G-quadruplex-containing antisense oligonucleotides

Abstract

The present invention relates to conjugates comprising (a) an antisense oligonucleotide (ASO) and (b) at least one G-quadruplex structure, wherein the ASO and the at least one G-quadruplex structure are heterologous to each other. The G-quadruplex of the conjugate may be further conjugated with ligands or functional moieties for addressable delivery and enhanced properties including potency and therapeutic index. Further encompassed are such conjugates for use as a medicament, a method of modulating the stability, translation, splicing, cleavage, or activity of a target nucleic acid molecule using such conjugates, and use of G-quadruplex in stabilizing antisense oligonucleotides.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This application makes reference to and claims the benefit of priority of the Singapore Patent Application No. 10201603451U filed on 29 Apr. 2016, the content of which is incorporated herein by reference for all purposes, including an incorporation of any element or part of the description, claims or drawings not contained herein and referred to in Rule 20.5(a) of the PCT, pursuant to Rule 4.18 of the PCT.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 690148_549USPC_SEQUENCE_LISTING.txt. The text file is 23 KB was created on Aug. 19, 2020, and is being submitted electronically via EFS-Web.

FIELD OF THE INVENTION

The present invention relates to the field of oligonucleotide therapeutics, in particular to the use of antisense oligonucleotides containing G-quadruplex structures, which can be further conjugated with ligands or functional moieties for addressable delivery and enhanced properties including potency and therapeutic index.

BACKGROUND OF THE INVENTION

Antisense technology utilizes the complementary hybridization of an antisense oligonucleotide (ASO) to modulate the amount, activity, or function of the target RNA. ASO can bind to regulatory elements on a pre-mRNA or mRNA and alter the post-transcriptional control or translational profile of the target (FIG. 1A).

The sequence specificity of ASO to the target RNA renders them excellent agents for the selective knockdown of any gene for which the pathological basis is known. With the advent of genomic-based screening, genetic association studies should lead to the discovery of novel gene targets, alone or in combination, for the treatment of various pathologies. Since ASO operates at the genetic level, this further allows it to address gene targets with “undruggable” proteins, which are refractory to small molecule or antibody binding due to a lack of druggable features or inaccessible intracellular localization.

Natural oligonucleotides (DNA or RNA) have a limited half-life in the circulation due to the ubiquitous presence of native nucleases in the body. This severely limits the therapeutic potential of natural ASO compounds. To overcome this handicap, extensive chemical modifications of the nucleotide building block have been investigated. These include modifications of the phosphodiester group, sugar moiety, and nitrogenous base, or even wholesale substitution of the backbone by nucleotide analogues such as phosphorodiamidate morpholino oligos (PMO) or peptide nucleic acids (PNA).

The most widely adopted modification is the phosphorothioate (PS) backbone, which involves substitution of one of the two non-bridging phosphate (PO) oxygen atoms by a sulfur. PS modification is typically applied uniformly across ASO compounds to improve their nuclease resistance. Moreover, the PS backbone leads to enhanced serum albumin binding of ASO, thus reducing their renal clearance and consequently prolonging their circulation time.

Another common modification is the bridged nucleic acid (BNA) analogue including locked nucleic acid (LNA) and constrained ethyl (cEt). BNA is composed of a sugar that is conformationally constrained at the 2′ and 4′ positions through a covalent linkage, which predisposes it into an RNA-like C3′-endo puckering. LNA incorporation within ASO leads to a stronger binding affinity with the RNA target (2 to 5° C. increase in melting temperature with each LNA nucleotide substitution), hence greatly enhancing the potency of the ASO. The enhanced potency allows much lower doses of systemic ASO to be administered, thus improving the therapeutic index of the oligo. However, such modifications have a drawback of being incompatible with RNase H cleavage of the RNA target. This issue was adequately addressed by the “gapmer” design, which places these nucleotide analogues at the two flanking ends of a middle gap that is made up of DNA units. In this manner, an ASO gapmer is bestowed with improved nuclease resistance and binding affinity for the target RNA, yet still allows for RNase H cleavage of the bound RNA partner within the gap. Additionally, the “mixmer” design wherein nucleotide analogues are interspersed between DNA units, as well as fully chemically modified ASO, have also been employed to inhibit translation initiation or progression on mRNA, or to alter the splicing profile of pre-mRNA.

However, despite the progress, there still remains a considerable need in the art for innovations that overcome the limitations of existing techniques. These include the delivery of ASO to the target organ and tissue type (with minimal off-site accumulation), as well as its release into the correct cellular compartment (cytoplasm or nucleus) from endosomal vesicles.

SUMMARY OF THE INVENTION

The present invention satisfies the aforementioned need by providing novel G-quadruplex-containing conjugates.

In a first aspect, the present invention provides a conjugate comprising or consisting of (a) an antisense oligonucleotide (ASO) and (b) at least one G-quadruplex structure, wherein the ASO and the at least one G-quadruplex structure are heterologous to each other.

In various embodiments, the ASO is at least 5, preferably up to 50, most preferably between 12 to 20 nucleotides in length.

In various embodiments, the ASO is chemically modified.

In various embodiments, the ASO is modified by phosphorothioate (PS), 2′-O-methyl (2′-OMe), 2′-fluoro (2′-F), 2′-methyoxyethyl (2′-MOE), locked nucleic acid (LNA), constrained ethyl (cEt), tricyclo-DNA (tcDNA), phosphorodiamidate morpholino oligo (PMO), or peptide nucleic acid (PNA), or a combination thereof.

In various embodiments, the ASO adopts a gapmer design.

In various embodiments, the ASO adopts a mixmer design.

In various embodiments, the conjugate comprises (a) one G-quadruplex structure 5′ to the ASO, (b) one G-quadruplex structure 3′ to the ASO, or (c) both.

In various embodiments, wherein the at least one G-quadruplex structure comprises

(a) a nucleic acid molecule comprising the nucleic acid sequence (g)_w(n)_a(g)_x(n)_b(g)_y(n)_c(g)_z, wherein g and n are natural or chemical analogues of guanine nucleobase and any nucleobase respectively, w, x, y, z are independently of each other integers of at least 0, a, b, c are independently of each other integers of at least 0, and the sum of integers w, x, y, z is at least 8;

(b) four nucleic acid molecules wherein each of said molecules comprises a sequence of (g), wherein z is an integer of at least 2; or

(c) two nucleic acid molecules wherein each of said molecules comprises a sequence of (g)_y(n)_b(g)_z, wherein b is an integer of at least 0, y and z are independently of each other integers of at least 0, and the sum of integers y and z is at least 4.

In various embodiments, the nucleic acid molecule comprises the nucleic acid sequence (g)_w(n)_a(g)_x((n)_b(g)_y(n)_c(g)_z wherein w, x, y, z are independently of each other integers of at least 3 and a, b, c are independently of each other integers of at least 1.

In various embodiments, the at least one G-quadruplex structure is chemically modified.

In various embodiments, the at least one G-quadruplex structure is chemically modified by phosphorothioate (PS), 2′-O-methyl (2′-OMe), 2′-fluoro (2′-F), 2′-methyoxyethyl (2′-MOE), locked nucleic acid (LNA), constrained ethyl (cEt), tricyclo-DNA (tcDNA), phosphorodiamidate morpholino oligo (PMO), or peptide nucleic acid (PNA), or a combination thereof.

In various embodiments, the loops of the at least one G-quadruplex structure comprise non-nucleosidic analogues without a base.

In various embodiments, the conjugate disclosed herein further comprises a linker connecting the at least one G-quadruplex structure to the ASO.

In various embodiments, the linker is composed of unmodified nucleotides.

In various embodiments, the linker is chemically modified.

In various embodiments, the linker is modified by phosphorothioate (PS), 2′-O-methyl (2′-OMe), 2′-fluoro (2′-F), 2′-methyoxyethyl (2′-MOE), locked nucleic acid (LNA), constrained ethyl (cEt), tricyclo-DNA (tcDNA), phosphorodiamidate morpholino oligo (PMO), or peptide nucleic acid (PNA), or a combination thereof.

In various embodiments, the linker comprises a reducible linkage (including but not limited to disulfide), an acid-labile linkage (including but not limited to acetal, ester, and hydrazone), or a protease-labile linkage (including but not limited to cathepsin and furin cleavage site).

In various embodiments, the linker is connected to a phosphate or phosphate analogue, sugar, or base on the G-tetrad core or loop of the at least one G-quadruplex structure.

In various embodiments, the linker is connected to a phosphate or phosphate analogue, sugar, or base on the ASO.

In various embodiments, the at least one G-quadruplex structure and the ASO are connected across the backbone, in the form of a contiguous nucleotide sequence.

In various embodiments, the conjugate further comprises single or multiple ligands or functional moieties conjugated to the at least one G-quadruplex structure.

In various embodiments, the ligand or functional moiety is selected from the group consisting of small molecules (including but not limited to sorafenib and vismodegib), carbohydrates (including but not limited to glucose, mannose, N-acetyl galactosamine (GalNAc), and N-acetyl glucosamine (GlcNAc)), vitamins (including but not limited to retinoid, thiamine, riboflavin, biotin, folate, cholecalciferol, and tocopherol), lipids (including but not limited to cholesterol, palmitate, stearate, and anandamide), aptamers (including but not limited to thrombin-binding aptamer), peptides, proteins, antibodies, fluorescent labels, and radiolabel tracers (including but not limited to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA)).

In various embodiments, the ligand or functional moiety is connected to a phosphate or phosphate analogue, sugar, base, or non-nucleosidic analogue on the G-tetrad core or loop of the at least one G-quadruplex structure.

In various embodiments, the ASO is complementary to a portion of a DNA, pre-mRNA, mRNA, regulatory RNA, or non-coding RNA.

In a second aspect, the invention is directed to the conjugate disclosed herein for use as a medicament.

In various embodiments, the conjugate is for use in the prevention and treatment of diseases, disorders, and conditions, including but not limited to cancer or chronic symptoms.

In a third aspect, the invention encompasses a method of modulating the stability, translation, splicing, cleavage, or activity of a target nucleic acid molecule, comprising contacting the target nucleic acid molecule with a conjugate disclosed herein having an ASO complementary to a portion of the target nucleic acid molecule.

In various embodiments, the target nucleic acid molecule is a DNA, pre-mRNA, mRNA, regulatory RNA, or non-coding RNA.

In a fourth aspect, the conjugate of the present invention is employed as a selective probe for imaging or diagnostic purposes.

In a final aspect, the invention concerns use of the G-quadruplex disclosed herein in stabilizing the ASO disclosed herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention will be better understood with reference to the detailed description when considered in conjunction with the non-limiting examples and the accompanying drawings.

FIG. 1 shows: (a) ASO binding to RNA target based on complementary hybridization, leading to translational blockage, alternative splicing, or RNase H degradation of the RNA. (b) Schematic diagram of a structure-enhanced antisense oligo (SEA oligo), with the ASO connected to a G-quadruplex structure through a linker. (c) Structural model showing the hybridization of SEA oligo with a target RNA. (d) Schematic diagram showing the various constructs of SEA oligo and their binding of the RNA target.

FIG. 2 shows schematic diagrams of G-quadruplexes and different sites of conjugations. FIG. 2-I: (a) Chemical structure and schematic representation of a G-tetrad. B) Different folding topologies adopted by G-quadruplex (G4) forming sequences. C) Possible sites of conjugation on the G4 core and the loops. D) Non-limiting examples of ligands and biomolecules that may be attached onto a G4 scaffold for enhanced delivery of ASO. FIG. 2-II: Non-limiting examples of ligands and nucleotide analogues that have been incorporated in the A) core and B) loop of G4.

FIG. 3 shows nuclease resistance of SEA oligo. FIG. 3-I: Nuclease resistivity assay of different G4 scaffolds. A) Schematic diagram of G4s with various folding topology and sequence origin. Guanine in syn and anti configuration, and cytosine are shown in white, grey, and black, respectively. B) Denaturing PAGE images of G4s (2 pmol) following incubation in human serum type AB for various time intervals; FIG. 3-II: comparative denaturing PAGE images of A) conventional antisense oligonucleotides (ASO) versus B) structure-enhanced antisense oligo (SEA oligo) following incubation in human serum type AB for various time intervals. Constructs with phosphate backbone and phosphorothioate backbone are indicated with subscript O and S respectively.

FIG. 4 shows compatibility of SEA oligos with RNase H enzyme degradation of target RNA. FIG. 4-I: RNase H assay of conventional ASO versus SEA oligo. A) Schematic representation of RNase H mode of action. B) Denaturing PAGE image of RNase H treated ASO and SEA oligo. FIG. 4-II: denaturing PAGE images demonstrating RNase H compatibility of SEA oligo with single G4 attachment (middle and right) in comparison with conventional ASO (left). ASO and SEA oligo were each hybridized with 2 pmol 5′ FAM-labelled RNA to form RNA/DNA heteroduplex with A) 5′ RNA overhang; B) 3′ RNA overhang, and treated with RNase H at 37° C. for 1 hour. FIG. 4-III: denaturing PAGE images demonstrating RNase H compatibility of SEA oligo (right) with double G4 attachments in comparison with conventional ASO (left). ASO and SEA oligo were each hybridized with 2 pmol 5′ FAM-labelled RNA to form RNA/DNA heteroduplex with 5′ and 3′ RNA overhang, and treated with RNase H at 37° C. for 1 hour.

FIG. 5 shows enhanced cellular uptake of G-quadruplex structures that are conjugated with lipids and lipid-soluble moieties. A) Comparative fluorescence-activated cells sorting (FACS) analysis of uptake of oligonucleotides by HeLa cells at 24 h—top: G4; bottom: G4 with internal cholesterol modifier (G4-iChol), untreated control (UTC). B) Time course of oligonucleotide uptake by HeLa cells at 37° C. Oligonucleotides screened are G4 (square), G4 with internal cholesterol modifier (G4-iChol, star), G4 with internal tocopherol modifier (G4-iToc, triangle) and G4 with 5′ stearyl modifier (Stea-G4, circle). C) Measurement of STAT3 gene knockdown in HeLa cells following 24 h treatment with 10 nM of the respective oligonucleotides pre-mixed in Lipofectamine® RNAiMAX.

FIG. 6 shows STAT3 gene knockdown by control ASO gapmer, G4-conjugated ASO gapmer (SEA003), peptide (GFWFG)-conjugated ASO gapmer (ASO-Pep1), single (SEA004-iPep1) and double (SEA005-2iPep1) peptide (GFWFG)-conjugated SEA oligo. HeLa cells were transfected with 10 nM of the respective oligonucleotides pre-mixed in Lipofectamine® RNAiMAX.

FIG. 7 shows the various combinations that single and multiple ligands can be conjugated onto a G4 structure. FIG. 7-I: Single or multiple ligands can be conjugated onto the G-tetrad core or loops in multiple combinations. FIG. 7-II: 1D imino (left) and aromatic (right) proton NMR spectra of (A) T95-2T, (B) T95-2T(GalNAc-15), (C) T95-2T(GalNAc-17), (D) T95-2T(GalNAc-16,17), and (E) T95-2T(GalNAc-15,16,17). Peaks corresponding to the N-acetyl amide proton of GalNAc are labeled with asterisks. Schematic illustrating the number of conjugated GalNAc units are shown on the right.

DETAILED DESCRIPTION OF THE INVENTION

The following detailed description refers to, by way of illustration, specific details and embodiments in which the invention may be practiced. These embodiments are described in sufficient detail to enable those skilled in the art to practice the invention. Other embodiments may be utilized and structural, and logical changes may be made without departing from the scope of the invention. The various embodiments are not necessarily mutually exclusive, as some embodiments can be combined with one or more other embodiments to form new embodiments.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control.

The objective of the present invention is to provide improved antisense technologies.

To this end, in a first aspect, the present invention provides a conjugate comprising, consisting essentially of, or consisting of (a) an antisense oligonucleotide (ASO) and (b) at least one G-quadruplex (G4) structure, wherein the ASO and the at least one G-quadruplex structure are heterologous to each other (FIGS. 1B & 1C are exemplary and non-limiting schematic diagrams illustrating such conjugates). The conjugate is henceforth denoted as structure-enhanced antisense oligo (SEA oligo).

The term “antisense oligonucleotide” or “ASO” is used broadly herein and encompasses a single-stranded oligomer comprising ribonucleotides, deoxyribonucleotides, modified ribonucleotides, modified deoxyribonucleotides or a combination thereof that is complementary to a portion of a target nucleic acid molecule. The target nucleic acid molecule of the ASO of the present invention may be a DNA, pre-mRNA, mRNA, regulatory RNA, or non-coding RNA.

Without wishing to be bound to any theory, the ASO binds to the target nucleic acid molecule through sequence-specific complementary hybridization and modulates the stability, translation, splicing, cleavage, or activity thereof. Those skilled in the art will recognize that the exact length of the ASO and its degree of complementarity with its target nucleic acid molecule will depend upon the specific target selected, including but not limited to the sequence and base composition of the target.

The ASO of the present invention is at least 5, preferably up to 50 nucleotides in length, for example, 5 to 50 nucleotides in length, 8 to 40 nucleotides in length, 12 to 30 nucleotides in length, or 20 to 25 nucleotides in length. In preferred embodiments, the ASO is at least 12, preferably up to 30 nucleotides in length. In some embodiments, the ASO is about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In the most preferred embodiments, the ASO is between 12 to 20 nucleotides in length.

The ASO of the invention is constructed and arranged such as to bind selectively with the target nucleic acid molecule under physiological conditions, i.e., to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions. The term “physiological conditions” is to be understood as referring to the physicochemical conditions (temperature, pH, ionic strength, viscosity, and the like) present intracellularly or extracellularly.

The term “complementary” is used herein to describe a first nucleotide sequence in relation to a second nucleotide sequence and refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize to and form a duplex structure under physiological conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence. Such hybridization is ordinarily the result of base-specific hydrogen bonding between complementary strands, preferably to form Watson-Crick or Hoogsteen base pairs, although other modes of hydrogen bonding, as well as base stacking can also lead to hybridization and are also encompassed herein. However, in particular embodiments, “complementary” means hybridization of Watson-Crick base pairing only. “Complementary” sequences, as used herein, may also include or be formed entirely from base pairs formed from non-natural and modified nucleotides, insofar the above requirements with respect to their ability to hybridize are fulfilled.

The ASO of the invention does not necessarily have to be fully complementary to the target nucleic acid molecule and some mismatches therebetween may be tolerated, given that the ASO is at least partially or substantially complementary to the target nucleic acid molecule to hybridize thereto and form a stable hybrid under physiological conditions. For instance, in some embodiments, the ASO is at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%, or preferably 100% complementary to the target nucleic acid molecule, as calculated based on the length of the ASO. Complementarity can be determined by means known in the art, in particular alignment tools such as BLAST programs (basic local alignment search tools) and PowerBLAST programs.

The ASO of the present invention may be modified in part or in full, for example, by chemical analogues including but not limited to phosphorothioate (PS), 2′-O-methyl (2′-OMe), 2′-fluoro (2′-F), 2′-methyoxyethyl (2′-MOE), locked nucleic acid (LNA), constrained ethyl (cEt), tricyclo-DNA (tcDNA), phosphorodiamidate morpholino oligo (PMO), or peptide nucleic acid (PNA), or a combination thereof. In certain embodiments, the ASO adopts a gapmer design. In certain embodiments, the ASO adopts a mixmer design. In certain embodiments, the ASO is fully chemically modified. These chemical modifications may improve nuclease resistance of the ASO or binding affinity of the ASO for its intended RNA target. The design of an ASO adopting a “gapmer” design or a “mixmer” design is within the purview of one of skill in the art.

The term “G-quadruplex” as used herein refers to a four-stranded helical nucleic acid structure comprising multiple stacked G-tetrads (FIG. 2-IA), each of which consists of four guanine bases or chemical analogues of guanine that associate in a cyclical manner through Hoogsteen hydrogen bonds and may be further stabilized through coordination to a cation in the center. The body of stacked G-tetrads, comprising a total of 2 or more layers, is collectively referred to as the G-tetrad core. Each of the four guanine columns constituting the G-tetrad core can arise from a single (continuous column) or two (discontinuous column) separate guanine stretch/es. The G-quadruplex structure of the present invention is thus a robust four-stranded helical structure spontaneously formed by G-rich oligonucleotide sequences under physiological conditions. Said G-quadruplex structure has two major structural components, a four-stranded G-tetrad core and three intervening loops (FIG. 2I-C).

G-quadruplex structures are highly diverse with regards to their relative strand orientations and loop types (FIG. 2I-B), resulting in different topologies including (a) parallel-type in which four strands point in the same direction; (b) hybrid “3+1” type in which three strands point in one direction and the fourth strand points in the opposite one; (iii) antiparallel-type in which two strands point in one direction and two strands point in the opposite direction. These topologies lead to different structural molecular shapes, with various loops and grooves of different size and accessibility (Phan A. T., FEBS J. 2010, 277, 1107). The structural polymorphism of G-quadruplexes depends on their nucleotide sequences and the environmental conditions.

In various embodiments, the G-quadruplex structure comprises (a) a nucleic acid molecule comprising the nucleic acid sequence (g)_w(n)_a(g)_x((n)_b(g)_y(n)_c(g)_z, wherein w, x, y, z are independently of each other integers of at least 0, a,b,c are independently of each other integers of at least 0, and the sum of integers w, x, y, z is at least 8; (b) four nucleic acid molecules, wherein each of said molecules comprises a sequence of (g)_z, wherein z is an integer of at least 2; or (c) two nucleic acid molecules, wherein each of said molecules comprises a sequence of (g)_y(n)_b(g)_z wherein b is an integer of at least 0, y and z are independently of each other integers of at least 0, and the sum of integers y and z is at least 4. In various embodiments, the nucleic acid molecule comprises the nucleic acid sequence (g)_w(n)_a(g)_x((n)_b(g)_y(n)_c(g)_z, wherein w, x, y, z are independently of each other integers of at least 3 and a, b, c are independently of each other integers of at least 1. The term “g”, as used herein, relates to a guanine nucleobase or its chemical analogues. The term “n”, as used herein, relates to a nucleotide having a base that is selected from the group consisting of adenine, guanine, cytosine, uracil, and thymine, or their chemical analogues.

The G-tetrad core and loops of the G-quadruplex structure may be chemically modified in part or in full, for example, with chemical analogues including but not limited to, PS, 2′-OMe, 2′-F, 2′-MOE, LNA, cEt, tcDNA, PMO, and PNA, or a combination thereof. In certain embodiments, the loops may comprise non-nucleosidic analogues without a base. There is a diverse range of G-quadruplex topologies arising from the combinatorial arrangement of the core and loops (FIG. 2I-B).

In accordance with the present invention, the ASO and the at least one G-quadruplex structure are heterologous to each other, meaning that they are not found together in a cell in nature.

The conjugate of the present invention comprises at least one G-quadruplex structure under physiological conditions. The term “at least one”, as used herein particularly in relation to the G-quadruplex structure, relates to one or more, in particular 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In preferred embodiments, the conjugate comprises up to 4, preferably up to 3, more preferably 1 or 2 G-quadruplex structure/s. In the most preferred embodiments, the conjugate comprises (a) one G-quadruplex structure 5′ to the ASO, (b) one G-quadruplex structure 3′ to the ASO, or (c) both (FIG. 1D).

In various embodiments, the conjugate further comprises a linker connecting the at least one G-quadruplex structure to the ASO (FIG. 1B).

The linker may be cleavable or non-cleavable in nature. In certain embodiments, the linker may be a nucleotide or nucleotide analogue, and may be unmodified, chemically modified in part or in full, for example, with chemical analogues including but not limited to, PS, 2′-OMe, 2′-F, 2′-MOE, LNA, cEt, tcDNA, PMO, and PNA, or a combination thereof. In certain embodiments, the linker may comprise a reducible linkage (including but not limited to disulfide), an acid-labile linkage (including but not limited to acetal, ester, and hydrazone), or a protease-labile linkage (including but not limited to cathepsin and furin cleavage site). The attachment point of the linker on the G-quadruplex structure can be any part of the G-tetrad core or loop. In certain embodiments, the linker is connected to a phosphate or phosphate analogue on the G-tetrad core or loop. In certain embodiments, the linker is connected to the sugar on the G-tetrad core or loop. In certain embodiments, the linker is connected to the base on the G-tetrad core or loop. The attachment point of the linker on the ASO can be any part of the ASO, preferably on either one flanking end or both flanking ends of the ASO. In certain embodiments, the linker is connected to a phosphate or phosphate analogue on the ASO. In certain embodiments, the linker is connected to the sugar on the ASO. In certain embodiments, the linker is connected to the base on the ASO. In the preferred embodiments, the G-quadruplex structure and the ASO are connected across the backbone, in the form of a contiguous nucleotide sequence, which is compatible with the automated synthesis of oligonucleotides.

Targeted delivery of ASO to its desired site of action remains one of the major challenges of the field. This entails delivery of ASO to the target organ and tissue type (with minimal off-site accumulation), as well as its release into the correct cellular compartment (cytoplasm or nucleus) from endosomal vesicles, otherwise known as the functional uptake of the oligonucleotide. Various approaches have been employed to accomplish this goal, including the packaging of ASO within delivery vehicles (e.g. liposomal particles or cationic polymers). However, toxicity and off-target issues still hamper their widespread utility.

Another approach involves the use of ligand conjugates of ASO, which will be directed towards organs or tissues showing an overexpression of the native receptors for the ligands. Recent advances include the conjugation of multiple N-acetyl galactosamine (GalNAc) units onto ASO, which tremendously enhances their delivery to liver hepatocytes with an abundance of the cognate asialoglycoprotein receptors (ASGPR). Since internal modifications within ASO could interfere with target hybridization, ligand conjugation sites are largely restricted to the two flanking ends. In certain cases, single-ligand conjugates were shown to be insufficient to induce efficient uptake, necessitating the design of a sophisticated scaffold for the presentation of multiple ligands for receptor recognition. This complicates and limits the scalability between different receptor-ligand pairs. Nevertheless, following the same principle, myriad other ligands can be conjugated onto ASO to assist in their targeted delivery. These can range in size from simple ligands such as small molecules, carbohydrates, vitamins, lipids, and peptides, up to macromolecules including aptamers, proteins, and even antibodies (FIG. 2-ID).

In this context, the G-quadruplex structure of the conjugate of the invention may be further conjugated with single or multiple ligands or functional moieties in a controllable and modular fashion, leading to desirable traits including addressable delivery, enhanced potency, or additional functionality of the ASO. By the term “ligand” or “functional moiety”, as used herein, any chemical molecule or group is meant that can be attached to the G-quadruplex structure, including but not limited to small molecules, carbohydrates, vitamins, lipids, peptides, aptamers, proteins, antibodies, and detectable tags.

The ligands or functional moieties may be pre-conjugated onto phosphoramidites, which are the monomeric building blocks for the automated synthesis of oligonucleotides, and incorporated onto the oligonucleotide chain during automated synthesis, or they may be incorporated onto the G-quadruplex structure post-synthetically using complementary conjugation chemistry. The conjugation site may be any position on the nucleotide building block of the G-tetrad core (FIG. 2-IIA) and loop (FIG. 2-IIB). In certain embodiments, the ligand is conjugated onto the phosphate or phosphate analogue on the G-tetrad core or loop. In certain embodiments, the ligand is connected to the sugar on the G-tetrad core or loop. In certain embodiments, the ligand is connected to the base on the G-tetrad core of loop. In certain embodiments, the ligand is connected to a non-nucleosidic analogue. The ligands that may be conjugated include, but are not limited to, small molecules (including but not limited to sorafenib and vismodegib), carbohydrates (including but not limited to glucose, mannose, GalNAc, and GlcNAc), vitamins (including but not limited to retinoid, thiamine, riboflavin, biotin, folate, cholecalciferol, and tocopherol), lipids (including but not limited to cholesterol, palmitate, stearate, and anandamide), aptamers (including but not limited to thrombin-binding aptamer), peptides, proteins, antibodies, fluorescent labels, and radiolabel tracers (including but not limited to DOTA).

Without wishing to be bound to any particular theory, the presence of a G-quadruplex structure at either one end (5′ or 3′) or both ends (5′ and 3′) of the ASO is compatible with RNase H degradation of the bound RNA target of the ASO (FIG. 4). The conjugate of the present invention exhibits numerous advantages over traditional ASO design, including but not limited to increased nuclease resistance (FIG. 3) and enhanced gene knockdown activity of the ASO relative to the standard ASO.

In addition, the presence of a G-quadruplex structure in the conjugate described herein creates a hub for oligonucleotide modification which does not interfere with the hybridization of the ASO/target complex. Unlike the standard ASO which can only accommodate up to two bulky moieties, one on each terminus of the ASO, the conjugate of the present invention can potentially accommodate as many attachments as the participating nucleotides within the G-quadruplex without structural distortion to the resulting ASO/target complex. Modification of a G-quadruplex structure within the conjugate therefore provides a method for overcoming the numerous barriers to delivery currently impeding progression of antisense therapeutic development in the industry.

In a second aspect, the invention is directed to the conjugate disclosed herein for use as a medicament.

The conjugate of the present invention may be used as a medicament, preferably for the prevention or treatment of diseases, disorders, and conditions. The terms “disease”, “disorder”, or “condition” are used interchangeably herein, and refer to any alteration in state of the body or of some of the organs, interrupting or disturbing the performance of the functions or causing symptoms such as discomfort, dysfunction, distress, or even death to the person afflicted or those in contact with a person, in particular to cancer or chronic symptoms.

Cancers treatable by the conjugate of the invention include, but are not limited to, breast cancer, lung cancer, head and neck cancer, brain cancer, abdominal cancer, colon cancer, colorectal cancer, esophageal cancer, parapharyngeal cancer, gastrointestinal cancer, glioma, liver cancer, hepatocellular cancer, parotid gland cancer, tongue cancer, neuroblastoma, osteosarcoma, ovarian cancer, renal cancer, pancreatic cancer, retinoblastoma, cervical cancer, uterine cancer, Wilm's tumor, multiple myeloma, skin cancer, lymphoma, leukemia, blood cancer, anaplastic thyroid tumor, sarcoma of the skin, melanoma, adenocystic tumor, hepatoid tumor, non-small cell lung cancer, chondrosarcoma, pancreatic islet cell tumor, prostate cancer, ovarian cancer, gall bladder cancer, urinary bladder cancer, renal cancer, urinary tract cancer, vulvar cancer, vaginal cancer, anal cancer, penile cancer, or carcinomas including but not limited to squamous cell carcinoma of the head and neck, colorectal carcinoma, glioblastoma, cervical carcinoma, endometrial carcinoma, gastric carcinoma, pancreatic carcinoma, leiomyosarcoma and breast carcinoma. In some embodiments, cancers treatable by the conjugates provided herein are hematological cancers, including but not limited to multiple myeloma, acute myelogenous leukemia, acute/chronic lymphoblastic leukemia, hairy-cell leukemia, follicular lymphoma, plasmacytoma, diffuse large B-cell lymphoma, Hodgkin's lymphoma, Non-Hodgkin's lymphoma and the like. In some embodiments, cancers treated by the conjugates provided herein are carcinomas. In some embodiments, cancers treated by the conjugates provided herein are hematological cancers. In some embodiments, cancers treated by the conjugates provided herein are sarcomas. In some embodiments, cancers treated by the conjugates provided herein are solid tumors.

Chronic symptoms treatable by the conjugate of the invention include, but are not limited to, to the following list of diseases; acquired immune deficiency syndrome (AIDS), attention deficit/hyperactivity disorder (ADHD), allergies, amyotrophic lateral sclerosis (ALS), Alzheimer's disease, arthritis, asthma, behcet's syndrome, bipolar disorder, bronchitis, cancer, cardiomegaly, cardiomyopathy, Crohn's disease, chronic cough, chronic fatigue syndrome (CFS), chronic obstructive pulmonary disease (COPD), congestive heart failure, cystic fibrosis, depression, diabetes, drug addiction, alcohol addiction, emphysema, fibromyalgia, gastroesophageal reflux disease (GERD), gout, hansen's disease, hunter syndrome, Huntington's disease, hyperlipidemia, hypertension, Marfan syndrome, mesenteric lymphadenitis, multiple sclerosis, migraines, myelofibrosis, nephrotic syndrome, obesity, Parkinson's disease, pneumoconiosis (interstitial lung diseases), pulmonary edema, pulmonary fibrosis, pulmonary hypertension, reactive airway disease, sarcoidosis, scleroderma, systemic lupus erythematosus, and ulcerative colitis.

As long as the genetic cause of a disease, disorder, or condition is known, a conjugate specific for the RNA of the causal genes may be developed in accordance with the present invention. Off-target effects of such conjugates may be minimized by optimizing the sequence design of the ASO.

Prior to its use as a medicament or in the treatment of a disease, disorder, or condition, the conjugate of the invention may need to be formulated into a pharmaceutical composition further comprising a pharmaceutically acceptable carrier. The skilled artisan would also realize that proper formulation is dependent upon the route of administration selected for the specific application, and the proper route and mode of administering the conjugate of the invention to a subject should be determined on a case-by-case basis. Suitable pharmaceutical compositions and dosage forms may be prepared using conventional methods known to those in the field of pharmaceutical formulation and described in the pertinent texts and literature, e.g., in Remington: The Science and Practice of Pharmacy.

In a third aspect, the invention encompasses a method of modulating the stability, translation, splicing, cleavage, or activity of a target nucleic acid molecule, comprising contacting the target nucleic acid molecule with a conjugate of the invention having an ASO complementary to a portion of the target nucleic acid molecule.

In various embodiments, the target nucleic acid molecule is a DNA, pre-mRNA, mRNA, regulatory RNA, or non-coding RNA.

The term “modulate” as used herein is meant to refer to any changes in biological state, i.e. increasing, decreasing, and the like.

It should be noted that, counterintuitively, ASO may also upregulate translation of a target RNA. For example, it has been shown that ASO binding to upstream ORF (uORF) of a mRNA leads to increased protein translation. In addition, ASO binding to the ends of mRNA can slow down native mRNA degradation (U.S. Pat. No. 2015/0050738 A1), thereby leading to higher protein production. Therefore, without wishing to be bound to any theory, the conjugate of the invention may be used to modulate the stability, translation, splicing, cleavage, or activity of its target nucleic acid molecule, either positively or negatively.

In a fourth aspect, the conjugate of the present invention is employed as a selective probe for imaging or diagnostic purposes.

In a final aspect, the invention concerns use of the G-quadruplex disclosed herein in stabilizing the ASO disclosed herein.

The present invention is further illustrated by the following examples. However, it should be understood, that the invention is not limited to the exemplified embodiments.

EXAMPLES

Example 1: Nuclease Resistance of SEA Oligo

Nuclease digestion assay. Oligonucleotides labelled with 6-FAM on 5′ or 3′ end were dissolved in buffer containing 20 mM potassium phosphate (KPi), 70 mM KCl, pH 7.0 to 20 μM concentration, heated to 95° C. and cooled slowly to room temperature. Aliquots of human serum type AB were mixed with FAM-labelled oligonucleotides (final concentration 2 μM) and incubated at 37° C. for time points of 0, 0.5, 1, 3, 24, 48, 120 h. At each time interval, 2 μL aliquots were added to stop buffer containing 95% formamide, 50 mM EDTA, 0.025% SDS, chilled on ice for 15 min and subsequently heat-denatured at 95° C. for 1 h. The denatured oligonucleotide samples were resolved by denaturing polyacrylamide gel electrophoresis on gels containing 20% acrylamide, 7 M urea, 1× Tris-Borate-EDTA, and visualized through fluorescence gel imaging.

Due to its robust nature, said G-quadruplex structure affords the ASO further nuclease resistance (FIG. 3), beyond that which is provided through chemical modifications of the ASO.

TABLE 1-1
Table of constructs used in the nuclease digestion assay.
	Construct	SEQ ID	Sequence (5′ to 3′; X = DNA; * =
Name	typea	NO:	phosphorothioate bond;   = 6-FAM)
So	ssDNA PO	1	AACACGTCTATACGC
Ss	ssDNA PS	2	A*A*C*A*C*G*T*C*T*A*T*A*C*G*C
G4	3-layer	3	TTGGGTGGGTGGGTGGGT
	parallel G4
	PO
G41	3-layer	4	TGAGGGTGGTGAGGGTGGGGAAGG
	c-myc
	parallel G4
	PO
G42	6-layer	5	GGGGTGGGAGGAGGGT
	interlocked
	dimer G4 PO
HT1	3-layer HT	6	TTGGGTTAGGGTTAGGGTTAGGGA
	(3 + 1) form
	1 G4 PO
HT2	2-layer HT	7	GGGTTAGGGTTAGGGTTAGGGT
	basket type
	G4 PO
HT3	3-layer HT	8	AGGGCTAGGGCTAGGGCTAGGG
	chair-type
	G4 PO
ZG4	4-layer	9	TGGTGGTGGTGGTTGTGGTGGTGGTGTT
	left-handed
	G4 PO
G4o-So	G4 PO +	10	TTGGGTGGGTGGGTGGGTAACACGTCTATACGC
	ssDNA PO
G4s-Ss	G4 PS +	11	T*T*G*G*G*T*G*G*G*T*G*G*G*T*G*G*G*T*A*A*
	ssDNA PS		C*A*C*G*T*C*T*A*T*A*C*G*C
G4o-So-	G4 PO +	12	TTGGGTGGGTGGGTGGGTAACACGTCTATACGCTGGGTG
G4o	ssDNA PO +		GGTGGGTGGGT
	G4 PO
G4s-Ss-	G4 PS +	13	T*T*G*G*G*T*G*G*G*T*G*G*G*T*G*G*G*T*A*A*
G4s	ssDNA PS +		C*A*C*G*T*C*T*A*T*A*C*G*C*T*G*G*G*T*G*
	G4 PS		G*G*T*G*G*G*T*G*G*G*T
assDNA = single-stranded DNA; G4 = G-quadruplex; HT = human telomeric; PO = phosphate backbone; PS = phosphorothioate backbone

Example 2: Compatibility of SEA Oligo with RNase H Degradation of RNA Target

Preparation of RNA/DNA heteroduplex substrates. 200 nM of 5′ FAM-labelled RNA was incubated with 3-fold excess of DNA in buffer containing 20 mM Tris-HCl (pH 7.5), 20 mM KCl. The reaction was heated to 90° C. for 5 min and cooled slowly to 37° C. RNase inhibitor (0.6 U/4), and 1 mM MgCl₂ were subsequently added, and the reaction was incubated at 37° C. for 16 h.

RNase H assay of RNA/DNA heteroduplex substrates. E. coli RNase H enzymes were pre-incubated in buffer containing 20 mM Tris-HCl (pH 7.5), 20 mM KCl, 1 mM MgCl₂, 1 mM tris(2-carboxyethyl)phosphine hydrochloride at 37° C. for 5 min. 1 μL of heteroduplex substrate (final concentration of 100 nM) was digested with 0.5 U of RNase H at 37° C. for 1 h, and the reaction was terminated by the addition of 2× volume of stop buffer (95% formamide, 18 mM EDTA, 0.025% SDS) and heat-denatured at 95° C. for 5 min. The digested substrates were resolved in 20% denaturing polyacrylamide gel and visualized via fluorescence imaging.

The presence of said G-quadruplex structure at either one end (5′ or 3′) or both ends (5′ and 3′) of the ASO (FIG. 1D) is compatible with RNase H-mediated degradation of the bound RNA target of the ASO (FIG. 4).

TABLE 2-1
List of oligonucleotides utilized in RNA/DNA
heteroduplex formation.
	SEQ
	ID	Sequence (X = DNA, Y = RNA,
Name	NO:	= 6-FAM; | = base-pairing)
F-rA-	14	ACUGUGCGUGGAAAGCGUAG
20
dA6	15	CTACGC
dA8	16	CTACGCTT
dA10	17	CTACCGTTTC
dA12	18	CTACGCTTTCCA
dA14	19	CTACGCTTTCCACG
dA16	20	CTACGCTTTCCACGCA
dA18	21	CTACGCTTTCCACGCACA
dA20#	22	CTACGCTTTCCACGCAGAGT
d6A	23	CACAGT
d8A	24	CGCACAGT
d10A	25	CACGCACACT
d12A	26	TCCACGCACAGT
d14A	27	TTTCCACGCACAGT
d16A	28	GCTTTCCACGCACAGT
d18A	29	ACGCTTTCCACGCACAGT
d20A#	30	CTACGCTTTCCACGCACAGT
dA8i	31	TTTCCACG
dA10i	32	CTTTCCACGC
dA12i	33	GCTTTCCACGCA
dA14i	34	CGCTTTCCACGCAC
dA16i	35	ACGCTTTCCACGCACA
dA6-G4	36	TTGGGTGGGTGGGTGGGTTCTACGC
dA8-G4	37	TTGGGTGGGTGGGTGGGTTCTACGCTT
dA10-	38	TTGGGTGGGTGGGTGGGTTCTACGCTTTC
G4
dA12-	39	TTGGGTGGGTGGGTGGGTTCTACGCTTTCCA
G4
dA14-	40	TTGGGTGGGTGGGTGGGTTCTACGCTTTCCACG
G4
dA16-	41	TTGGGTGGGTGGGTGGGTTCTACGCTTTCCACGCA
G4
dA18-	42	TTGGGTGGGTGGGTGGGTTCTACGCTTTCCACGCACA
G4
dA20-	43	TTGGGTGGGTGGGTGGGTTCTACGCTTTCCACGCACAGT
G4&
dG4-6A	44	CACAGTTTGGGTGGGTGGGTGGGTT
dG4-8A	45	CGCACAGTTTGGGTGGGTGGGTGGGTT
dG4-	46	CACGCACAGTTTGGGTGGGTGGGTGGGTT
10A
dG4-	47	TCCACGCACAGTTTGGGTGGGTGGGTGGGTT
12A
dG4-	48	TTTCCACGCACAGTTTGGGTGGGTGGGTGGGTT
14A
dG4-	49	GCTTTCCACGCACAGTTTGGGTGGGTGGGTGGGTT
16A
dG4-	50	ACGCTTTCCACGCACAGTTTGGGTGGGTGGGTGGGTT
18A
dG4-	51	CTACGCTTTCCACGCACAGTTTGGGTGGGTGGGTGGGTT
20A$
dG4-A6	52	CTACGCTTGGGTGGGTGGGTGGGTT
dG4-	53	CTACGCTTTCTTGGGTGGGTGGGTGGGTT
A10
dG4-	54	CTACGCTTTCCACGTTGGGTGGGTGGGTGGGTT
A14
dG4-	55	CTACGCTTTCCACGCACATTGGGTGGGTGGGTGGGTT
A18
dG4-	56	CTACGCTTTCCACGCACAGTTTGGGTGGGTGGGTGGGTT
A20$
d6A-G4	57	TTGGGTGGGTGGGTGGGTTCACAGT
d10A-	58	TTGGGTGGGTGGGTGGGTTCACGCACAGT
G4
d14A-	59	TTGGGTGGGTGGGTGGGTTTTTCCACGCACAGT
G4
d18A-	60	TTGGGTGGGTGGGTGGGTTACGCTTTCCACGCACAGT
G4
d20A-	61	TTGGGTGGGTGGGTGGGTTCTACGCTTTCCACGCACAGT
G4&
dG4T-	62	TTGGGTGGGTGGGTGGGTTTTCCACGTTGGGTGGGTGGGTGGGT
A8i-
TTG4
dG4T-	63	TTGGGTGGGTGGGTGGGTCTTTCCACGCTTGGGTGGGTGGGTGGGT
A10i-
TTG4
dG4T-	64	TTGGGTGGGTGGGTGGGTGCTTTCCACGCATTGGGTGGGTGGGTGGGT
A12i-
TTG4
dG4T-	65	TTGGGTGGGTGGGTGGGTCGCTTTCCACGCACTTGGGTGGGTGGGTGGGT
A14i-
TTG4
dG4T-	66	TTGGGTGGGTGGGTGGGTACGCTTTCCACGCACATTGGGTGGGTGGGTGGGT
A16i-
TTG4
dG4-	67	TTGGGTGGGTGGGTGGGTTTCCACGGGGTGGGTGGGTGGGT
A8i-G4
dG4-	68	TTGGGTGGGTGGGTGGGCTTTCCACGCGGGTGGGTGGGTGGGT
A10i-
G4
dG4-	69	TTGGGTGGGTGGGTGGGGCTTTCCACGCAGGGTGGGTGGGTGGGT
A12i-
G4
dG4-	70	TTGGGTGGGTGGGTGGGCGCTTTCCACGCACGGGTGGGTGGGTGGGT
A14i-
G4
dG4-	71	TTGGGTGGGTGGGTGGGACGCTTTCCACGCACAGGGTGGGTGGGTGGGT
A16i-
G4
dG4T-	72	TTGGGTGGGTGGGTGGGTTTTCCACGTGGGTGGGTGGGTGGGT
A8i-
TG4
dG4T-	73	TTGGGTGGGTGGGTGGGTCTTTCCACGCTGGGTGGGTGGGTGGGT
A10i-
TG4
dG4T-	74	TTGGGTGGGTGGGTGGGTGCTTTCCACGCATGGGTGGGTGGGTGGGT
A12i-
TG4
dG4T-	75	TTGGGTGGGTGGGTGGGTCGCTTTCCACGCACTGGGTGGGTGGGTGGGT
A14i-
TG4
dG4T-	76	TTGGGTGGGTGGGTGGGTACGCTTTCCACGCACATGGGTGGGTGGGTGGGT
A16i-
TG4
dG4TT-	77	TTGGGTGGGTGGGTGGGTTTTTCCACGTTGGGTGGGTGGGTGGGT
A8i-
TTG4
dG4TT-	78	TTGGGTGGGTGGGTGGGTTCTTTCCACGCTTGGGTGGGTGGGTGGGT
A10i-
TTG4
dG4TT-	79	TTGGGTGGGTGGGTGGGTTGCTTTCCACGCATTGGGTGGGTGGGTGGGT
A12i-
TTG4
dG4TT-	80	TTGGGTGGGTGGGTGGGTTCGCTTTCCACGCACTTGGGTGGGTGGGTGGGT
A14i-
TTG4
dG4TT-	81	TTGGGTGGGTGGGTGGGTTACGCTTTCCACGCACATTGGGTGGGTGGGTGGGT
A16i-
TTG4
#dA20 and d20A; &dA20-G4 and A20-G4; $dG4-A20 and dG4-20A have the same sequence.

TABLE 2-2
List of constructs of RNA/DNA heteroduplex
with RNA overhang on 5′ or 3′.
     Sequence (X = DNA, Y = RNA,   = 6-FAM;
Name | = base-pairing)
A6   5′   ACUGUGCGUGGAAAGCGUAG
     ||||||
     3′                 CGCATC
A8   5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||
     3′               TTCGCATC
A10  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||
     3′             CTTTCGCATC
A12  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||
     3′           ACCTTTCGCATC
A14  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||
     3′         GCACCTTTCGCATC
A16  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||||
     3′       ACGCACCTTTCGCATC
A18  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||||||
     3′     ACACGCACCTTTCGCATC
A20# 5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||||||||
     3′   TGACACGCACCTTTCGCATC
A6-  5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||
     3′                 CGCATCTTGGGTGGGTGGGTGGGTT
A8-  5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||
     3′               TTCGCATCTTGGGTGGGTGGGTGGGTT
A10- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||
     3′             CTTTCGCATCTTGGGTGGGTGGGTGGGTT
A12- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||||
     3′           ACCTTTCGCATCTTGGGTGGGTGGGTGGGTT
A14- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||||||
     3′         GCACCTTTCGCATCTTGGGTGGGTGGGTGGGTT
A16- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||||||||
     3′       ACGCACCTTTCGCATCTTGGGTGGGTGGGTGGGTT
A18- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||||||||||
     3′     ACACGCACCTTTCGCATCTTGGGTGGGTGGGTGGGTT
A20- 5′   ACUGUGCGUGGAAAGCGUAG
G4&  ||||||||||||||||||||
     3′   TGACACGCACCTTTCGCATCTTGGGTGGGTGGGTGGGTT
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
A6   ||||||
     3′                 TTGGGTGGGTGGGTGGGTTCGCATC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
A10  ||||||||||
     3′              TGGGTGGGTGGGTGGGTTCTTTCGCATC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
A14  ||||||||||||||
     3′         TTGGGTGGGTGGGTGGGTTGCACCTTTCGCATC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
A18  ||||||||||||||||||
     3′     TTGGGTGGGTGGGTGGGTTACACGCACCTTTCGCATC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
A20$ ||||||||||||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCACCTTTCGCATC
6A   5′   ACUGUGCGUGGAAAGCGUAG
     ||||||
     3′   TGACAC
8A   5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||
     3′   TGACACGC
10A  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||
     3′   TGACACGCAC
12A  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||
     3′   TGACACGCACCT
14A  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||
     3′   TGACACGCACCTTT
16A  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||||
     3′   TGACACGCACCTTTCG
18A  5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||||||
     3′   TGACACGCACCTTTCGCA
20A# 5′   ACUGUGCGUGGAAAGCGUAG
     ||||||||||||||||||||
     3′   TGACACGCACCTTTCGCATC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
6A   ||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACAC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
8A   ||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
10A  ||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCAC
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
12A  ||||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCACCT
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
14A  ||||||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCACCTTT
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
16A  ||||||||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCACCTTTCG
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
18A  ||||||||||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCACCTTTCGCA
G4-  5′                      ACUGUGCGUGGAAAGCGUAG
20A$ ||||||||||||||||||||
     3′   TTGGGTGGGTGGGTGGGTTTGACACGCACCTTTCGCATC
6A-  5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||
     3′   TGACACTTGGGTGGGTGGGTGGGTT
10A- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||
     3′   TGACACGCACTTGGGTGGGTGGGTGGGTT
14A- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||||||
     3′   TGACACGCACCTTTTTGGGTGGGTGGGTGGGTT
18A- 5′   ACUGUGCGUGGAAAGCGUAG
G4   ||||||||||||||||||
     3′   TGACACGCACCTTTCGCATTGGGTGGGTGGGTGGGTT
20A- 5′   ACUGUGCGUGGAAAGCGUAG
G4&  ||||||||||||||||||||
     3′   TGACACGCACCTTTCGCATCTTGGGTGGGTGGGTGGGTT
#A20 and 20A; &A20 G4 and A20-G4; $G4-A20 and G4-20A are the same construct.

TABLE 2-3
List of RNA/DNA heteroduplex with RNA overhang on 5′ and 3′.
Name      Sequence (X = DNA, Y = RNA,   = 6-FAM; | = base-pairing)
A8i       5′   ACUGUGCGUGGAAAGCGUAG
          ||||||||
          3′         GCACCTTT
A10i      5′   ACUGUGCGUGGAAAGCGUAG
          ||||||||||
          3′        CGCACCTTTC
A12i      5′   ACUGUGCGUGGAAAGCGUAG
          ||||||||||||
          3′       ACGCACCTTTCG
A14i      5′   ACUGUGCGUGGAAAGCGUAG
          ||||||||||||||
          3′      CACGCACCTTTCGC
A16i      5′   ACUGUGCGUGGAAAGCGUAG
          ||||||||||||||||
          3′     ACACGCACCTTTCGCA
G4T-A8i-  5′                  ACUGUGCGUGGAAAGCGUAG
TTG4      ||||||||
          3′     TGGGTGGGTGGGTGGGGTTGCACCTTTTGGGTGGGTGGGTGGGTT
G4T-A10i- 5′                  ACUGUGCGUGGAAAGCGUAG
TTG4      ||||||||||
          3′    TGGGTGGGTGGGTGGGGTTCGCACCTTTCTGGGTGGGTGGGTGGGTT
G4T-A12i- 5′                  ACUGUGCGUGGAAAGCGUAG
TTG4      ||||||||||||
          3′   TGGGTGGGTGGGTGGGGTTACGCACCTTTCGTGGGTGGGTGGGTGGGTT
G4T-A14i- 5′                  ACUGUGCGUGGAAAGCGUAG
TTG4      |||||||||||||
          3′  TGGGTGGGTGGGTGGGGTTCACGCACCTTTCGCTGGGTGGGTGGGTGGGTT
G4T-A16i- 5′                  ACUGUGCGUGGAAAGCGUAG
TTG4      ||||||||||||||||
          3′ TGGGTGGGTGGGTGGGGTTACACGCACCTTTCGCATGGGTGGGTGGGTGGGTT
G4-A8i-G4 5′                  ACUGUGCGUGGAAAGCGUAG
          ||||||||
          3′       TGGGTGGGTGGGTGGGGGCACCTTTGGGTGGGTGGGTGGGTT
G4-A10i-  5′                  ACUGUGCGUGGAAAGCGUAG
G4        ||||||||||
          3′      TGGGTGGGTGGGTGGGGCGCACCTTTCGGGTGGGTGGGTGGGTT
G4-A12i-  5′                  ACUGUGCGUGGAAAGCGUAG
G4        ||||||||||||
          3′     TGGGTGGGTGGGTGGGGACGCACCTTTCGGGGTGGGTGGGTGGGTT
G4-A14i-  5′                  ACUGUGCGUGGAAAGCGUAG
G4        ||||||||||||||
          3′   MTGGGTGGGTGGGTGGGTCACGCACCTTTCGCGGGTGGGTGGGTGGGTT
G4-A16i-  5′                  ACUGUGCGUGGAAAGCGUAG
G4        ||||||||||||||||
          3′   TGGGTGGGTGGGTGGGGACACGCACCTTTCGCAGGGTGGGTGGGTGGGTT
G4T-A8i-  5′                  ACUGUGCGUGGAAAGCGUAG
TG4       |||||||||
          3′      TGGGTGGGTGGGTGGGGTGCACCTTTTGGGTGGGTGGGTGGGTT
G4T-A10i- 5′                  ACUGUGCGUGGAAAGCGUAG
TG4       ||||||||||
          3′     TGGGTGGGTGGGTGGGGTCGCACCTTTCTGGGTGGGTGGGTGGGTT
G4T-A12i- 5′                  ACUGUGCGUGGAAAGCGUAG
TG4       ||||||||||||
          3′    TGGGTGGGTGGGTGGGGTACGCACCTTTCGTGGGTGGGTGGGTGGGTT
G4T-A14i- 5′                  ACUGUGCGUGGAAAGCGUAG
TG4       ||||||||||||||
          3′   TGGGTGGGTGGGTGGGGTCACGCACCTTTCGCTGGGTGGGTGGGTGGGTT
G4T-A16i- 5′                  ACUGUGCGUGGAAAGCGUAG
TG4       ||||||||||||||||
          3′  TGGGTGGGTGGGTGGGGTACACGCACCTTTCGCATGGGTGGGTGGGTGGGTT
G4TT-A8i- 5′                  ACUGUGCGUGGAAAGCGUAG
TTG4      ||||||||
          3′     TGGGTGGGTGGGTGGGGTTGCACCTTTTTGGGTGGGTGGGTGGGTT
G4TT-     5′                  ACUGUGCGUGGAAAGCGUAG
A10i-TTG4 ||||||||||
          3′    TGGGTGGGTGGGTGGGGTTCGCACCTTTCTTGGGTGGGTGGGTGGGTT
G4TT-     5′                  ACUGUGCGUGGAAAGCGUAG
A12i-TTG4 ||||||||||||
          3′   TGGGTGGGTGGGTGGGGTTACGCACCTTTCGTTGGGTGGGTGGGTGGGTT
G4TT-     5′                  ACUGUGCGUGGAAAGCGUAG
A14i-TTG4 ||||||||||||||
          3′  TGGGTGGGTGGGTGGGGTTCACGCACCTTTCGCTTGGGTGGGTGGGTGGGTT
G4TT-     5′                  ACUGUGCGUGGAAAGCGUAG
A16i-TTG4 ||||||||||||||||
          3′ TGGGTGGGTGGGTGGGGTTACACGCACCTTTCGCATTGGGTGGGTGGGTGGGTT

Example 3: Enhanced Gene Knockdown Activity with Lipid-Conjugated SEA Oligo

Measurement of cellular uptake of oligo by flow cytometry. HeLa cells were seeded (100,000 cells per well) onto 12-well plates 24 h prior to experiment in complete DMEM media at 37° C. and 5% CO₂. Cells were incubated in complete media containing FAM-labeled oligonucleotides at a final concentration of 0.1 μM for 1, 5, 9, or 24 h at 37° C. At the set time points, the growth medium was removed and cells were washed twice with PBS (500 μL) and harvested by scrapping. Cell suspension in PBS (500 μL) was transferred into 5 mL round bottom tubes. Cells were fixed with freshly made 4% (w/v) paraformaldehyde for 10 min. After fixing, cells were washed twice by centrifugation at 130×g for 10 min in PBS (1 mL) and resuspended with PBS (500 μL) for flow cytometry (BD FACSCalibur). For each sample, 10,000 events were collected in a selected gate that corresponds to the untreated single cell population. FITC fluorescence was measured by air-cooled argon laser at 488-nm. Flowjo software was used to analyze the gated shift in histograms with FITC for cells treated with different FAM-labeled oligonucleotides with reference to the untreated cell populations. All data were collected as duplicates and shown as mean±standard deviation.

G-quadruplex structures conjugated with lipids and lipid-soluble moieties at either the 5′-terminus (stearate) or the loop (cholesterol and α-tocopherol) show enhanced uptake by HeLa cells (FIG. 5).

TABLE 3-1
Table of constructs used in the
lipid-conjugated SEA oligo study.
			Sequence (5′ to 3′; X = DNA; X = LNA;
			Chol = Cholesterol modifier;
		SEQ	Toc = Tocopherol modifier; Stea = Stearyl
		ID	modifier; SS = disulfide linker;
Name	Study	NO:	* = phosphorothioate bond;   = 6-FAM)
G4	Cells	82	TTGGGTGGGTGGGTGGGT
	uptake
G4-	Cells	83	TTGGGTGGG Toc TGGGTGGGT
iChol	uptake
G4-iToc	Cells	84	TTGGGTGGG Chol TGGGTGGGT
	uptake
Stea-G4	Cells	85	Stea TTGGGTGGGTGGGTGGGT
	uptake
Control	Gene	86	C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
ASO#	knockdown
Chol-	Gene	87	Chol  C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
ASO	knockdown
Toc-ASO	Gene	88	Toc  C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
	knockdown
SEA001-	Gene	89	TTGGGTGGG Chol TGGGTGGGT SS
iChol	knockdown		C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
SEA002-	Gene	90	TTGGGTGGG Toc TGGGTGGGT SS
iToc	knockdown		C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
#Control ASO is the LNA version of a clinical phase 2 gapmer, AZD9150.

Example 4: Enhanced Gene Knockdown Activity with Peptide-Conjugated SEA Oligo

Preparation of peptide-conjugated oligonucleotides. 3-nitro-2-pyridine sulfenyl (NPys)-modified peptide (5 equiv) was added to a solution mixture of thiol-modified oligonucleotide (1 equiv) in H₂O (3.15 μL/nmol), formamide (4.3 μL/nmol) and 2M TEAA (0.6 μL/nmol). The reaction mixture was vortexed, centrifuged and kept at room temperature for 3 h, with the process of vortex and centrifugation repeated every hour. The reaction mixture was filtered with micro spin filter (pore size 0.2 μm, nylon) prior to purification with RP-UHPLC (column, YMC-Triact C18, 120 Å, 4.6×250 mm; Buffer A, 0.1 M TEAA; Buffer B, MeCN; flow rate: 1.0 mL/min).

Cell transfection study of ASO, peptide-conjugated ASO, and peptide-conjugated SEA oligo. HeLa cells were seeded in 12-well plates (TPP®) at 25% confluency in complete DMEM media containing 10% FBS (Gibco®) 24 h prior to ASO treatment. ASO, peptide-ASO conjugate, and peptide-G4-ASO conjugates were pre-mixed with Lipofectamine RNAiMAX according to the manufacturer's protocol and added to the cell culture media to a final concentration of 10 nM for a further incubation of 24 h. Total RNA was isolated by TRIzol reagent (Invitrogen) according to the manufacturer's protocol. One microgram of total RNA per sample was reverse transcribed to cDNA using M-MLV reverse transcriptase (Promega) and random hexamer/oligo-dT primers. One fiftieth of the resulting reactions were used for quantitative PCR (qPCR) with primer pairs for STAT3 (Forward: 5′-ACATGCCACTTTGGTGTTTCATAA-3′ (SEQ ID NO: 91); Reverse: 5′-TCTTCGTAGATTGTGCTGATAGAGAAC-3′ (SEQ ID NO: 92)) and β-actin (Forward: 5′-CGGACTATGACTTAGTTGCGTTACA-3′ (SEQ ID NO: 93); Reverse: 5′-GCCATGCCAATCTCATCTTGT-3′(SEQ ID NO: 94)). The qPCR reactions were performed for 40 cycles of annealing at 55° C. for 10 s, extension at 72° C. for 20 s, and denaturation at 95° C. for 10 s.

The mRNA level was normalized using the endogenous β-actin (ACTB) mRNA as an internal control. Relative STAT3 mRNA levels were determined from the calculated threshold cycle (Cq) by the LightCycler®480 CW 1.5.1 software and compared to untreated controls (UTC) using ΔΔCq calculation method. Each sample was analyzed in duplicate.

STAT3 gene knockdown by ASO gapmer, SEA oligo, peptide-conjugated ASO gapmer, and peptide-conjugated SEA oligo in HeLa cells are shown in FIG. 6. The ASO gapmer utilized is the LNA equivalent of AZD9150 (U.S. Pat. No. 9,359,608 B2; Hong et al., Sci. Transl. Med. 2015, 7, 314ra185). The peptide employed (GFWFG) was previously shown to promote endosomal escape enhancement (LOnn et al., Sci. Rep. 2016, 6, 32301) of biomacromolecules.

TABLE 4-1
Table of constructs used in the
peptide-conjugated SEA Oligo study.
			Sequence (5′ to 3′; X = DNA;
			X = LNA; Pep1 = GFWFG peptide;
		SEQ	Pep1-T = GFWFG peptide conjugated
		ID	on dT; SS = disulfide
Name	Study	NO:	linker; * = phosphorothioate bond)
Control	Gene	86	C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
ASO#	knock
	down
SEA003	Gene	95	TTGGGTGGGTGGGTGGGT SS
	knock		C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
	down
ASO-	Gene	96	C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
Pep1	knock		SS Pep1
	down
SEA004-	Gene	97	TTGGGTGGG Pep1-T GGGTGGGT SS
iPep1	knock		C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
	down
SEA005-	Gene	98	TTGGG Pep1-T GGGTGGG Pep1-T GGGT SS
2iPep1	knock		C*T*A*T*T*T*G*G*A*T*G*T*C*A*G*C
	down
#Control ASO is the LNA version of a clinical phase 2 gapmer, AZD9150.

Example 5: GalNAc-Conjugated G-Quadruplex and SEA Oligo

Preparation of mono- and poly-GalNAc-conjugated G-quadruplex. GalNAc-conjugated guanine phosphoramidite was synthesized according to procedures by Manoharan, M. et. al. (U.S. Pat. No. 2016/0376585 A1) and incorporated onto oligonucleotides via an automated DNA synthesizer using standard solid-phase oligonucleotide synthesis. The GalNAc-containing oligonucleotides were treated 1 M 1,8-Diazabicyclo[5.4.0]undec-7-ene in anhydrous acetonitrile prior to deprotection with concentrated ammonium hydroxide, and purified by RP-UHPLC (column, YMC-Triact C18, 120 Å, 4.6×250 mm; Buffer A, 0.1 M TEAA; Buffer B, MeCN; flow rate: 1.0 mL/min). The samples were dialyzed successively against 2 mM KCl and water, lyophilized and resuspended in buffer containing 10 mM KPi, 10% D₂O, pH 7.0 prior to characterization by NMR spectroscopy.

Single or multiple ligands can be conjugated onto the G-tetrad core or loops of the G-quadruplex structure in multiple combinations (FIG. 7-I). Here we demonstrated the conjugation of mono-(FIG. 7-IIB,C), di-(FIG. 7-IID), and tri-(FIG. 7-IIE) GalNAc units onto the G-tetrad core.

Conjugation of multiple GalNAc units onto ASO (U.S. Pat. Nos. 9,181,549 B2, 9,249,179 B2, 9,370,582 B2, 2015/0368642 A1; Sliedregt et al., J. Med. Chem. 1999, 42, 609; Rozema et al., Proc. Natl. Acad. Sci. USA 2007, 104, 12982; Khorev et al., Bioorg. Med. Chem. 2008, 16, 5216; Prakash et al., Nucleic Acids Res. 2014, 42, 8796; Nair et al., J. Am. Chem. Soc. 2014, 136, 16958; Matsuda et al., ACS Chem. Biol. 2015, 10, 1181; Rajeev et al., Chembiochem 2015, 16, 903) was previously shown to lead to enhanced delivery to liver hepatocytes, resulting in highly effective gene knockdown of liver targets involved in lipid metabolism (e.g. APOB (U.S. Pat. No. 8,735,364 B2; Straarup et al., Nucleic Acids Res. 2010, 38, 7100), PCSK9 (U.S. Pat. No. 8,912,160 B2), APOC3 (U.S. Pat. No. 9,163,239 B2), LPA (U.S. Pat. No. 9,181,550 B2), and ANGPTL3(U.S. Pat. No. 9,139,831 B2)).

The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. Other embodiments are within the following claims.

One skilled in the art would readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. Further, it will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The compositions, methods, procedures, treatments, molecules and specific compounds described herein are presently representative of preferred embodiments are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art which are encompassed within the spirit of the invention are defined by the scope of the claims. The listing or discussion of a previously published document in this specification should not necessarily be taken as an acknowledgement that the document is part of the state of the art or is common general knowledge.

The invention illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by exemplary embodiments and optional features, modification and variation of the inventions embodied therein herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

The content of all documents and patent documents cited herein is incorporated by reference in their entirety.

The disclosures of the following documents are hereby incorporated into the present application by reference in their entirety:

PATENT DOCUMENTS
Gapmer:
U.S. Pat. No. 6,326,199 B1	December 2001	Cook et al.
U.S. Pat. No. 7,015,315 B1	March 2006	Cook et al.
U.S. Pat. No. 8,703,728 B2	April 2014	Swayze et al.
U.S. Pat. No. 9,045,754 B2	June 2015	Bhanot et al.
End-stabilizing oligo:
2015/0050738 A1		Ozsolak et al.
GalNAc conjugation:
U.S. Pat. No. 9,181,549 B2	November 2015	Prakash et al.
U.S. Pat. No. 9,249,179 B2	February 2016	Hadwiger et al.
U.S. Pat. No. 9,370,582 B2	June 2016	Manoharan et al.
US 2015/0368642 A1	December 2015	Albæk et al.
US 2016/0376585 A1	December 2016	Manoharan et al.
STAT3:
U.S. Pat. No. 9,359,608 B2	June 2016	Swayze et al.
APOB:
U.S. Pat. No. 8,735,364 B2	January 2008	Crooke and Graham
PCSK9:
U.S. Pat. No. 8,912,160 B2	December 2014	Freier et al.
APOC3:
U.S. Pat. No. 9,163,239 B2	October 2015	Prakash et al.
LPA:
U.S. Pat. No. 9,181,550 B2	November 2015	Prakash et al.
ANGPTL3:
U.S. Pat. No. 9,139,831 B2	September 2015	Crooke et al.
Modified G-quadruplex nanoparticles:
US 2016/0310519 A1	October 2016	Phan et al.
LNA:
WO1999014226 A2	March 1999	Wengel and Nielsen
WO2000066604 A2	November 2000	Wengel J
WO2003095467 A1	November 2003	Sorensen et al.
cEt:
WO2012109395 A1	August 2012	Freier and Swayze

OTHER PUBLICATIONS

• Oligotherapeutics:
• Sharma et al., Fut. Med. Chem. 2015, 7, 2221
• ASO:
• Zamecnik et al., Proc. Natl. Acad. Sci. USA 1978, 75, 280
• Stephenson et al., Proc. Natl. Acad. Sci. USA 1978, 75, 285
• Crooke et al., Nucleic Acid Ther. 2017, 27, 70
• Crooke et al., Nat. Biotechnol. 2017, 35, 230
• Bennett et al., Annu. Rev. Pharmacol. Toxicol. 2017, 57, 81
• Phosphorothioate:
• Eckstein F., J. Am. Chem. Soc. 1966, 88, 4292
• Gapmer:
• Monia et al., Biochemistry 1993, 268, 14514
• LNA:
• Obika et al., Tetrahedron Lett. 1997, 38, 8735
• Koshkin et al., Tetrahedron 1998, 54, 3607
• cEt:
• Seth et al., J. Med. Chem. 2009, 52, 10
• Automated synthesis of oligo:
• Matteucci and Caruthers, J. Am. Chem. Soc. 1981, 103, 3185
• GalNAc conjugation:
• Sliedregt et al., J. Med. Chem. 1999, 42, 609
• Rozema et al., Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 12982
• Khorev et al., Bioorg. Med. Chem. 2008, 16, 5216
• Prakash et al., Nucleic Acids Res. 2014, 42, 8796
• Nair et al., J. Am. Chem. Soc. 2014, 136, 16958
• Matsuda et al., ACS Chem. Biol. 2015, 10, 1181
• Rajeev et al., Chembiochem 2015, 16, 903
• STAT3:
• Hong et al., Sci. Transl. Med. 2015, 7, 314ra185
• APOB:
• Straarup et al., Nucleic Acids Res. 2010, 38, 7100
• Endosomal escape enhancement peptide:
• LÖnn et al., Sci. Rep. 2016, 6, 32301
• G-quadruplex:
• Phan A. T., FEBS J. 2010, 277, 1107

Claims

1. A conjugate consisting of: (1)(a) an antisense oligonucleotide (ASO), wherein the ASO is at least 5 nucleotides in length and (b) at least one G-quadruplex structure, or(2)(a) an antisense oligonucleotide (ASO), wherein the ASO is at least 5 nucleotides in length, (b) at least one G-quadruplex structure, and (c) a linker connecting the at least one G-quadruplex structure to the ASO, or(3)(a) an antisense oligonucleotide (ASO), wherein the ASO is at least 5 nucleotides in length, (b) at least one G-quadruplex structure, and (d) single or multiple ligands or functional moieties conjugated to the at least one G-quadruplex structure, or(4)(a) an antisense oligonucleotide (ASO), wherein the ASO is at least 5 nucleotides in length, (b) at least one G-quadruplex structure, (c) a linker connecting the at least one G-quadruplex structure to the ASO, and (d) single or multiple ligands or functional moieties conjugated to the at least one G-quadruplex structure,wherein the ASO and the at least one G-quadruplex structure are heterologous to each other, and wherein the conjugate has increased nuclease resistance relative to the unconjugated ASO.

2. The conjugate of claim 1, wherein the ASO is chemically modified.

3. The conjugate of claim 1, wherein the ASO adopts a gapmer design or a mixmer design.

4. The conjugate of claim 1, wherein the conjugate comprises (a) one G-quadruplex structure 5′ to the ASO, (b) one G-quadruplex structure 3′ to the ASO, or (c) both.

5. The conjugate of claim 1, wherein the at least one G-quadruplex structure comprises (a) a nucleic acid molecule comprising the nucleic acid sequence (g)w(n)a(g)x(n)b(g)y(n)c(g)z, wherein g and n are natural or chemical analogues of guanine nucleobase and any nucleobase respectively, w, x, y, z are independently of each other integers of at least 0, a, b, c are independently of each other integers of at least 0, and the sum of integers w, x, y, z is at least 8;(b) four nucleic acid molecules wherein each of said molecules comprises a sequence of (g)z, wherein z is an integer of at least 2; or(c) two nucleic acid molecules wherein each of said molecules comprises a sequence of (g)y(n)b(g)z, wherein b is an integer of at least 0, y and z are independently of each other integers of at least 0, and the sum of integers y and z is at least 4.

6. The conjugate according to claim 5, wherein the nucleic acid molecule comprises the nucleic acid sequence (g)w(n)a(g)x(n)b(g)y(n)c(g)z wherein g and n are natural or chemical analogues of guanine nucleobase and any nucleobase respectively, w, x, y, z are independently of each other integers of at least 3 and a, b, c are independently of each other integers of at least 1.

7. The conjugate of claim 1, wherein the at least one G-quadruplex structure is chemically modified.

8. The conjugate of claim 1, wherein loops of the at least one G-quadruplex structure comprise non-nucleosidic analogues without a base.

9. The conjugate of claim 1, wherein the linker is composed of unmodified nucleotides or wherein the linker is composed of chemically modified nucleotides, in part or in full.

10. The conjugate of claim 1, wherein the linker comprises a reducible linkage, an acid-labile linkage, or a protease-labile linkage.

11. The conjugate of claim 1, wherein the linker is connected to a phosphate or phosphate analogue, sugar, or base on the G-tetrad core or loop of the at least one G-quadruplex structure.

12. The conjugate of claim 1, wherein the linker is connected to a phosphate or phosphate analogue, sugar, or base on the ASO.

13. The conjugate of claim 1, wherein the at least one G- quadruplex structure and the ASO are connected across the backbone, in the form of a contiguous nucleotide sequence.

14. The conjugate of claim 1, wherein the ligand or functional moiety is selected from the group consisting of small molecules, carbohydrates, vitamins, lipids, aptamers, peptides, proteins, antibodies, fluorescent labels, and radiolabel tracers.

15. The conjugate of claim 1, wherein the ligand or functional moiety is connected to a phosphate or phosphate analogue, sugar, base or non-nucleosidic analogue on the G-tetrad core or loop of the at least one G-quadruplex structure.

16. The conjugate of claim 1, wherein the ASO is complementary to a portion of a DNA, pre-mRNA, mRNA, regulatory RNA, or non-coding RNA.

17. A method for preventing or treating diseases, disorders, and conditions, comprising administering a therapeutically effective amount of the conjugate of claim 1 to a subject in need thereof.

18. A method of modulating the stability, translation, splicing, cleavage, or activity of a target nucleic acid molecule, comprising contacting the target nucleic acid molecule with a conjugate of claim 1 having an ASO complementary to a portion of the target nucleic acid molecule.

19. A method of imaging or diagnosing, the method comprising contacting a selective probe with a target nucleic acid molecule, wherein the selective probe comprises a conjugate of claim 1.