constrained to 0. Y=Bottom+(Top−Bottom)/(1+(IC50/X){circumflex over ( )}HillSlope).









TABLE 118







Reduction of human HTT RNA in transgenic mice









Compound
Dose
HTT (% control)












No.
(ug)
Cortex
ED50 (ug)
Spinal Cord
ED50 (ug)





PBS

100 

100 



443139
3
106 
96
117 
288



10
 87‡

 98‡



30
65

84



100
50

65



300
31

54


1394371
3
100 
43
76
16



10
74

59



30
67

36



100
25

25



300
 9

16





‡Indicates less than 4 samples were available





Claims
  • 1.-56. (canceled)
  • 57. An oligomeric compound comprising a modified oligonucleotide according to the following chemical notation:
  • 58. (canceled)
  • 59. (canceled)
  • 60. The oligomeric compound of claim 57, wherein the modified oligonucleotide is a pharmaceutically acceptable salt.
  • 61. The oligomeric compound of claim 60, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.
  • 62. The oligomeric compound of claim 57, wherein the oligomeric compound is a singled-stranded oligomeric compound.
  • 63. A modified oligonucleotide according to the following chemical structure:
  • 64. The modified oligonucleotide of claim 63, which is a pharmaceutically acceptable salt comprising one or more cations selected from sodium, potassium, calcium, and magnesium.
  • 65. A modified oligonucleotide according to the following chemical structure:
  • 66.-79. (canceled)
  • 80. A population of oligomeric compounds of claim 57, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.
  • 81.-106. (canceled)
  • 107. A pharmaceutical composition comprising the oligomeric compound of claim 57 and a pharmaceutically acceptable carrier or diluent.
  • 108. The pharmaceutical composition of claim 107, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 109. The pharmaceutical composition of claim 108, wherein the pharmaceutical composition consists essentially of the oligomeric compound and PBS.
  • 110. The pharmaceutical composition of claim 108, wherein the pharmaceutical composition consists essentially of the oligomeric compound and aCSF.
  • 111.-128. (canceled)
  • 129. A pharmaceutical composition comprising the modified oligonucleotide of claim 63; and a pharmaceutically acceptable carrier or diluent.
  • 130. The pharmaceutical composition of claim 129, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 131. The pharmaceutical composition of claim 130, wherein the pharmaceutical composition consists essentially of the modified oligonucleotide and PBS.
  • 132. The pharmaceutical composition of claim 130, wherein the pharmaceutical composition consists essentially of the modified oligonucleotide and aCSF.
  • 133. A pharmaceutical composition comprising the modified oligonucleotide of claim 64; and a pharmaceutically acceptable carrier or diluent.
  • 134. The pharmaceutical composition of claim 133, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 135. The pharmaceutical composition of claim 134, wherein the pharmaceutical composition consists essentially of the modified oligonucleotide and PBS.
  • 136. The pharmaceutical composition of claim 134, wherein the pharmaceutical composition consists essentially of the modified oligonucleotide and aCSF.
  • 137. A pharmaceutical composition comprising the modified oligonucleotide of claim 65; and a pharmaceutically acceptable carrier or diluent.
  • 138. The pharmaceutical composition of claim 137, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 139. The pharmaceutical composition of claim 138, wherein the pharmaceutical composition consists essentially of the modified oligonucleotide and PBS.
  • 140. The pharmaceutical composition of claim 138, wherein the pharmaceutical composition consists essentially of the modified oligonucleotide and aCSF.
  • 141. A population of modified oligonucleotides of claim 63, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.
  • 142. A population of modified oligonucleotides of claim 64, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.
  • 143. A population of modified oligonucleotides of claim 65, wherein all of the phosphorothioate internucleoside linkages of the modified oligonucleotide are stereorandom.
  • 144. A pharmaceutical composition comprising the population of oligomeric compounds of claim 80; and a pharmaceutically acceptable carrier or diluent.
  • 145. The pharmaceutical composition of claim 144, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 146. A pharmaceutical composition comprising the population of modified oligonucleotides of claim 141; and a pharmaceutically acceptable carrier or diluent.
  • 147. The pharmaceutical composition of claim 146, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 148. A pharmaceutical composition comprising the population of modified oligonucleotides of claim 142; and a pharmaceutically acceptable carrier or diluent.
  • 149. The pharmaceutical composition of claim 148, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
  • 150. A pharmaceutical composition comprising the population of modified oligonucleotides of claim 143; and a pharmaceutically acceptable carrier or diluent.
  • 151. The pharmaceutical composition of claim 150, wherein the pharmaceutically acceptable diluent comprises phosphate buffered saline (PBS) or artificial cerebrospinal fluid (aCSF).
PCT Information
Filing Document Filing Date Country Kind
PCT/US2022/014231 1/28/2022 WO
Provisional Applications (1)
Number Date Country
63143686 Jan 2021 US