Nucleotide triphosphates and their incorporation into oligonucleotides

Abstract

The present invention relates to novel nucleotide triphosphates, methods of synthesis and process of incorporating these nucleotide triphosphates into oligonucleotides, and isolation of novel nucleic acid catalysts (e.g., ribozymes or DNAzymes). Also, provided are the use of novel enzymatic nucleic acid molecules to inhibit HER2/neu/ErbB2 gene expression and their applications in human therapy.

Description

BACKGROUND OF THE INVENTION

[0002] This invention relates to novel nucleotide triphosphates (NTPs); methods for synthesizing nucleotide triphosphates; and methods for incorporation of novel nucleotide triphosphates into oligonucleotides. The invention further relates to incorporation of these nucleotide triphosphates into nucleic acid molecules using polymerases under several novel reaction conditions.

[0003] The following is a brief description of nucleotide triphosphates. This summary is not meant to be complete, but is provided only to assist understanding of the invention that follows. This summary is not an admission that all of the work described below is prior art to the claimed invention.

[0004] The synthesis of nucleotide triphosphates and their incorporation into nucleic acids using polymerase enzymes has greatly assisted in the advancement of nucleic acid research. The polymerase enzyme utilizes nucleotide triphosphates as precursor molecules to assemble oligonucleotides. Each nucleotide is attached by a phosphodiester bond formed through nucleophilic attack by the 3′ hydroxyl group of the oligonucleotide's last nucleotide onto the 5′ triphosphate of the next nucleotide. Nucleotides are incorporated one at a time into the oligonucleotide in a 5′ to 3′ direction. This process allows RNA to be produced and amplified from virtually any DNA or RNA templates.

[0005] Most natural polymerase enzymes incorporate standard nucleotide triphosphates into nucleic acid. For example, a DNA polymerase incorporates dATP, dTTP, dCTP, and dGTP into DNA and an RNA polymerase generally incorporates ATP, CTP, UTP, and GTP into RNA. There are however, certain polymerases that are capable of incorporating non-standard nucleotide triphosphates into nucleic acids (Joyce, 1997, PNAS 94, 1619-1622, Huang et al., Biochemistry 36, 8231-8242).

[0006] Before nucleosides can be incorporated into RNA transcripts using polymerase enzymes they must first be converted into nucleotide triphosphates which can be recognized by these enzymes. Phosphorylation of unblocked nucleosides by treatment with POCl3 and trialkyl phosphates was shown to yield nucleoside 5′-phosphorodichloridates (Yoshikawa et al., 1969, Bull. Chem. Soc. (Japan) 42, 3505). Adenosine or 2′-deoxyadenosine 5′-triphosphate was synthesized by adding an additional step consisting of treatment with excess tri-n-butylammonium pyrophosphate in DMF followed by hydrolysis (Ludwig, 1981, Acta Biochim. et Biophys. Acad. Sci. Hung. 16, 131-133).

[0007] Non-standard nucleotide triphosphates are not readily incorporated into RNA transcripts by traditional RNA polymerases. Mutations have been introduced into RNA polymerase to facilitate incorporation of deoxyribonucleotides into RNA (Sousa & Padilla, 1995, EMBO J. 14,4609-4621, Bonner et al., 1992, EMBO J. 11, 3767-3775, Bonner et al., 1994, J. Biol. Chem. 42, 25120-25128, Aurup et al., 1992, Biochemistry 31, 9636-9641).

[0008] McGee et al., International PCT Publication No. WO 95/35102, describes the incorporation of 2′-NH2—NTP's, 2′-F—NTP's, and 2′-deoxy-2′-benzyloxyamino UTP into RNA using bacteriophage T7 polymerase.

[0009] Wieczorek et al., 1994, Bioorganic & Medicinal Chemistry Letters 4, 987-994, describes the incorporation of 7-deaza-adenosine triphosphate into an RNA transcript using bacteriophage T7 RNA polymerase.

[0010] Lin et al., 1994, Nucleic Acids Research 22, 5229-5234, reports the incorporation of 2′-NH2—CTP and 2′-NH2—UTP into RNA using bacteriophage T7 RNA polymerase and polyethylene glycol containing buffer. The article describes the use of the polymerase synthesized RNA for in vitro selection of aptamers to human neutrophil elastase (HNE).

SUMMARY OF THE INVENTION

[0011] This invention relates to novel nucleotide triphosphate (NTP) molecules, and their incorporation into nucleic acid molecules, including nucleic acid catalysts. The NTPs of the instant invention are distinct from other NTPs known in the art. The invention further relates to incorporation of these nucleotide triphosphates, into oligonucleotides, using an RNA polymerase; the invention further relates to novel transcription conditions for the incorporation of modified (non-standard) and unmodified NTP's, into nucleic acid molecules. Further, the invention relates to methods for synthesis of novel NTP's

[0012] In a first aspect, the invention features NTP's having the formula triphosphate-OR, for example the following formula I: 1

[0013] where R is any nucleoside; specifically the nucleosides 2′-O-methyl-2,6-diaminopurine riboside; 2′-deoxy-2′amino-2,6-diaminopurine riboside; 2′-(N-alanyl) amino-2′-deoxy-uridine; 2′-(N-phenylalanyl)amino-2′-deoxy-uridine; 2′-deoxy-2′-(N-β-alanyl) amino; 2′-deoxy-2′-(lysiyl) amino uridine; 2′-C-allyl uridine; 2′-O-amino-uridine; 2′-O-methylthiomethyl adenosine; 2′-O-methylthiomethyl cytidine; 2′-O-methylthiomethyl guanosine; 2′-O-methylthiomethyl-uridine; 2′-deoxy-2′-(N-histidyl) amino uridine; 2′-deoxy-2′-amino-5-methyl cytidine; 2′-(N-β-carboxamidine-β-alanyl)amino-2′-deoxy-uridine; 2′-deoxy-2′-(N-β-alanyl)-guanosine; 2′-O-amino-adenosine; 2′-(N-lysyl)amino-2′-deoxy-cytidine; 2′-Deoxy-2′-(L-histidine) amino Cytidine; 5-Imidazoleacetic acid 2′-deoxy uridine, 5-[3-(N-4-imidazoleacetyl)aminopropynyl]-2′-O-methyl uridine, 5-(3-aminopropynyl)-2′-O-methyl uridine, 5-(3-aminopropyl)-2′-O-methyl uridine, 5-[3-(N-4-imidazoleacetyl)aminopropyl]-2′-O-methyl uridine, 5-(3-aminopropyl)-2′-deoxy-2-fluoro uridine, 2′-Deoxy-2′-(β-alanyl-L-histidyl)amino uridine, 2′-deoxy-2′-p-alaninamido-uridine, 3-(2′-deoxy-2′-fluoro-β-D-ribofuranosyl)piperazino[2,3-D]pyrimidine-2-one, 5-[3-(N-4-imidazoleacetyl)aminopropyl]-2′-deoxy-2′-fluoro uridine, 5-[3-(N-4-imidazoleacetyl)aminopropynyl]-2′-deoxy-2′-fluoro uridine, 5-E-(2-carboxyvinyl-2′-deoxy-2′-fluoro uridine, 5-[3-(N-4-aspartyl)aminopropynyl-2′-fluoro uridine, 5-(3-aminopropyl)-2′-deoxy-2-fluoro cytidine, and 5-[3-(N-4-succynyl)aminopropyl-2′-deoxy-2-fluoro cytidine.

[0014] In a second aspect, the invention features inorganic and organic salts of the nucleoside triphosphates of the instant invention.

[0015] In a third aspect, the invention features a process for the synthesis of pyrimidine nucleotide triphosphate (such as UTP, 2′-O-MTM-UTP, dUTP and the like) including the steps of monophosphorylation where the pyrimidine nucleoside is contacted with a mixture having a phosphorylating agent (such as phosphorus oxychloride, phospho-tris-triazolides, phospho-tris-triimidazolides and the like), trialkyl phosphate (such as triethylphosphate or trimethylphosphate or the like) and a hindered base (such as dimethylaminopyridine, DMAP and the like) under conditions suitable for the formation of pyrimidine monophosphate; and pyrophosphorylation where the pyrimidine monophosphate is contacted with a pyrophosphorylating reagent (such as tributylammonium pyrophosphate) under conditions suitable for the formation of pyrimidine triphosphates.

[0016] The term “nucleotide” as used herein is as recognized in the art to include natural bases (standard), and modified bases well known in the art. Such bases are generally located at the 1′ position of a sugar moiety. Nucleotides generally include a base, a sugar and a phosphate group. The nucleotides can be unmodified or modified at the sugar, phosphate and/or base moiety, (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, non-standard nucleotides and other; see, for example, Usman and McSwiggen, Ann. Rev. Med. Chem. 30:285-294; Eckstein et al., International PCT Publication No. WO 92/07065; Usman et al., International PCT Publication No. WO 93/15187; all of which are hereby incorporated by reference herein). There are several examples of modified nucleic acid bases known in the art, e.g., as recently summarized by Limbach et al., 1994, Nucleic Acids Res. 22, 2183. Some of the non-limiting examples of base modifications that can be introduced into nucleic acids without significantly effecting their catalytic activity include, inosine, purine, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2,4,6-trimethoxy benzene, 3-methyl uracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g., 5-methylcytidine), 5-alkyluridines (e.g., ribothymidine), 5-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or 6-alkylpyrimidines (e.g. 6-methyluridine) and others (Burgin et al., 1996, Biochemistry, 35, 14090).

[0017] By “modified bases” in this aspect is meant nucleotide bases other than adenine, guanine, cytosine, thymine, and uracil at 1′ position or their equivalents; such bases may be used within the catalytic core of an enzymatic nucleic acid molecule and/or in the substrate-binding regions of such a molecule. Such modified nucleotides include dideoxynucleotides which have pharmaceutical utility well known in the art, as well as utility in basic molecular biology methods such as sequencing.

[0018] By “ribonucleotide” is meant a nucleotide with a hydroxyl group at the 2′ position of a β-D-ribo-furanose moiety.

[0019] By “unmodified nucleoside” or “unmodified nucleotide” is meant one of the bases adenine, cytosine, guanine, uracil joined to the 1′ carbon of β-D-ribo-furanose with substitutions on either moiety.

[0020] By “modified nucleoside” or “modified nucleotide” is meant any nucleotide base which contains a modification in the chemical structure of an unmodified nucleotide base, sugar and/or phosphate.

[0021] By “pyrimidines” is meant nucleotides comprising modified or unmodified derivatives of a six membered pyrimidine ring. An example of a pyrimidine is modified or unmodified uridine.

[0022] By “nucleotide triphosphate” or “NTP” is meant a nucleoside bound to three inorganic phosphate groups at the 5′ hydroxyl group of the modified or unmodified ribose or deoxyribose sugar where the 1′ position of the sugar may comprise a nucleic acid base or hydrogen. The triphosphate portion may be modified to include chemical moieties which do not destroy the functionality of the group (i.e., allow incorporation into an RNA molecule).

[0023] In another embodiment, nucleotide triphosphates (NTPs) of the instant invention are incorporated into an oligonucleotide using an RNA polymerase enzyme. RNA polymerases include but are not limited to mutated and wild type versions of bacteriophage T7, SP6, or T3 RNA polymerases. Applicant has also found that the NTPs of the present invention can be incorporated into oligonucleotides using certain DNA polymerases, such as Taq polymerase.

[0024] In yet another embodiment, the invention features a process for incorporating modified NTP's into an oligonucleotide including the step of incubating a mixture having a DNA template, RNA polymerase, NTP, and an enhancer of modified NTP incorporation under conditions suitable for the incorporation of the modified NTP into the oligonucleotide.

[0025] By “enhancer of modified NTP incorporation” is meant a reagent which facilitates the incorporation of modified nucleotides into a nucleic acid transcript by an RNA polymerase. Such reagents include, but are not limited to, methanol, LiCl, polyethylene glycol (PEG), diethyl ether, propanol, methyl amine, ethanol, and the like.

[0026] In another embodiment, the modified nucleotide triphosphates can be incorporated by transcription into a nucleic acid molecules including enzymatic nucleic acid, antisense, 2-5A antisense chimera, oligonucleotides, triplex forming oligonucleotide (TFO), aptamers and the like (Stull et al., 1995 Pharmaceutical Res. 12, 465).

[0027] By “antisense” it is meant a non-enzymatic nucleic acid molecule that binds to target RNA by means of RNA-RNA or RNA-DNA or RNA-PNA (protein nucleic acid; Egholm et al., 1993 Nature 365, 566) interactions and alters the activity of the target RNA (for a review, see Stein and Cheng, 1993 Science 261, 1004; Agrawal et al, U.S. Pat. No. 5,591,721; Agrawal, U.S. Pat. No. 5,652,356). Typically, antisense molecules are complementary to a target sequence along a single contiguous sequence of the antisense molecule. However, in certain embodiments, an antisense molecule can bind to substrate such that the substrate molecule forms a loop, and/or an antisense molecule can bind such that the antisense molecule forms a loop. Thus, the antisense molecule can be complementary to two (or even more) non-contiguous substrate sequences or two (or even more) non-contiguous sequence portions of an antisense molecule can be complementary to a target sequence or both.

[0028] By “2-5A antisense chimera” it is meant, an antisense oligonucleotide containing a 5′ phosphorylated 2′-5′-linked adenylate residues. These chimeras bind to target RNA in a sequence-specific manner and activate a cellular 2-5A-dependent ribonuclease which, in turn, cleaves the target RNA (Torrence et al., 1993 Proc. Natl. Acad. Sci. USA 90, 1300).

[0029] By “triplex forming oligonucleotides (TFO)” it is meant an oligonucleotide that can bind to a double-stranded DNA in a sequence-specific manner to form a triple-strand helix. Formation of such triple helix structure has been shown to inhibit transcription of the targeted gene (Duval-Valentin et al., 1992 Proc. Natl. Acad. Sci. USA 89, 504).

[0030] By “oligonucleotide” as used herein is meant a molecule having two or more nucleotides. The polynucleotide can be single, double or multiple stranded and can have modified or unmodified nucleotides or non-nucleotides or various mixtures and combinations thereof.

[0031] By “nucleic acid catalyst” is meant a nucleic acid molecule capable of catalyzing (altering the velocity and/or rate of) a variety of reactions including the ability to repeatedly cleave other separate nucleic acid molecules (endonuclease activity) in a nucleotide base sequence-specific manner. Such a molecule with endonuclease activity can have complementarity in a substrate binding region to a specified gene target, and also has an enzymatic activity that specifically cleaves RNA or DNA in that target. That is, the nucleic acid molecule with endonuclease activity is able to intramolecularly or intermolecularly cleave RNA or DNA and thereby inactivate a target RNA or DNA molecule. This complementarity functions to allow sufficient hybridization of the enzymatic RNA molecule to the target RNA or DNA to allow the cleavage to occur. 100% complementarity is preferred, but complementarity as low as 50-75% can also be useful in this invention. The nucleic acids can be modified at the base, sugar, and/or phosphate groups. The term enzymatic nucleic acid is used interchangeably with phrases such as ribozymes, catalytic RNA, enzymatic RNA, catalytic DNA, catalytic oligonucleotides, nucleozyme, DNAzyme, RNA enzyme, endoribonuclease, endonuclease, minizyme, leadzyme, oligozyme, finderon or DNA enzyme. All of these terminologies describe nucleic acid molecules with enzymatic activity. The specific enzymatic nucleic acid molecules described in the instant application are not limiting in the invention and those skilled in the art will recognize that all that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site which is complementary to one or more of the target nucleic acid regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart a nucleic acid cleaving activity to the molecule (Cech et al., U.S. Pat. No. 4,987,071; Cech et al., 1988, 260 JAMA 3030).

[0032] By “enzymatic portion” or “catalytic domain” is meant that portion/region of the enzymatic nucleic acid molecule essential for cleavage of a nucleic acid substrate.

[0033] By “substrate binding arm” or “substrate binding domain” is meant that portion/region of an enzymatic nucleic acid molecule which is complementary to (i.e., able to base-pair with) a portion of its substrate. Generally, such complementarity is 100%, but can be less if desired. For example, as few as 10 bases out of 14 can be base-paired. That is, these arms contain sequences within a enzymatic nucleic acid molecule which are intended to bring enzymatic nucleic acid molecule and target together through complementary base-pairing interactions. The enzymatic nucleic acid molecule of the invention can have binding arms that are contiguous or non-contiguous and may be varying lengths. The length of the binding arm(s) are preferably greater than or equal to four nucleotides; specifically 12-100 nucleotides; more specifically 14-24 nucleotides long. If two binding arms are chosen, the design is such that the length of the binding arms are symmetrical (i.e., each of the binding arms is of the same length; e.g., five and five nucleotides, six and six nucleotides or seven and seven nucleotides long) or asymmetrical (i.e., the binding arms are of different length; e.g., six and three nucleotides; three and six nucleotides long; four and five nucleotides long; four and six nucleotides long; four and seven nucleotides long; and the like). Binding arms can be complementary to the specified substrate, to a portion of the indicated substrate, to the indicated substrate sequence and additional adjacent sequence, or a portion of the indicated sequence and additional adjacent sequence.

[0034] By “nucleic acid molecule” as used herein is meant a molecule having nucleotides. The nucleic acid molecule can be single, double or multiple stranded and can comprise modified or unmodified nucleotides or non-nucleotides or various mixtures and combinations thereof. In preferred embodiments of the present invention, a nucleic acid molecule, e.g., an antisense molecule, a triplex DNA, or an enzymatic nucleic acid molecule, is greater than about 12 nucleotides in length. In particularly preferred embodiments, the nucleic acid molecule is between 12 and 100 nucleotides in length, e.g., in specific embodiments 35, 36, 37, or 38 nucleotides in length for particular ribozymes. In particular embodiments, the nucleic acid molecule is 15-100, 17-100, 20-100, 21-100, 23-100, 25-100, 27-100, 30-100, 32-100, 35-100, 40-100, 50-100, 60-100, 70-100, or 80-100 nucleotides in length. Instead of 100 nucleotides being the upper limit in particularly preferred embodiments, the upper limit of the length range in some preferred embodiments can be, for example, 30, 40, 50, 60, 70, or 80 nucleotides. Thus, for any of the length ranges, the length range for particular embodiments has a lower limit as specified, with an upper limit as specified which is greater than the lower limit. For example, in a particular embodiment, the length range can be 35-50 nucleotides in length. All such ranges are expressly included. Also in particular embodiments, a nucleic acid molecule can have a length which is any of the specific lengths within the range specified above, for example, 21 nucleotides in length.

[0035] By “complementarity” is meant that a nucleic acid can form hydrogen bond(s) with another RNA sequence by either traditional Watson-Crick or other non-traditional types. In reference to the nucleic molecules of the present invention, the binding free energy for a nucleic acid molecule with its target or complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., enzymatic nucleic acid cleavage, antisense or triple helix inhibition. Determination of binding free energies for nucleic acid molecules is well-known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785. A percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). “Perfectly complementary” means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence.

[0036] In one embodiment, the modified nucleotide triphosphates of the instant invention can be used for combinatorial chemistry or in vitro selection of nucleic acid molecules with novel function. Modified oligonucleotides can be enzymatically synthesized to generate libraries for screening.

[0037] In another embodiment, the invention features nucleic acid based techniques (e.g., enzymatic nucleic acid molecules), antisense nucleic acids, 2-5A antisense chimeras, triplex DNA, antisense nucleic acids containing RNA cleaving chemical groups) isolated using the methods described in this invention and methods for their use to diagnose, down regulate or inhibit gene expression.

[0038] In one embodiment, the invention features enzymatic nucleic acid molecules targeted against HER2 RNA, specifically including ribozymes in the class II (zinzyme) motif.

[0039] Targets, for example HER2, for useful ribozymes and antisense nucleic acids can be determined, for example, as described in Draper et al., WO 93/23569; Sullivan et al., WO 93/23057; Thompson et al., WO 94/02595; Draper et al., WO 95/04818; McSwiggen et al., U.S. Pat. Nos. 5,525,468 and 5,646,042, all are hereby incorporated by reference herein in their totalities. Other examples include the following PCT applications, which concern inactivation of expression of disease-related genes: WO 95/23225, and WO 95/13380; all of which are incorporated by reference herein.

[0040] In the context of this invention, “inhibit” it is meant that the activity of target genes or level of mRNAs or equivalent RNAs encoding target genes is reduced below that observed in the absence of the nucleic acid molecules of the instant invention (e.g., enzymatic nucleic acid molecules), antisense nucleic acids, 2-5A antisense chimeras, triplex DNA, antisense nucleic acids containing RNA cleaving chemical groups). In one embodiment, inhibition with enzymatic nucleic acid molecule preferably is below that level observed in the presence of an enzymatically attenuated nucleic acid molecule that is able to bind to the same site on the mRNA, but is unable to cleave that RNA. In another embodiment, inhibition with nucleic acid molecules, including enzymatic nucleic acid and antisense molecules, is preferably greater than that observed in the presence of, for example, an oligonucleotide with scrambled sequence or with mismatches. In another embodiment, inhibition of target genes with the nucleic acid molecule of the instant invention is greater than in the presence of the nucleic acid molecule than in its absence.

[0041] In another embodiment, the invention features a process for incorporating a plurality of compounds of formula I. 2

[0042] In another embodiment, the invention features a nucleic acid molecule with catalytic activity having formula II: 3

[0043] In the formula shown above X, Y, and Z represent independently a nucleotide or a non-nucleotide linker, which may be the same or different; • indicates hydrogen bond formation between two adjacent nucleotides which may or may not be present; Y′ is a nucleotide complementary to Y; Z′ is a nucleotide complementary to Z; q is an integer greater than or equal to 3 and preferably less than 20, more preferably 4, 5, 6, 7, 8, 9, 10, 11, 12, or 15; m is an integer greater than 1 and preferably less than 10, more preferably 2, 3, 4, 5, 6, or 7; n is an integer greater than 1 and preferably less than 10, more preferably 3, 4, 5, 6, or 7; o is an integer greater than or equal to 3 and preferably less than 20, more preferably 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 15; q and o can be the same length (q=o) or different lengths (q≠o); each X(q) and X(o) are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid sequence (the target can be an RNA, DNA or RNA/DNA mixed polymers); W is a linker of ≧2 nucleotides in length or a non-nucleotide linker less than about 200 atoms in length; A, U, C. and G represent the nucleotides; G is a nucleotide, preferably 2′-O-methyl or ribo; A is a nucleotide. preferably 2′-O-methyl or ribo; U is a nucleotide, preferably 2′-amino (e.g., 2′-NH2 or 2′-O—NH2), 2′-O-methyl or ribo; C represents a nucleotide, preferably 2′-amino (e.g., 2′-NH2 or 2′-O—NH2), and—represents a chemical linkage (e.g. a phosphate ester linkage, amide linkage. phosphorothioate, phosphorodithioate or other linkage known in the art).

[0044] In yet another embodiment, the invention features a nucleic acid molecule with catalytic activity having formula III: 4

[0045] In the formula shown above X, Y, and Z represent independently a nucleotide or a non-nucleotide linker, which may be same or different; • indicates hydrogen bond formation between two adjacent nucleotides which may or may not be present; Z′ is a nucleotide complementary to Z; q is an integer greater than or equal to 3 and preferably less than 20, more specifically 4, 5, 6, 7, 8, 9, 10, 11, 12, or 15; n is an integer greater than 1 and preferably less than 10, more specifically 3, 4, 5, 6, or 7; o is an integer greater than or equal to 3 and preferably less than 20, more specifically 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 15; q and o may be the same length (q=o) or different lengths (q≠o); each X(q) and X(o) are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid sequence (the target can be an RNA, DNA or RNA/DNA mixed polymers); X(o) preferably has a G at the 3′-end, X(q) preferably has a G at the 5′-end; W is a linker of ≧2 nucleotides in length or can be a non-nucleotide linker less than about 200 atoms in length; Y is a linker of ≧1 nucleotides in length, preferably G, 5′-CA-3′, or 5′-CAA-3′, or can be a non-nucleotide linker less than about 200 atoms in length; A, U, C, and G represent nucleotides; G is a nucleotide, preferably 2′-O-methyl, 2′-deozy-2′-fluoro, or 3′-OH; A is a nucleotide, preferably 2′-O-methyl, 2′-deozy-2′-fluoro, or 2′-OH; U is a nucleotide, preferably 2′-O-methyl, 2′-deozy-2′-fluoro, or 2′-OH; C represents a nucleotide, preferably 2′-amino (e.g., 2′-NH2 or 2′-O—NH2, and—represents a chemical linkage (e.g. a phosphate ester linkage, amide linkage, phosphorothioate, phosphorodithioate or others known in the art).

[0046] In one embodiment, the invention features a method of inhibiting expression of HER2 in a cell, comprising the step of contacting the cell with a chemotherapeutic agent and an enzymatic nucleic acid molecule having a formula III under conditions suitable for the inhibition of expression of HER2.

[0047] In another embodiment, the invention features a method of treatment of a patient having a condition associated with the level of HER2, wherein the patient is administered a chemotherapeutic agent and an enzymatic nucleic acid molecule having a formula III under conditions suitable for the treatment.

[0048] In another embodiment, the invention features a method for treating conditions associated with the level of HER2 gene using a chemotherapeutic agent in combination with an enzymatic nucleic acid molecule having a formula III under conditions suitable for the treatment.

[0049] In a preferred embodiment, the invention features a method for treating cancer using a chemotherapeutic agent in combination with an enzymatic nucleic acid molecule having a formula III under conditions suitable for the treatment.

[0050] Suitable chemotherapeutic agents include chemotherapeutic agents selected from the group consisting of Paclitaxel, Doxorubicin, Cisplatin, and Herceptin.

[0051] In another embodiment, enzymatic nucleic acid molecules of the instant invention are used to treat cancers selected from the group consisting of breast cancer, non-small cell lung cancer, bladder cancer, prostate cancer, and pancreatic cancer.

[0052] The enzymatic nucleic acid molecules of Formula II and Formula III can independently comprise a cap structure which may independently be present or absent.

[0053] By “sufficient length” is meant an oligonucleotide of greater than or equal to 3 nucleotides that is of a length great enough to provide the intended function under the expected condition. For example, for binding arms of enzymatic nucleic acid “sufficient length” means that the binding arm sequence is long enough to provide stable binding to a target site under the expected binding conditions. Preferably, the binding arms are not so long as to prevent useful turnover.

[0054] By “stably interact” is meant interaction of the oligonucleotides with target nucleic acid (e.g., by forming hydrogen bonds with complementary nucleotides in the target under physiological conditions).

[0055] By “chimeric nucleic acid molecule” or “chimeric oligonucleotide” is meant that the molecule can be comprised of both modified or unmodified DNA or RNA.

[0056] By “cap structure” is meant chemical modifications, which have been incorporated at a terminus of the oligonucleotide. These terminal modifications protect the nucleic acid molecule from exonuclease degradation, and can help in delivery and/or localization within a cell. The cap can be present at the 5′-terminus (5′-cap) or at the 3′-terminus (3′-cap) or can be present on both termini. In non-limiting examples, the 5′-cap is selected from the group consisting of inverted abasic residue (moiety), 4′,5′-methylene nucleotide, 1-(beta-D-erythrofuranosyl) nucleotide, 4′-thio nucleotide, carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides, modified base nucleotide, phosphorodithioate linkage, threo-pentofuranosyl nucleotide, acyclic 3′,4′-seco nucleotide, acyclic 3,4-dihydroxybutyl nucleotide, acyclic 3,5-dihydroxypentyl nucleotide, 3′-3′-inverted nucleotide moiety, 3′-3′-inverted a basic moiety; 3′-2′-inverted nucleotide moiety; 3′-2′-inverted a basic moiety; 1,4-butanediol phosphate, 3′-phosphoramidate, hexylphosphate, aminohexyl phosphate; 3′-phosphate, 3′-phosphorothioate, phosphorodithioate, or bridging or non-bridging methylphosphonate moiety (for more details, see Beigelman et al., International PCT publication No. WO 97/26270, incorporated by reference herein).

[0057] In another embodiment, the 3′-cap can be selected from a group consisting of 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide; 4′-thio nucleotide; carbocyclic nucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate; 3-aminopropyl phosphate; 6-aminohexyl phosphate; 1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide; phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide; 5′-5′-inverted nucleotide moiety; 5′-5′-inverted a basic moiety; 5′-phosphoramidate; 5′-phosphorothioate; 1,4-butanediol phosphate 5′-amino; bridging and/or non-bridging 5′-phosphoramidate, phosphorothioate and/or phosphorodithioate; bridging or non-bridging methylphosphonate and 5′-mercapto moieties (for more details, see Beaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by reference herein).

[0058] By the term “non-nucleotide” is meant any group or compound which can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound is a basic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine. The terms “abasic” or “abasic nucleotide” as used herein encompass sugar moieties lacking a base or having other chemical groups in place of base at the 1′ position.

[0059] In connection with 2′-modified nucleotides as described for the present invention, by “amino” is meant 2′-NH2 or 2′-O—NH2, which can be modified or un-modified. Such modified groups are described, for example, in Eckstein et al., U.S. Pat. No. 5,672,695 and Matulic-Adamic et al., WO 98/28317, respectively, which are both incorporated by reference in their entireties.

[0060] As used herein “cell” is used in its usual biological sense, and does not refer to an entire multicellular organism. The cell can, for example, be in vitro, e.g., in cell culture, or present in a multicellular organism, including, e.g., birds, plants and mammals such as cows, sheep, apes, monkeys, swine, dogs, and cats.

[0061] In another aspect, the invention provides mammalian cells containing one or more nucleic acid molecules and/or expression vectors of this invention. The one or more nucleic acid molecules can independently be targeted to the same or different sites.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0062] The drawings will first briefly be described.

[0063] Drawings:

[0064] FIG. 1 displays a schematic representation of NTP synthesis using nucleoside substrates.

[0065] FIG. 2 shows a scheme for an in vitro selection method. A pool of nucleic acid molecules is generated with a random core region and one or more region(s) with a defined sequence. These nucleic acid molecules are bound to a column containing immobilized oligonucleotide with a defined sequence, where the defined sequence is complementary to region(s) of defined sequence of nucleic acid molecules in the pool. Those nucleic acid molecules capable of cleaving the immobilized oligonucleotide (target) in the column are isolated and converted to complementary DNA (cDNA), followed by transcription using NTPs to form a new nucleic acid pool.

[0066] FIG. 3 shows a scheme for a two column in vitro selection method. A pool of nucleic acid molecules is generated with a random core and two flanking regions (region A and region B) with defined sequences. The pool is passed through a column which has immobilized oligonucleotides with regions A′ and B′ that are complementary to regions A and B of the nucleic acid molecules in the pool, respectively. The column is subjected to conditions sufficient to facilitate cleavage of the immobilized oligonucleotide target. The molecules in the pool that cleave the target (active molecules) have A′ region of the target bound to their A region, whereas the B region is free. The column is washed to isolate the active molecules with the bound A′ region of the target. This pool of active molecules can also contain some molecules that are not active to cleave the target (inactive molecules) but have dissociated from the column. To separate the contaminating inactive molecules from the active molecules, the pool is passed through a second column (column 2) which contains immobilized oligonucleotides with the A′ sequence but not the B′ sequence. The inactive molecules will bind to column 2 but the active molecules will not bind to column 2 because their A region is occupied by the A′ region of the target oligonucleotide from column 1. Column 2 is washed to isolate the active molecules for further processing as described in the scheme shown in FIG. 2.

[0067] FIG. 4 is a diagram of a novel 48 nucleotide enzymatic nucleic acid motif which was identified using in vitro methods described in the instant invention. The molecule shown is only exemplary. The 5′ and 3′ terminal nucleotides (referring to the nucleotides of the substrate binding arms rather than merely the single terminal nucleotide on the 5′ and 3′ ends) can be varied so long as those portions can base-pair with target substrate sequence. In addition, the guanosine (G) shown at the cleavage site of the substrate can be changed to other nucleotides so long as the change does not eliminate the ability of enzymatic nucleic acid molecules to cleave the target sequence. Substitutions in the nucleic acid molecule and/or in the substrate sequence can be readily tested, for example, as described herein.

[0068] FIG. 5 is a schematic diagram of HCV luciferase assay used to demonstrate efficacy of class I enzymatic nucleic acid molecule motif.

[0069] FIG. 6 is a graph indicating the dose curve of an enzymatic nucleic acid molecule targeting site 146 on HCV RNA.

[0070] FIG. 7 is a bar graph showing enzymatic nucleic acid molecules targeting 4 sites within the HCV RNA are able to reduce RNA levels in cells.

[0071] FIG. 8 shows secondary structures and cleavage rates for characterized Class II enzymatic nucleic acid motifs.

[0072] FIG. 9 is a diagram of a novel 35 nucleotide enzymatic nucleic acid motif which was identified using in vitro methods described in the instant invention. The molecule shown is only exemplary. The 5′ and 3′ terminal nucleotides (referring to the nucleotides of the substrate binding arms rather than merely the single terminal nucleotide on the 5′ and 3′ ends) can be vaned so long as those portions can base-pair with target substrate sequence. In addition, the guanosine (G) shown at the cleavage site of the substrate can be changed to other nucleotides so long as the change does not eliminate the ability of enzymatic nucleic acid molecules to cleave the target sequence. Substitutions in the nucleic acid molecule and/or in the substrate sequence can be readily tested, for example, as described herein.

[0073] FIG. 10 is a bar graph showing substrate specificities for Class II (zinzyme) ribozymes.

[0074] FIG. 11 is a bar graph showing Class II enzymatic nucleic acid molecules targeting 10 representative sites within the HER2 RNA in a cellular proliferation screen.

[0075] FIG. 12 is a synthetic scheme outlining the synthesis of 5-[3-aminopropynyl(propyl)]uridine 5′-triphosphates and 4-imidazoleaceticacid conjugates.

[0076] FIG. 13 is a synthetic scheme outlining the synthesis of 5-[3-(N-4-imidazoleacetyl) aminopropynyl(propyl)]uridine 5′-triphosphates.

[0077] FIG. 14 is a synthetic scheme outlining the synthesis of carboxylate tethered uridine 5′-triphosphoates.

[0078] FIG. 15 is a synthetic scheme outlining the synthesis of 5-(3-aminoalkyl) and 5-[3(N-succinyl)aminopropyl] functionalized cytidines.

[0079] FIG. 16 is a diagram of a class I ribozyme stem truncation and loop replacement analysis.

[0080] FIG. 17 is a diagram of class I ribozymes with truncated stem(s) and/or non-nucleotide linkers used in loop structures.

[0081] FIG. 18 is a diagram of “no-ribo” class II ribozymes.

[0082] FIG. 19 is a graph showing cleavage reactions with class II ribozymes under differing divalent metal concentrations.

[0083] FIG. 20 is a diagram of differing class II ribozymes with varying ribo content and their relative rates of catalysis.

[0084] FIG. 21 is a graph showing class II ribozyme (zinzyme) mediated reduction of HER2 RNA in SKBR3 breast carcinoma cells. Cells were treated with 100 nm, and 200 nm of zinzyme (RPI 18656) targeting site 972 of HER2 RNA and a corresponding scrambled attenuated control complexed with 2.5 μg/ml of lipid. Active zinzymes and scrambled attenuated controls were compared to untreated cells after 24 hours post treatment.

[0085] FIG. 22 is a graph showing class II ribozyme (zinzyme) mediated dose response anti-proliferation assay in SKBR3 breast carcinoma cells. Cells were treated with 100 nm, and 200 nm of zinzyme (RPI 18656) targeting site 972 of HER2 RNA and a corresponding scrambled attenuated control complexed with 2.0 μg/ml of lipid. Active zinzymes and scrambled attenuated controls were compared to untreated cells after 24 hours post treatment.

[0086] FIG. 23 is a graph which shows the dose dependent reduction of HER2 RNA in SKOV-3 cells treated with RPI 19293 from 0 to 100 nM with 5.0 μg/ml of cationic lipid.

[0087] FIG. 24 is a graph which shows the dose dependent reduction of HER2 RNA and inhibition of cellular proliferation in SKBR-3 cells treated with RPI 19293 from 0 to 400 nM with 5.0 μg/ml of cationic lipid.

[0088] FIG. 25 shows a non-limiting example of the replacement of a 2′-O-methyl 5′-CA-3′with a ribo G in the class II (zinzyme) motif. The representative motif shown for the purpose of the figure is a “seven-ribo” zinzyme motif, however, the interchangeability of a G and a CA in the position shown in FIG. 25 of the class II (zinzyme) motif extends to any combination of 2-O-methyl and ribo residues. For instance, a 2′-O-methyl G can replace the 2′-O-methyl 5′-CA-3′ and vise versa.

[0089] FIG. 26 is a graph which shows a screen of class II ribozymes (zinzymes) targeting site 972 of HER2 RNA which contain ribo-G reductions (RPI 19727=no ribo, RPI 19728=one ribo, RPI 19293=two ribo, RPI 19729=three ribo, RPI 19730=four ribo, 19731=five ribo, and RPI 19292=seven ribo) for anti-proliferative activity in SKBR3 cells.

[0090] FIG. 27 is a bar graph showing the anti-proliferative activity of RPI 19293 (Herzyme) treatment in combination with Paclitaxel (TAX) in SK-OV-3 cells as compared to a scrambled control.

[0091] FIG. 28 is a bar graph showing the anti-proliferative activity of RPI 19293 (Herzyme) in combination with Doxorubicin (DOX) treatment in SK-OV-3 cells as compared to a scrambled control.

[0092] FIG. 29 is a bar graph showing the anti-proliferative activity of RPI 19293 (Herzyme) in combination with Cisplatin (CIS) treatment in SK-OV-3 cells as compared to a scrambled control.

[0093] FIG. 30 is a bar graph showing the anti-proliferative activity of RPI 19293 (Herzyme) in combination with Paclitaxel (TAX) treatment in SK-BR-3 cells as compared to a scrambled control.

[0094] FIG. 31 is a bar graph showing the anti-proliferative activity of RPI 19293 (Herzyme) in combination with Doxorubicin (DOX) treatment in SK-BR-3 cells as compared to a scrambled control.

[0095] FIG. 32 is a bar graph showing the anti-proliferative activity of RPI 19293 (Herzyme) in combination with Cisplatin (CIS) treatment in SK-BR-3 cells as compared to a scrambled control.

[0096] Nucleotide Synthesis

[0097] Addition of dimethylaminopyridine (DMAP) to the phosphorylation protocols known in the art can greatly increase the yield of nucleotide monophosphates while decreasing the reaction time (FIG. 1). Synthesis of the nucleosides of the invention have been described in several publications and Applicants previous applications (Beigelman et al., International PCT publication No. WO 96/18736; Dudzcy et al., Int. PCT Pub. No. WO 95/11910; Usman et al., Int. PCT Pub. No. WO 95/13378; Matulic-Adamic et al., 1997, Tetrahedron Lett. 38, 203; Matulic-Adamic et al., 1997, Tetrahedron Lett. 38, 1669; all of which are incorporated herein by reference). These nucleosides are dissolved in triethyl phosphate and chilled in an ice bath. Phosphorus oxychloride (POCl3) is then added followed by the introduction of DMAP. The reaction is then warmed to room temperature and allowed to proceed for 5 hours. This reaction allows the formation of nucleotide monophosphates which can then be used in the formation of nucleotide triphosphates. Tributylamine is added followed by the addition of anhydrous acetonitrile and tributylammonium pyrophosphate. The reaction is then quenched with TEAB and stirred overnight at room temperature (about 20° C.). The triphosphate is purified using Sephadex® column purification or equivalent and/or HPLC and the chemical structure is confirmed using NMR analysis. Those skilled in the art will recognize that the reagents, temperatures of the reaction, and purification methods can easily be alternated with substitutes and equivalents and still obtain the desired product.

[0098] Nucleotide Triphosphates The invention provides nucleotide triphosphates which can be used for a number of different functions. The nucleotide triphosphates formed from nucleosides found in Table I are unique and distinct from other nucleotide triphosphates known in the art. Incorporation of modified nucleotides into DNA or RNA oligonucleotides can alter the properties of the molecule. For example, modified nucleotides can hinder binding of nucleases, thus increasing the chemical half-life of the molecule. This is especially important if the molecule is to be used for cell culture or in vivo. It is known in the art that the introduction of modified nucleotides into these molecules can greatly increase the stability and thereby the effectiveness of the molecules (Burgin et al., 1996, Biochemistry 35, 14090-14097; Usman et al., 1996, Curr. Opin. Struct. Biol. 6, 527-533).

[0099] Modified nucleotides are incorporated using either wild type or mutant polymerases. For example, mutant T7 polymerase is used in the presence of modified nucleotide triphosphate(s), DNA template and suitable buffers. Those skilled in the art will recognize that other polymerases and their respective mutant versions can also be utilized for the incorporation of NTP's of the invention. Nucleic acid transcripts were detected by incorporating radiolabelled nucleotides (α-32P NTP). The radiolabeled NTP contained the same base as the modified triphosphate being tested. The effects of methanol, PEG and LiCl were tested by adding these compounds independently or in combination. Detection and quantitation of the nucleic acid transcripts was performed using a Molecular Dynamics Phosphorlmager. Efficiency of transcription was assessed by comparing modified nucleotide triphosphate incorporation with all-ribonucleotide incorporation control. Wild-type polymerase was used to incorporate NTP's using the manufacturer's buffers and instructions (Boehringer Mannheim).

[0100] Transcription Conditions

[0101] Incorporation rates of modified nucleotide triphosphates into oligonucleotides can be increased by adding to traditional buffer conditions, several different enhancers of modified NTP incorporation. Applicant has utilized methanol and LiCl in an attempt to increase incorporation rates of dNTP using RNA polymerase. These enhancers of modified NTP incorporation can be used in different combinations and ratios to optimize transcription. Optimal reaction conditions differ between nucleotide triphosphates and can readily be determined by standard experimentation. Overall, however, Applicant has found that inclusion of enhancers of modified NTP incorporation such as methanol or inorganic compound such as lithium chloride increase the mean transcription rates.

[0102] Mechanism of action of Nucleic Acid Molecules of the Invention

[0103] Antisense: Antisense molecules can be modified or unmodified RNA, DNA, or mixed polymer oligonucleotides and primarily function by specifically binding to matching sequences resulting in inhibition of peptide synthesis (Wu-Pong, November 1994, BioPharm, 20-33). The antisense oligonucleotide binds to target RNA by Watson Crick base-pairing and blocks gene expression by preventing ribosomal translation of the bound sequences either by steric blocking or by activating RNase H enzyme. Antisense molecules can also alter protein synthesis by interfering with RNA processing or transport from the nucleus into the cytoplasm (Mukhopadhyay & Roth, 1996, Crit. Rev. in Oncogenesis 7, 151-190).

[0104] In addition, binding of single stranded DNA to RNA can result in nuclease degradation of the heteroduplex (Wu-Pong, supra; Crooke, supra). To date, the only backbone modified DNA chemistry which acts as substrates for RNase H are phosphorothioates and phosphorodithioates. Recently, it has been reported that 2′-arabino and 2′-fluoro arabino-containing oligos can also activate RNase H activity.

[0105] A number of antisense molecules have been described that utilize novel configurations of chemically modified nucleotides, secondary structure, and/or RNase H substrate domains (Woolf et al., International PCT Publication No. WO 98/13526; Thompson et al., U.S. Ser. No. 60/082,404 which was filed on Apr. 20, 1998; Hartmann et al., U.S. Ser. No. 60/101,174 which was filed on Sep. 21, 1998) all of these are incorporated by reference herein in their entirety.

[0106] Triplex Forming Oligonucleotides (TFO): Single stranded DNA can be designed to bind to genomic DNA in a sequence specific manner. TFOs are comprised of pyrimidine-rich oligonucleotides which bind DNA helices through Hoogsteen Base-pairing (Wu-Pong, supra). The resulting triple helix composed of the DNA sense, DNA antisense, and TFO disrupts RNA synthesis by RNA polymerase. The TFO mechanism can result in gene expression or cell death since binding can be irreversible (Mukhopadhyay & Roth, supra)

[0107] 2-5A Antisense Chimera: The 2-5A system is an interferon-mediated mechanism for RNA degradation found in higher vertebrates (Mitra et al., 1996, Proc Nat Acad Sci USA 93, 6780-6785). Two types of enzymes, 2-5A synthetase and RNase L, are required for RNA cleavage. The 2-5A synthetases require double stranded RNA to form 2′-5′ oligoadenylates (2-5A). 2-5A then acts as an allosteric effector for utilizing RNase L which has the ability to cleave single stranded RNA. The ability to form 2-5A structures with double stranded RNA makes this system particularly useful for inhibition of viral replication.

[0108] (2′-5′) oligoadenylate structures can be covalently linked to antisense molecules to form chimeric oligonucleotides capable of RNA cleavage (Torrence, supra). These molecules putatively bind and activate a 2-5A dependent RNase, the oligonucleotide/enzyme complex then binds to a target RNA molecule which can then be cleaved by the RNase enzyme.

[0109] Enzymatic Nucleic Acid: In general, enzymatic nucleic acids act by first binding to a target RNA. Such binding occurs through the target-binding portion of an enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cut the target RNA. Strategic cleavage of such a target RNA destroys its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.

[0110] The enzymatic nature of an enzymatic nucleic acid has significant advantages, such as the concentration of enzymatic nucleic acid molecules necessary to affect a therapeutic treatment is lower. This advantage reflects the ability of the enzymatic nucleic acid molecules to act enzymatically. Thus, a single enzymatic nucleic acid molecule can cleave many molecules of target RNA. In addition, the enzymatic nucleic acid molecule is a highly specific inhibitor, with the specificity of inhibition depending not only on the base-pairing mechanism of binding to the target RNA, but also on the mechanism of target RNA cleavage. Single mismatches, or base-substitutions, near the site of cleavage can be chosen to completely eliminate catalytic activity of enzymatic nucleic acid molecules.

[0111] Nucleic acid molecules having an endonuclease enzymatic activity are able to repeatedly cleave other separate RNA molecules in a nucleotide base sequence-specific manner. Such enzymatic nucleic acid molecules can be targeted to virtually any RNA transcript, and efficient cleavage achieved in vitro (Zaug et al, 324, Nature 429 1986; Uhlenbeck, 1987 Nature 328, 596; Kim et al., 84 Proc. Natl. Acad. Sci. USA 8788, 1987; Dreyfus, 1988, Einstein Quart. J. Bio. Med., 6, 92; Haseloff and Gerlach, 334 Nature 585, 1988; Cech, 260 JAMA 3030, 1988; and Jefferies et al., 17 Nucleic Acids Research 1371, 1989; Santoro et al., 1997 infra).

[0112] Because of their sequence-specificity, trans-cleaving enzymatic nucleic acid molecules show promise as therapeutic agents for human disease (Usman & McSwiggen, 1995 Ann. Rep. Med. Chem. 30, 285-294; Christoffersen and Marr, 1995 J. Med. Chem. 38, 2023-2037). Enzymatic nucleic acid molecules can be designed to cleave specific RNA targets within the background of cellular RNA. Such a cleavage event renders the RNA non-functional and abrogates protein expression from that RNA. In this manner, synthesis of a protein associated with a disease state can be selectively inhibited.

[0113] Synthesis of Nucleic acid Molecules Synthesis of nucleic acids greater than about 100 nucleotides in length is difficult using automated methods, and the therapeutic cost of such molecules is prohibitive. In this invention, small nucleic acid motifs (“small” refers to nucleic acid motifs less than about 100 nucleotides in length, preferably less than about 80 nucleotides in length, and more preferably less than about 50 nucleotides in length; e.g., antisense oligonucleotides, hammerhead or the hairpin ribozymes) are preferably used for exogenous delivery. The simple structure of these molecules increases the ability of the nucleic acid to invade targeted regions of RNA structure. Exemplary molecules of the instant invention were chemically synthesized, and others can similarly be synthesized. Oligodeoxyribonucleotides were synthesized using standard protocols as described in Caruthers et al., 1992, Methods in Enzymology 211, 3-19, which is incorporated herein by reference.

[0114] The method of synthesis used for normal RNA including certain enzymatic nucleic acid molecules follows the procedure as described in Usman et al., 1987, J. Am. Chem. Soc., 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433; and Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684 Wincott et al., 1997, Methods Mol. Bio., 74, 59, and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. In a non-limiting example, small scale syntheses were conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 μmol scale protocol with a 7.5 min coupling step for alkylsilyl protected nucleotides and a 2.5 min coupling step for 2′-O-methylated nucleotides. Table II outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 μmol scale can be done on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 μL of 0.11 M=6.6 μmol) of 2′-O-methyl phosphoramidite and a 75-fold excess of S-ethyl tetrazole (60 μL of 0.25 M=15 μmol) can be used in each coupling cycle of 2′-O-methyl residues relative to polymer-bound 5′-hydroxyl. A 66-fold excess (120 μL of 0.11 M=13.2 μmol) of alkylsilyl (ribo) protected phosphoramidite and a 150-fold excess of S-ethyl tetrazole (120 μL of 0.25 M=30 μmol) can be used in each coupling cycle of ribo residues relative to polymer-bound 5′-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, were 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer; detritylation solution was 3% TCA in methylene chloride (ABI); capping was performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); oxidation solution was 16.9 mM I2, 49 mM pyridine, 9% water in THF (PERSEPTIVET™). Burdick & Jackson Synthesis Grade acetonitrile was used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) was made up from the solid obtained from American International Chemical, Inc.

[0115] Deprotection of the RNA was performed using either a two-pot or one-pot protocol. For the two-pot protocol, the polymer-bound trityl-on oligoribonucleotide was transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aq. methylamine (1 mL) at 65° C. for 10 min. After cooling to −20° C., the supernatant was removed from the polymer support. The support was washed three times with 1.0 mL of EtOH:MeCN:H20/3:1:1, vortexed and the supernatant was then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, were dried to a white powder. The base deprotected oligoribonucleotide was resuspended in anhydrous TEA/HF/NMP solution (300 μL of a solution of 1.5 mL N-methylpyrrolidinone, 750 μL TEA and 1 mL TEA•3HF to provide a 1.4 M HF concentration) and heated to 65° C. After 1.5 h, the oligomer was quenched with 1.5 M NH4HCO3.

[0116] Alternatively, for the one-pot protocol, the polymer-bound trityl-on oligoribonucleotide was transferred to a 4 mL glass screw top vial and suspended in a solution of 33% ethanolic methylamine/DMSO: 1/1 (0.8 mL) at 65° C. for 15 min. The vial was brought to r.t. TEA•3HF (0.1 mL) was added and the vial was heated at 65° C. for 15 min. The sample was cooled at −20° C. and then quenched with 1.5 M NH4HCO3.

[0117] For purification of the trityl-on oligomers, the quenched NH4HCO3 solution was loaded onto a C-18 containing cartridge that had been prewashed with acetonitrile followed by 50 mM TEAA. After washing the loaded cartridge with water, the RNA was detritylated with 0.5% TFA for 13 min. The cartridge was then washed again with water, salt exchanged with 1 M NaCl and washed with water again. The oligonucleotide was then eluted with 30% acetonitrile.

[0118] Inactive hammerhead ribozymes or binding attenuated control (BAC) oligonucleotides) were synthesized by substituting a U for G5 and a U for A14 (numbering from Hertel, K. J., et al., 1992, Nucleic Acids Res., 20, 3252). Similarly, one or more nucleotide substitutions can be introduced in other enzymatic nucleic acid molecules to inactivate the molecule and such molecules can serve as a negative control.

[0119] The average stepwise coupling yields were >98% (Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684). Those of ordinary skill in the art will recognize that the scale of synthesis can be adapted to be larger or smaller than the example described above including but not limited to 96-well format, all that is important is the ratio of chemicals used in the reaction.

[0120] Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and joined together post-synthetically, for example, by ligation (Moore et al., 1992, Science 256, 9923; Draper et al., International PCT publication No. WO 93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides & Nucleotides, 16, 951; Bellon et al., 1997, Bioconjugate Chem. 8, 204).

[0121] The nucleic acid molecules of the present invention are modified extensively to enhance stability by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-flouro, 2′-O-methyl, 2′-H (for a review see Usman and Cedergren, 1992, TIBS 17, 34; Usman et al, 1994, Nucleic Acids Symp. Ser. 31, 163). Ribozymes are purified by gel electrophoresis using general methods or are purified by high pressure liquid chromatography (HPLC; see Wincott et al., supra, the totality of which is hereby incorporated herein by reference) and are re-suspended in water.

[0122] The sequences of the ribozymes and antisense constructs that are chemically synthesized and used in this study are shown in Tables XIII to XVI and XIX. Those in the art will recognize that these sequences are representative only of many more such sequences where the enzymatic portion of the ribozyme (all but the binding arms) is altered to affect activity. The ribozyme and antisense construct sequences listed in Tables XIII to XVI and XIX can be formed of ribonucleotides or other nucleotides or non-nucleotides. Such ribozymes with enzymatic activity are equivalent to the ribozymes described specifically in the Tables.

[0123] Optimizing Nucleic Acid Catalyst Activity

[0124] Catalytic activity of the enzymatic nucleic acid molecules described and identified using the methods of the instant invention, can be optimized as described by Draper et al., supra and using the methods well known in the art. The details will not be repeated here, but include altering the length of the enzymatic nucleic acid molecules' binding arms, or chemically synthesizing enzymatic nucleic acid molecules with modifications (base, sugar and/or phosphate) that prevent their degradation by serum ribonucleases and/or enhance their enzymatic activity (see e.g., Eckstein et al., International Publication No. WO 92/07065; Perrault et al., 1990 Nature 344, 565; Pieken et al., 1991 Science 253, 314; Usman and Cedergren, 1992 Trends in Biochem. Sci. 17, 334; Usman et al., International Publication No. WO 93/15187; Rossi et al., International Publication No. WO 91/03162; Sproat, U.S. Pat. No. 5,334,711; and Burgin et al., supra; all of these describe various chemical modifications that can be made to the base, phosphate and/or sugar moieties of enzymatic nucleic acid molecules). All these publications are hereby incorporated by reference herein. Modifications which enhance their efficacy in cells, as well as removal of bases from stem loop structures to shorten synthesis times and reduce chemical requirements are desired.

[0125] There are several examples in the art describing sugar, base and phosphate modifications that can be introduced into nucleic acid molecules with significant enhancement in their nuclease stability and efficacy. For example, oligonucleotides are modified to enhance stability and/or enhance biological activity by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-flouro, 2′-O-methyl, 2′-H, nucleotide base modifications (for a review see Usman and Cedergren, 1992, TIBS. 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163; Burgin et al., 1996, Biochemistry, 35, 14090). Sugar modification of nucleic acid molecules have been extensively described in the art (see Eckstein et al., International Publication PCT No. WO 92/07065; Perrault et al. Nature, 1990, 344, 565-568; Pieken et al. Science, 1991, 253, 314-317; Usman and Cedergren, Trends in Biochem. Sci., 1992, 17, 334-339; Usman et al. International Publication PCT No. WO 93/15187; Sproat, U.S. Pat. No. 5,334,711 and Beigelman et al., 1995, J. Biol. Chem., 270, 25702; Beigelman et al., International PCT publication No. WO 97/26270; Beigelman et al., U.S. Pat. No. 5,716,824; Usman et al., U.S. Pat. No. 5,627,053; Woolf et al., International PCT Publication No. WO 98/13526; Thompson et al., U.S. Ser. No. 60/082,404 which was filed on Apr. 20, 1998; Karpeisky et al., 1998, Tetrahedron Lett., 39, 1131; Earnshaw and Gait, 1998, Biopolymers (Nucleic acid Sciences), 48, 39-55; Verma and Eckstein, 1998, Annu. Rev. Biochem., 67, 99-134; and Burlina et al., 1997, Bioorg. Med. Chem., 5, 1999-2010; all of these references are hereby incorporated by reference herein in their totalities). Such publications describe general methods and strategies to determine the location of incorporation of sugar, base and/or phosphate modifications and the like into ribozymes without inhibiting catalysis, and are incorporated by reference herein. In view of such teachings, similar modifications can be used as described herein to modify the nucleic acid molecules of the instant invention.

[0126] While chemical modification of oligonucleotide internucleotide linkages with phosphorothioate, phosphorodithioate, and/or 5′-methylphosphonate linkages improves stability, too many of these modifications may cause some toxicity. Therefore, when designing nucleic acid molecules, the amount of these intemucleotide linkages should be minimized, but can be balanced to provide acceptable stability while reducing potential toxicity. The reduction in the concentration of these linkages should lower toxicity resulting in increased efficacy and higher specificity of these molecules.

[0127] Nucleic acid catalysts having chemical modifications which maintain or enhance enzymatic activity are provided. Such nucleic acid molecules are generally more resistant to nucleases than unmodified nucleic acid. Thus, in a cell and/or in vivo the activity may not be significantly lowered. As exemplified herein, such enzymatic nucleic acid molecules are useful in a cell and/or in vivo even if activity over all is reduced 10-fold (Burgin et al., 1996, Biochemistry, 35, 14090). Such enzymatic nucleic acid molecules herein are said to “maintain” the enzymatic activity.

[0128] Therapeutic nucleic acid molecules (e.g., enzymatic nucleic acid molecules and antisense nucleic acid molecules) delivered exogenously must optimally be stable within cells until translation of the target RNA has been inhibited long enough to reduce the levels of the undesirable protein. This period of time varies between hours to days depending upon the disease state. Clearly, these nucleic acid molecules must be resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of nucleic acid molecules described in the instant invention and in the art have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability as described above.

[0129] By “enhanced enzymatic activity” is meant to include activity measured in cells and/or in vivo where the activity is a reflection of both catalytic activity and enzymatic nucleic acid molecules stability. In this invention, the product of these properties is increased or not significantly (less than 10-fold) decreased in vivo compared to unmodified enzymatic nucleic acid molecules.

[0130] In one embodiment, nucleic acid catalysts having chemical modifications which maintain or enhance enzymatic activity are provided. Such nucleic acid is also generally more resistant to nucleases than unmodified nucleic acid. Thus, in a cell and/or in vivo the activity may not be significantly lowered. As exemplified herein such enzymatic nucleic acid molecules are useful in a cell and/or in vivo even if activity over all is reduced 10-fold (Burgin et al., 1996, Biochemistry, 35, 14090). Such enzymatic nucleic acid molecules herein are said to “maintain” the enzymatic activity on all RNA enzymatic nucleic acid molecule.

[0131] Use of these molecules can lead to better treatment of the disease progression by affording the possibility of combination therapies (e.g., multiple enzymatic nucleic acid molecules targeted to different genes, enzymatic nucleic acid molecules coupled with known small molecule inhibitors, or intermittent treatment with combinations of enzymatic nucleic acid molecules (including different enzymatic nucleic acid molecules motifs) and/or other chemical or biological molecules. The treatment of patients with nucleic acid molecules can also include combinations of different types of nucleic acid molecules. Therapies can be devised which include a mixture of enzymatic nucleic acid molecules (including different enzymatic nucleic acid molecules motifs), antisense and/or 2-5A chimera molecules to one or more targets to alleviate symptoms of a disease.

[0132] Administration of nucleotide mono, di or triphosphates and Nucleic Acid Molecules

[0133] Methods for the delivery of nucleic acid molecules are described in Akhtar et al., 1992, Trends Cell Bio., 2, 139; and Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995 which are both incorporated herein by reference. Sullivan et al., PCT WO 94/02595, further describes the general methods for delivery of enzymatic RNA molecules. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those familiar to the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres. For some indications, nucleic acid molecules can be directly delivered ex vivo to cells or tissues with or without the aforementioned vehicles. Alternatively, the nucleic acid/vehicle combination can be locally delivered by direct injection or by use of a catheter, infusion pump or stent. Other routes of delivery include, but are not limited to, intravascular, intramuscular, subcutaneous or joint injection, aerosol inhalation, oral (tablet or pill form), topical, systemic, ocular, intraperitoneal and/or intrathecal delivery. More detailed descriptions of nucleic acid delivery and administration are provided in Sullivan et al., supra, Draper et al., PCT WO93/23569, Beigelman et al., PCT WO99/05094, and Klimuk et al., PCT WO99/04819 all of which are incorporated by reference herein.

[0134] The molecules of the instant invention can be used as pharmaceutical agents. Pharmaceutical agents prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state in a patient.

[0135] The negatively charged nucleotide mono, di or triphosphates of the invention can be administered and introduced into a patient by any standard means, such as those described above and other methods known in the art, with or without stabilizers, buffers, and the like, to form a pharmaceutical composition. When it is desired to use a liposome delivery mechanism, standard protocols for formation of liposomes can be followed. The compositions of the present invention can also be formulated and used as tablets, capsules or elixirs for oral administration; suppositories for rectal administration; sterile solutions; suspensions for injectable administration; and the like.

[0136] The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the above compounds, e.g., ammonium, sodium, calcium, magnesium, lithium, tributylammoniun, and potassium salts.

[0137] A pharmacological composition or formulation refers to a composition or formulation in a form suitable for administration, e.g., systemic administration, into a cell or patient, preferably a human. Suitable forms, in part, depend upon the use or the route of entry, for example oral, transdermal, or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the negatively charged polymer is desired to be delivered). For example, pharmacological compositions injected into the blood stream should be soluble. Other factors for pharmaceutical formulation are known in the art, and include, for example, considerations such as toxicity and formulations which impede or prevent the enzymatic nucleic acid molecule from exerting its effect.

[0138] By “systemic administration” is meant in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body. Administration routes which lead to systemic absorption include, without limitations: intravenous, subcutaneous, intraperitoneal, inhalation, oral, intrapulmonary and intramuscular. Each of these administration routes expose the desired negatively charged polymers, e.g., NTP's, to an accessible diseased tissue. The rate of entry of a drug into the circulation has been shown to be a function of molecular weight or size. The use of a liposome or other drug carrier comprising the compounds of the instant invention can potentially localize the drug, for example, in certain tissue types, such as the tissues of the reticular endothelial system (RES). A liposome formulation which facilitates the association of drug with the surface of cells such as lymphocytes and macrophages is also useful. This approach can provide enhanced delivery of the drug to target cells by taking advantage of the specificity of macrophage and lymphocyte immune recognition of abnormal cells, such as cancer cells.

[0139] The invention also features compositions comprising surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al Chem. Rev. 1995, 95, 2601-2627; Ishiwata et al., Chem. Pharm. Bull. 1995, 43, 1005-1011). Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., Science 1995, 267, 1275-1276; Oku et al., 1995, Biochim. Biophys. Acta, 1238, 86-90). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of drugs, particularly compared to conventional cationic liposomes which are known to accumulate in tissues of the MPS (Liu et al., J. Biol. Chem. 1995, 42, 24864-24870; Choi et al., International PCT Publication No. WO 96/10391; Ansell et al., International PCT Publication No. WO 96/10390; Holland et al., International PCT Publication No. WO 96/10392; all of these are incorporated by reference herein). Long-circulating liposomes are also likely to protect drugs from nuclease degradation to a greater extent compared to cationic liposomes, based on their ability to avoid accumulation in metabolically aggressive MPS tissues, such as the liver and spleen. All of these references are incorporated by reference herein.

[0140] The present invention also features compositions prepared for storage or administration which include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985) hereby incorporated by reference herein. Suitable carriers can include, for example, preservatives, stabilizers, dyes and flavoring agents, such as sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. Id. at 1449. In addition, antioxidants and suspending agents can be included in acceptable carriers.

[0141] By “patient” is meant an organism which is a donor or recipient of explanted cells or the cells themselves. “Patient” also refers to an organism or the cells of an organism to which the compounds of the invention can be administered. Preferably, the patient is a mammal, e.g., a human, primate or a rodent.

[0142] A pharmaceutically effective dose is that dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of mammal being treated, the physical characteristics of the specific mammal under consideration, concurrent medication, and other factors which those skilled in the medical arts will recognize. Generally, an amount between 0.1 mg/kg and 100 mg/kg body weight/day of active ingredients is administered dependent upon potency of the negatively charged polymer. In a one aspect, the invention provides enzymatic nucleic acid molecules that can be delivered exogenously to specific cells as required.

[0143] The nucleic acid molecules of the present invention can also be administered to a patient in combination with other therapeutic compounds to increase the overall therapeutic effect. The use of multiple compounds to treat an indication can increase the beneficial effects while reducing the presence of side effects. Examples of chemotherapeutic agents that can be combined with the nucleic acid molecules of the invention include, but are not limited to, Paclitaxel, Doxorubicin, Cisplatin, and/or antibodies such as Herceptin.

EXAMPLES

[0144] The following are non-limiting examples showing the synthesis, incorporation and analysis of nucleotide triphosphates and activity of enzymatic nucleic acids of the instant invention.

[0145] Applicant synthesized pyrimidine nucleotide triphosphates using DMAP in the reaction. For purines, applicant utilized standard protocols previously described in the art (Yoshikawa et al supra;. Ludwig, supra). Described below is one example of a pyrimdine nucleotide triphosphate and one purine nucleotide triphosphate synthesis.

Example 1

Synthesis of Purine Nucleotide Triphosphates: 2′-O-methyl-guanosine-5′-triphosphate

[0146] 2′-O-methyl guanosine nucleoside (0.25 grams, 0.84 mmol) was dissolved in triethyl phosphate (5.0) ml by heating to 100° C. for 5 minutes. The resulting clear, colorless solution was cooled to 0° C. using an ice bath under an argon atmosphere. Phosphorous oxychloride (1.8 eq., 0.141 ml) was then added to the reaction mixture with vigorous stirring. The reaction was monitored by HPLC, using a sodium perchlorate gradient. After 5 hours at 0° C., tributylamine (0.65 ml) was added followed by the addition of anhydrous acetonitrile (10.0 ml), and after 5 minutes (reequilibration to 0° C.) tributylammonium pyrophosphate (4.0 eq., 1.53 g) was added. The reaction mixture was quenched with 20 ml of 2 M TEAB after 15 minutes at 0° C. (HPLC analysis with above conditions showed consumption of monophosphate at 10 minutes) then stirred overnight at room temperature, the mixture was evaporated in vacuo with methanol co-evaporation (4×) then diluted in 50 ml 0.05 M TEAB. DEAE sephadex purification was used with a gradient of 0.05 to 0.6 M TEAB to obtain pure triphosphate (0.52 g, 66.0% yield) (elutes around 0.3 M TEAB); the purity was confirmed by HPLC and NMR analysis.

Example 2

Synthesis of Pyrimidine Nucleotide Triphosphates: 2′-O-methylthiomethyl-uridine-5′-triphosphate

[0147] 2′-O-methylthiomethyl uridine nucleoside (0.27 grams, 1.0 mmol) was dissolved in triethyl phosphate (5.0 ml). The resulting clear, colorless solution was cooled to 0° C. with an ice bath under an argon atmosphere. Phosphorus oxychloride (2.0 eq., 0.190 ml) was then added to the reaction mixture with vigorous stirring. Dimethylaminopyridine (DMAP, 0.2 eq., 25 mg) was added, the solution warmed to room temperature and the reaction was monitored by HPLC, using a sodium perchlorate gradient. After 5 hours at 20° C., tributylamine (1.0 ml) was added followed by anhydrous acetonitrile (10.0 ml), and after 5 minutes tributylammonium pyrophosphate (4.0 eq., 1.8 g) was added. The reaction mixture was quenched with 20 ml of 2 M TEAB after 15 minutes at 20° C. (HPLC analysis with above conditions showed consumption of monophosphate at 10 minutes) then stirred overnight at room temperature. The mixture was evaporated in vacuo with methanol co-evaporation (4×) then diluted in 50 ml 0.05 M TEAB. DEAE fast flow Sepharose purification with a gradient of 0.05 to 1.0 M TEAB was used to obtain pure triphosphate (0.40 g, 44% yield) (elutes around 0.3M TEAB) as determined by HPLC and NMR analysis.

Example 3

Utilization of DMAP in Uridine 5′-Triphosphate Synthesis

[0148] The reactions were performed on 20 mg aliquots of nucleoside dissolved in 1 ml of triethyl phosphate and 19 ul of phosphorus oxychloride. The reactions were monitored at 40 minute intervals automatically by HPLC to generate yield-of-product curves at times up to 18 hours. A reverse phase column and ammonium acetate/sodium acetate buffer system (50 mM & 100 mM respectively at pH 4.2) was used to separate the 5′, 3′, 2′ monophosphates (the monophosphates elute in that order) from the 5′-triphosphate and the starting nucleoside. The data is shown in Table III. These conditions doubled the product yield and resulted in a 10-fold improvement in the reaction time to maximum yield (1200 minutes down to 120 minutes for a 90% yield). Selectivity for 5′-monophosphorylation was observed for all reactions. Subsequent triphosphorylation occurred in nearly quantitative yield.

[0149] Materials Used in Bacteriophage T7 RNA Polymerase Reactions

[0150] Buffer 1: Reagents are mixed together to form a 10×stock solution of buffer 1 (400 mM Tris-Cl [pH 8.1], 200 mM MgCl2, 100 mM DTT, 50 mM spermidine, and 0.1% triton® X-100). Prior to initiation of the polymerase reaction methanol, LiCl is added and the buffer is diluted such that the final reaction conditions for condition 1 consisted of: 40 mM tris (pH 8.1), 20 mM MgCl2, 10 mM DTT, 5 mM spermidine, 0.01% triton® X-100, 10% methanol, and 1 mM LiCl.

[0151] BUFFER 2: Reagents are mixed together to form a 10×stock solution of buffer 2 (400 mM Tris-Cl [pH 8.1], 200 mM MgCl2, 100 mM DTT, 50 mM spermidine, and 0.1% triton® X-100). Prior to initiation of the polymerase reaction PEG, LiCl is added and the buffer is diluted such that the final reaction conditions for buffer 2 consisted of: 40 mM tris (pH 8.1), 20 mM MgCl2, 10 mM DTT, 5 mM spermidine, 0.01% triton® X-100, 4% PEG, and 1 mM LiCl.

[0152] BUFFER 3: Reagents are mixed together to form a 10×stock solution of buffer 3 (400 mM Tris-Cl [pH 8.0], 120 mM MgCl2, 50 mM DTT, 10 mM spermidine and 0.02% triton® X-100). Prior to initiation of the polymerase reaction PEG is added and the buffer is diluted such that the final reaction conditions for buffer 3 consisted of: 40 mM tris (pH 8.0), 12 mM MgCl2, 5 mM DTT, 1 mM spermidine, 0.002% triton® X-100, and 4% PEG.

[0153] BUFFER 4: Reagents are mixed together to form a 10×stock solution of buffer 4 (400 mM Tris-Cl [pH 8.0], 120 mM MgCl2, 50 mM DTT, 10 mM spermidine and 0.02% triton® X-100). Prior to initiation of the polymerase reaction PEG, methanol is added and the buffer is diluted such that the final reaction conditions for buffer 4 consisted of: 40 mM tris (pH 8.0), 12 mM MgCl2, 5 mM DTT, 1 mM spermidine, 0.002% triton® X-100, 10% methanol, and 4% PEG.

[0154] BUFFER 5: Reagents are mixed together to form a 10×stock solution of buffer 5 (400 mM Tris-Cl [pH 8.0], 120 mM MgCl2, 50 mM DTT, 10 mM spermidine and 0.02% triton® X-100). Prior to initiation of the polymerase reaction PEG, LiCl is added and the buffer is diluted such that the final reaction conditions for buffer 5 consisted of: 40 mM tris (pH 8.0), 12 mM MgCl2, 5 mM DTT, 1 mM spermidine, 0.002% triton® X-100, 1 mM LiCl and 4% PEG.

[0155] BUFFER 6: Reagents are mixed together to form a 10×stock solution of buffer 6 (400 mM Tris-Cl [pH 8.0], 120 mM MgCl2, 50 mM DTT, 10 mM spermidine and 0.02% triton® X-100). Prior to initiation of the polymerase reaction PEG, methanol is added and the buffer is diluted such that the final reaction conditions for buffer 6 consisted of: 40 mM tris (pH 8.0), 12 mM MgCl2, 5 mM DTT, 1 mM spermidine, 0.002% triton® X-100, 10% methanol, and 4% PEG.

[0156] BUFFER 7: Reagents are mixed together to form a 10×stock solution of buffer 6 (400 mM Tris-Cl [pH 8.0], 120 mM MgCl2, 50 mM DTT, 10 mM spermidine and 0.02% triton® X-100). Prior to initiation of the polymerase reaction PEG, methanol and LiCl is added and the buffer is diluted such that the final reaction conditions for buffer 6 consisted of: 40 mM tris (pH 8.0), 12 mM MgCl2, 5 mM DTT, 1 mM spermidine, 0.002% triton® X-I00, 10% methanol, 4% PEG, and 1 mM LiCl.

Example 4

Screening of Modified Nucleotide Triphosphates with Mutant T7 RNA Polymerase

[0157] Modified nucleotide triphosphates were tested in buffers 1 through 6 at two different temperatures (25 and 37° C.). Buffers 1-6 tested at 25° C. were designated conditions 1-6 and buffers 1-6 tested at 37° C. were designated conditions 7-12 (Table IV). In each condition, Y639F mutant T7 polymerase (Sousa and Padilla, supra) (0.3-2 mg/20 ml reaction), NTP's (2 mM each), DNA template (10 pmol), inorganic pyrophosphatase (5 U/ml) and α32p NTP (0.8 mCi/pmol template) were combined and heated at the designated temperatures for 1-2 hours. The radiolabeled NTP used was different from the modified triphosphate being tested. The samples were resolved by polyacrylamide gel electrophoresis. Using a Phosphorlmager (Molecular Dynamics, Sunnyvale, Calif.), the amount of full-length transcript was quantified and compared with an all-RNA control reaction. The data is presented in Table V; results in each reaction are expressed as a percent compared to the all-ribonucleotide triphosphate (rNTP) control. The control was run with the mutant T7 polymerase using commercially available polymerase buffer (Boehringer Mannheim, Indianapolis, Ind.).

Example 5

Incorporation of Modified NTP's Using Wild-Type T7 RNA Polymerase

[0158] Bacteriophage T7 RNA polymerase was purchased from Boehringer Mannheim at 0.4 U/EL concentration. Applicant used the commercial buffer supplied with the enzyme and 0.2 μCi alpha-32P NTP in a 50 μL reaction with nucleotides triphosphates at 2 mM each. The template was a double-stranded PCR fragment, which was used in previous screens. Reactions were carried out at 37° C. for 1 hour. Ten μL of the sample was run on a 7.5% analytical PAGE and bands were quantitated using a Phosphorlmager. Results are calculated as a comparison to an “all ribo” control (non-modified nucleotide triphosphates) and the results are in Table VI.

Example 6

Incorporation of Multiple Modified Nucleotide Triphosphates Into Oligonucleotides

[0159] Combinations of modified nucleotide triphosphates were tested with the transcription protocol described in example 4, to determine the rates of incorporation of two or more of these triphosphates. Incorporation of 2′-Deoxy-2′-(L-histidine) amino uridine (2′-his-NH2-UTP) was tested with unmodified cytidine nucleotide triphosphates, rATP and rGTP in reaction condition number 9. The data is presented as a percentage of incorporation of modified NTP's compared to the all rNTP control and is shown in Table VII a.

[0160] Two modified cytidines (2′-NH2—CTP or 2′dCTP) were incorporated along with 2′-his-NH2—UTP with identical efficiencies. 2′-his-NH2—UTP and 2′-NH2—CTP were then tested with various unmodified and modified adenosine triphosphates in the same buffer (Table VII b). The best modified adenosine triphosphate for incorporation with both 2′-his-NH2-UTP and 2′-NH2—CTP was 2′-NH2—DAPTP.

Example 7

Optimization of Reaction Conditions for Incorporation of Modified Nucleotide Triphosphate

[0161] The combination of 2′-his-NH2—UTP, 2′-NH2—CTP, 2′-NH2—DAP, and rGTP was tested in several reaction conditions (Table VIII) using the incorporation protocol described in example 9. The results demonstrate that of the buffer conditions tested, incorporation of these modified nucleotide triphosphates occur in the presence of both methanol and LiCl.

Example 8

Selection of Novel Enzymatic Nucleic Acid Molecule Motifs Using 2′-deoxy-2′ Amino Modified GTP and CTP

[0162] For selection of new enzymatic nucleic acid molecule motifs, pools of enzymatic nucleic acid molecules were designed to have two substrate binding arms (5 and 16 nucleotides long) and a random region in the middle. The substrate has a biotin on the 5′ end, 5 nucleotides complementary to the short binding arm of the pool, an unpaired G (the desired cleavage site), and 16 nucleotides complementary to the long binding arm of the pool. The substrate was bound to column resin through an avidin-biotin complex. The general process for selection is shown in FIG. 2. The protocols described below represent one possible method that can be utilized for selection of enzymatic nucleic acid molecules and are given as a non-limiting example of enzymatic nucleic acid molecule selection with combinatorial libraries.

[0163] Construction of Libraries: The oligonucleotides listed below were synthesized by Operon Technologies (Alameda, Calif.). Templates were gel purified and then run through a Sep-Pak™ cartridge (Waters, Millford, Mass.) using the manufacturers protocol. Primers (MST3, MST7c, MST3del) were used without purification.

[0164] Primers:

[0165] MST3 (30 mer): 5′-CAC TTA GCA TTA ACC CTC ACT AAA GGC CGT-3′ (SEQ ID NO: 1528)

[0166] MST7c (33 mer): 5′-TAA TAC GAC TCA CTA TAG GAA AGG TGT GCA ACC-3′ (SEQ ID NO: 1529)

[0167] MST3del (18 mer): 5′-ACC CTC ACT AAA GGC CGT-3′ (SEQ ID NO: 1530)

[0168] Templates:

[0169] MSN60c (93 mer): 5′-ACC CTC ACT AAA GGC CGT (N)60 GGT TGC ACA CCT TTG-3′ (SEQ IDNO: 1531)

[0170] MSN40c (73 mer): 5′-ACC CTC ACT AAA GGC CGT (N)40 GGT TGC ACA CCT TTG-3′ (SEQ ID NO: 1532)

[0171] MSN20c (53 mer): 5′-ACC CTC ACT AAA GGC CGT (N)20 GGT TGC ACA CCT TTG-3′ (SEQ ID NO: 1533)

[0172] N60 library was constructed using MSN60c as a template and MST3/MST7c as primers. N40 and N20 libraries were constructed using MSN40c (or MSN20c) as template and MST3del/MST7c as primers.

[0173] Single-stranded templates were converted into double-stranded DNA by the following protocol: 5 nmol template, 10 nmol each primer, in 10 ml reaction volume using standard PCR buffer, dNTP's, and taq DNA polymerase (all reagents from Boerhinger Mannheim). Synthesis cycle conditions were 94° C., 4 minutes; (94° C., 1 minute; 42° C., 1 minute; 72° C., 2 minutes)×4; 72° C., 10 minutes. Products were checked on agarose gel to confirm the length of each fragment (N60=123 bp, N40=91 bp, N20=71 bp) and then were phenol/chloroform extracted and ethanol precipitated. The concentration of the double-stranded product was 25 μM.

[0174] Transcription of the initial pools was performed in a 1 ml volume comprising: 500 pmol double-stranded template (3×1014 molecules), 40 mM tris-HCl (pH 8.0), 12 mM MgCl2, 1 mM spermidine, 5 mM DTT, 0.002% triton X-100, 1 mM LiCl, 4% PEG 8000, 10% methanol, 2 mM ATP (Pharmacia), 2 mM GTP (Pharmacia), 2 mM 2′-deoxy-2′-amino-CTP (USB), 2 mM 2′-deoxy-2′-amino-UTP (USB), 5 U/ml inorganic pyrophosphatase (Sigma), 5 U/μl T7 RNA polymerase (USB; Y639F mutant was used in some cases at 0.1 mg/ml (Sousa and Padilla, supra)), 37° C., 2 hours. Transcribed libraries were purified by denaturing PAGE (N60=106 ntds, N40=74, N20=54) and the resulting product was desalted using Sep-Pak™ columns and then ethanol precipitated.

[0175] Initial column-Selection: The following biotinylated substrate was synthesized using standard protocols (Usman et al., 1987 J. Am. Chem. Soc., 109, 7845; Scaringe et al., 1990 Nucleic Acids Res., 18, 5433; and Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684):

[0176] Biotin-C18 spacer-5′-GCC GUG GGU UGC ACA CCU UUC C-3′(SEQ ID NO: 1534)-C18 spacer-thiol-modifier C6 S-S-inverted abasic Substrate was purified by denaturing PAGE and ethanol precipitated. 10 nmol of substrate was linked to a NeutrAvidin™ column using the following protocol: 400 μl UltraLink Immobilized NeutrAvidin™ slurry (200 μl beads, Pierce, Rockford, Ill.) were loaded into a polystyrene column (Pierce). The column was washed twice with 1 ml of binding buffer (20 mM NaPO4 (pH 7.5), 150 mM NaCl) and then capped off (i.e., a cap was put on the bottom of the column to stop the flow). 200 μl of the substrate suspended in binding buffer was applied and allowed to incubate at room temperature for 30 minutes with occasional vortexing to ensure even linking and distribution of the solution to the resin. After the incubation, the cap was removed and the column was washed with 1 ml binding buffer followed by 1 ml column buffer (50 mM tris-HCL (pH 8.5), 100 mM NaCl, 50 mM KCl). The column was then ready for use and capped off. 1 nmol of the initial pool RNA was loaded on the column in a volume of 200 μl column buffer. It was allowed to bind the substrate by incubating for 30 minutes at room temperature with occasional vortexing. After the incubation, the cap was removed and the column was washed twice with 1 ml column buffer and capped off. 200 μl of elution buffer (50 mM tris-HCl (pH 8.5), 100 mM NaCl, 50 mM KCl, 25 mM MgCl2) was applied to the column followed by 30 minute incubation at room temperature with occasional vortexing. The cap was removed and four 200 μl fractions were collected using elution buffer.

[0177] Second column (counter selection): A diagram for events in the second column is generally shown in FIG. 3 and substrate oligonucleotide used is shown below:

[0178] 5′-GGU UGC ACA CCU UUC C-3′ (SEQ ID NO: 1535)-C18 spacer-biotin-inverted abasic This column substrate was linked to UltraLink NeutrAvidin™ resin as previously described (40 pmol) which was washed twice with elution buffer. The eluent from the first column purification was then run on the second column. The use of this column allowed for binding of RNA that non-specifically diluted from the first column, while RNA that performed a catalytic event and had product bound to it, flowed through the second column. The fractions were ethanol precipitated using glycogen as carrier and rehydrated in sterile water for amplification.

[0179] Amplification: RNA and primer MST3 (10-100 pmol) were denatured at 90° C. for 3 minutes in water and then snap-cooled on ice for one minute. The following reagents were added to the tube (final concentrations given): 1×PCR buffer (Boerhinger Mannheim), 1 mM dNTP's (for PCR, Boerhinger Mannheim), 2 U/μl RNase-Inhibitor (Boerhinger Mannheim), 10 U/μl Superscript™ II Reverse Transcriptase (BRL). The reaction was incubated for 1 hour at 42° C., then at 95° C. for 5 minutes in order to destroy the Superscript™. The following reagents were then added to the tube to increase the volume five-fold for the PCR step (final concentrations/amounts given): MST7c primer (10-100 pmol, same amount as in RT step), 1X PCR buffer, taq DNA polymerase (0.025-0.05 U/μl, Boerhinger Mannheim). The reaction was cycled as follows: 94° C., 4minutes; (94° C., 30s; 42-54° C., 30s; 72° C., 1 minute)×4-30 cycles; 72° C., 5minutes; 30° C., 30 minutes. Cycle number and annealing temperature were decided on a round by round basis. In cases where heteroduplex was observed, the reaction was diluted five-fold with fresh reagents and allowed to progress through 2 more amplification cycles. Resulting products were analyzed for size on an agarose gel (N60=123 bp, N40=103 bp, N20=83 bp) and then ethanol precipitated.

[0180] Transcriptions: Transcription of amplified products was done using the conditions described above with the following modifications: 10-20% of the amplification reaction was used as template, reaction volume was 100-500 μl, and the products sizes varied slightly (N60=106 ntds, N40=86, N20=66). A small amount of 32P-GTP was added to the reactions for quantitation purposes.

[0181] Subsequent rounds: Subsequent rounds of selection used 20 pmols of input RNA and 40 pmol of the 22 nucleotide substrate on the column.

[0182] Activity of pools: Pools were assayed for activity under single turnover conditions every three to four rounds. Activity assay conditions were as follows: 50 mM tris-HCl (pH 8.5), 25 mM MgCl2, 100 mM NaCl, 50 mM KCl, trace 32P-labeled substrate, 10 nM RNA pool. 2× pool in buffer and, separately, 2×substrate in buffer were incubated at 90° C. for 3 minutes, then at 37° C. for 3 minutes. Equal volume 2×substrate was then added the 2× pool tube (t=0). Initial assay time points were taken at 4 and 24 hours: 5 μl was removed and quenched in 8 μl cold Stop buffer (96% formamide, 20 mM EDTA, 0.05% bromphenyl blue/xylene cyanol). Samples were heated 90° C., 3 minutes, and loaded on a 20% sequencing gel. Quantitation was performed using a Molecular Dynamics Phosphorimager and ImageQuaNT™ software. The data is shown in Table IX.

[0183] Samples from the pools of oligonucleotide were cloned into vectors and sequenced using standard protocols (Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press). The enzymatic nucleic acid molecules were transcribed from a representative number of these clones using methods described in this application. Individuals from each pool were tested for RNA cleavage from N60 and N40 by incubating the enzymatic nucleic acid molecules from the clones with 5/16 substrate in 2 mM MgCl2, pH 7.5, 10 mM KCl at 37° C. The data in Table XI shows that the enzymatic nucleic acid molecules isolated from the pool are individually active.

[0184] Kinetic Activity: Kinetic activity of the enzymatic nucleic acid molecule shown in Table XI, was determined by incubating enzymatic nucleic acid molecule (10 nM) with substrate in a cleavage buffer (pH 8.5, 25 mM MgCl2, 100 mM NaCl, 50 mM KCl) at 37° C.

[0185] Magnesium Dependence: Magnesium dependence of round 15 of N20 was tested by varying MgCl2 while other conditions were held constant (50 mM tris [pH 8.0], 100 mM NaCl, 50 mM KCl, single turnover, 10 nM pool). The data is shown in Table XII, which demonstrates increased activity with increased magnesium concentrations.

Example 9

Selection of Novel Enzymatic Nucleic Acid Molecule Motifs Using 2′-Deoxy-2′-(N-histidyl) Amino UTP, 2′-Fluoro-ATP, and 2′-deoxy-2′-amino CTP and GTP

[0186] The method described in example 8 was repeated using 2′-Deoxy-2′-(N-histidyl) amino UTP, 2′-Fluoro-ATP, and 2′-deoxy-2′-amino CTP and GTP. However, rather than causing cleavage on the initial column with MgCl2, the initial random modified-RNA pool was loaded onto substrate-resin in the following buffer; 5 mM NaOAc pH 5.2, 1 M NaCl at 4° C. After ample washing, the resin was moved to 22° C. and the buffer switch 20 mM HEPES pH 7.4, 140 mM KCl, 10 mM NaCl, 1 mM CaCl2, 1 mM MgCl2. In one selection of N60 oligonucleotides, no divalent cations (MgCl2, CaCl2) was used. The resin was incubated for 10 minutes to allow reaction and the eluant collected.

[0187] The enzymatic nucleic acid molecule pools were capable of cleaving 1-3% of the present substrate even in the absence of divalent cations, the background (in the absence of modified pools) was 0.2-0.4%.

Example 10

Synthesis of 5-substituted 2′-modified Nucleosides

[0188] When designing monomeric nucleoside triphosphates for selection of therapeutic catalytic RNAs, one has to take into account nuclease stability of such molecules in biological sera. A common approach to increase RNA stability is to replace the sugar 2′-OH group with other groups like 2′-fluoro, 2′-O-methyl or 2′-amino. Fortunately such 2′-modified pyrimidine 5′triphosphates are shown to be substrates for RNA polymerases. (Aurup, H.; Williams, D. M.; Eckstein, F. Biochemistry 1992, 31, 9637; and Padilla, R.; Sousa, R. Nucleic Acids Res. 1999, 27, 1561.) On the other hand it has been shown that variety of substituents at pyrimidine 5-position is well tolerated by T7 RNA polymerase (Tarasow, T. M.; Eaton, B. E. Biopolymers 1998, 48, 29), most likely because the natural hydrogen-bonding pattern of these nucleotides is preserved. We chose 2′-fluoro and 2′-O-methyl pyrimidine nucleosides as starting materials for attachment of different functionalities to the 5-position of the base. Both rigid (alkynyl) and flexible (alkyl) spacers were used. The choice of imidazole, amino and carboxylate pendant groups is based on their ability to act as general acids, general bases, nucleophiles and metal ligands, all of which can improve the catalytic effectiveness of selected nucleic acids. FIGS. 12-15 illustrate the synthesis of these compounds.

[0189] As shown in FIG. 12, 2′-O-methyluridine was 3′,5′-bis-acetylated using acetic anhydride in pyridine and then converted to its 5-iodo derivative 1a using I2/ceric ammonium nitrate reagent (Asakura, J.; Robins, M. J. J. Org. Chem. 1990, 55, 4928) (Scheme 1). Both reactions proceeded in a quantitative yield and no chromatographic purifications were needed. Coupling between 1 and N-trifluoroacetyl propargylamine using copper(I) iodide and tetrakis(triphenylphosphine)palladium(0) catalyst as described by Hobbs (Hobbs, F. W.,Jr. J. Org. Chem. 1989, 54, 3420) yielded 2a in 89% yield. Selective O-deacylation with aqueous NaOH afforded 3a which was phosphorylated with POCl3/triethylphosphate (TEP) in the presence of 1,8-bis(dimethylamino)naphthalene (Proton-Sponge) (Method A) (Kovácz, T; Ötvös, L. Tetrahedron Lett. 1988, 29, 4525). The intermediate nucleoside phosphorodichloridate was condensed in situ with tri-n-butylammonium pyrophosphate. At the end, the N-TFA group was removed with concentrated ammonia. 5′-Triphosphate was purified on Sephadex® DEAE A-25 ion exchange column using a linear gradient of 0. 1-0.8 M triethylammonium bicarbonate (TEAB) for elution. Traces of contaminating inorganic pyrophosphate are removed using C-18 RP HPLC to afford analytically pure material. Conversion into Na-salt was achieved by passing the aqueous solution of triphosphate through Dowex 50WX8 ion exchange resin in Na+ form to afford 4a in 45% yield. When Proton-Sponge was omitted in the first phosphorylation step, yields were reduced to 10-20%. Catalytic hydrogenation of 3a yielded 5-aminopropyl derivative 5a which was phosphorylated under conditions identical to those described for propynyl derivative 3a to afford triphosphate 6a in 50% yield.

[0190] For the preparation of imidazole derivatized triphosphates 9a and 11a, we developed an efficient synthesis of N-diphenylcarbamoyl 4-imidazoleacetic acid (ImAADPC): Transient protection of carboxyl group as TMS-ester using TMS-Cl/pyridine followed by DPC-Cl allowed for a clean and quantitative conversion of 4-imidazoleacetic acid (ImAA) to its N-DPC protected derivative.

[0191] Complete deacylation of 2a afforded 5-(3-aminopropynyl) derivative 8a which was condensed with 4-imidazoleacetic acid in the presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide (EDC) to afford 9a in 68% yield. Catalytic hydrogenation of 8a yielded 5-(3-aminopropyl) derivative 10a which was condensed with IMAADPC to yield conjugate 11a in 32% yield. Yields in these couplings were greatly improved when 5′-OH was protected with DMT group (not shown) thus efficiently preventing undesired 5′-O-esterification. Both 9a and 11a failed to yield triphosphate products in reaction with POCl3/TEP/Proton-Sponge.

[0192] On the contrary, phosphorylation of 3′-O-acetylated derivatives 12a and 13a using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one followed by pyrophosphate addition and oxidation (Method B, Scheme 2; Ludwig, J., Eckstein, F., J. Org. Chem. 1989, 54, 631) afforded the desired triphosphates 14a and 15a in 57% yield, respectively (FIG. 13).

[0193] 2′-Deoxy-2′-fluoro nucleoside 5′-triphosphates containing amino-(4b, 6b) and imidazole-(14b, 15b) linked groups were synthesized in a manner analogous to that described for the preparation of 2′-O-methyl nucleoside 5′-triphosphates (Schemes 1 and 2). Again, only Ludwig-Eckstein's phosphorylation worked for the preparation of 4-imidazoleacetyl derivatized triphosphates.

[0194] It is worth noting that when “one-pot-two-steps” phosphorylation reaction (Kovácz, T; Ötvös, L. Tetrahedron Lett. 1988, 29, 4525) of 5b was quenched with 40% aqueous methylamine instead of TEAB or H2O, the γ-amidate 7b was generated as the only detectable product. Similar reaction was reported recently for the preparation of the γ-amidate of pppA2′p5′A2′p5′A.12

[0195] As shown in FIG. 14, carboxylate group was introduced into 5-position of uridine both on the nucleoside level and post-synthetically (Scheme 3). 5-Iodo-2′-deoxy-2′-fluorouridine (16) was coupled with methyl acrylate using modified Heck reaction13 to yield 17 in 85% yield. 5′-O-Dimethoxytritylation, followed by in situ 3′-O-acetylation and subsequent detritylation afforded 3′-protected derivative 18. Phosphorylation using 2-chloro-4H-1,3,2-benzodioxa-phosphorin-4-one followed by pyrophosphate addition and oxidation (Ludwig, J.; Eckstein, F. J. Org. Chem. 1989, 54, 631) afforded the desired triphosphate in 54% yield. On the other hand, 5-(3-aminopropyl)uridine 5′-triphosphate 6b was coupled with N-hydroxysuccinimide ester of Fmoc-Asp-OFm to afford, after removal of Fmoc and Fm groups with diethylamine, the desired aminoacyl conjugate 20 in 50% yield.

[0196] As shown in FIG. 15, cytidine derivatives comprising 3-aminopropyl and 3(N-succinyl)aminopropyl groups were synthesized according to Scheme 4. Peracylated 5-(3-aminopropynyl)uracil derivative 2b is reduced using catalytic hydrogenation and then converted in seven steps and 5% overall yield into 3′-acetylated cytidine derivative 25. This synthesis was plagued by poor solubility of intermediates and formation of the N4-cyclized byproduct during ammonia treatment of the 4-triazolyl intermediate. Phosphorylation of 25 as described in reference 11 yielded triphosphate 26 and N4-cyclized product 27 in 1:1 ratio. They were easily separated on Sephadex DEAE A-25 ion exchange column using 0.1-0.8 M TEAB gradient. Results indicate that under basic conditions the free primary amine can displace any remaining intact 4-NHBz group leading to the cyclized product. This is similar to displacement of 4-triazolyl group by primary amine as mentioned above.

[0197] We reasoned that utilization of N4-unprotected cytidine will solve this problem. This lead to an improved synthesis of 26: lodination of 2′-deoxy-2′-fluorocytidine (28) provided the 5-iodo derivative 29 in 58% yield. This compound was then smoothly converted into 5-(3-aminopropynyl) derivative 30. Hydrogenation afforded 5-(3-aminopropyl) derivative 31 which was phosphorylated directly with POCl3/PPi to afford 26 in 37% yield. Coupling of the 5′-triphosphate 26 with succinic anhydride yielded succinylated derivative 32 in 36% yield.

Example 11

Synthesis of 5-Imidazoleacetic acid 2′-deoxy-5′-triphosphate Uridine

[0198] 5-dintrophenylimidazoleacetic acid 2′-deoxy uridine nucleoside (80 mg) was dissolved in 5 ml of triethylphosphate while stirring under argon, and the reaction mixture was cooled to 0° C. Phosphorous oxychloride (1.8 eq, 22 ml) was added to the reaction mixture at 0° C., three more aliquots were added over the course of 48 hours at room temperature. The reaction mixture was then diluted with anhydrous MeCN (5 ml) and cooled to 0° C., followed by the addition of tributylamine (0.65 ml) and tributylammonium pyrophosphate (4.0 eq, 0.24 g). After 45 minutes, the reaction was quenched with 10 ml aq. methyl amine for four hours. After co-evaporation with MeOH (3×), purified material on DEAE Sephadex was followed by RP chromatography to afford 15 mg of triphosphate.

Example 12

Synthesis of 2′-(N-lysyl)-amino-2′-deoxy-cytidine Triphosphate

[0199] 2′-(N-lysyl)-amino-2′-deoxy cytidine (0.180 g, 0.22 mmol) was dissolved in triethyl phosphate (2.00 ml) under Ar. The solution was cooled to 0° C. in an ice bath. Phosphorus oxychloride (99.999%, 3 eq., 0.0672 mL) was added to the solution and the reaction was stirred for two hours at 0° C. Tributylammonium pyrophosphate (4 eq., 0.400 g) was dissolved in 3.42 mL of acetonitrile and tribuytylamine (0.165 mL). Acetonitrile (1 mL) was added to the monophosphate solution followed by the pyrophosphate solution which was added dropwise. The resulting solution was clear. The reaction was allowed to warm up to room temperature. After stirring for 45 minutes, methylamine (5 mL) was added and the reaction and stirred at room temperature for 2 hours. A biphasic mixture appeared (little beads at the bottom of the flask). TLC (7:1:2 iPrOH:NH4OH:H2O) showed the appearance of triphosphate material. The solution was concentrated, dissolved in water and loaded on a newly prepared DEAE Sephadex A-25 column. The column was washed with a gradient up to 0.6 M TEAB buffer and the product eluted off in fractions 90-95. The fractions were analyzed by ion exchange HPLC. Each fraction showed one triphosphate peak that eluted at ˜4.000 minutes. The fractions were combined and pumped down from methanol to remove buffer salt to yield 15.7 mg of product.

Example 13

Synthesis of 2′-deoxy-2′-(L-histidine)amino Cytidine Triphosphate

[0200] 2′-[N-Fmoc, Nimid-dinitrophenyl-histidyl]amino-2′-cytidine (0.310 g, 4.04 mmol) was dissolved in triethyl phosphate (3 ml) under Ar. The solution was cooled to 0° C. Phosphorus oxychloride (1.8 eq., 0.068 mL) was added to the solution and stored overnight in the freezer. The next morning TLC (10% MeOH in CH2Cl2) showed significant starting material, one more equivalent of POCl3 was added. After two hours, TLC still showed starting material. Tributylamine (0.303 mL) and Tributylammonium pyrophosphate (4 eq., 0.734 g) dissolved in 6.3 mL of acetonitrile (added dropwise) were added to the monophosphate solution. The reaction was allowed to warm up to room temperature. After stirring for 15 min, methylamine (10 mL) was added at room temperature and stirring continued for 2 hours. TLC (7:1:2 iPrOH:NH40H:H2O) showed the appearance of triphosphate material. The solution was concentrated, dissolved in water and loaded on a DEAE Sephadex A-25 column. The column was washed with a gradient up to 0.6 M TEAB buffer and the product eluted off in fractions 170-179. The fractions were analyzed by ion exchange HPLC. Each fraction showed one triphosphate peak that eluted at ˜6.77 minutes. The fractions were combined and pumped down from methanol to remove buffer salt to afford 17 mg of product.

Example 14

Screening for Novel Enzymatic Nucleic Acid Molecule Motifs Using Modified NTPs (Class I Motif)

[0201] Our initial pool contained 3×1014 individual sequences of 2′-amino-dCTP/2′-amino-dUTP RNA. We optimized transcription conditions in order to increase the amount of RNA product by inclusion of methanol and lithium chloride. 2′-amino-2′-deoxynucleotides do not interfere with the reverse transcription and amplification steps of selection and confer nuclease resistance. We designed the pool to have two binding arms complementary to the substrate, separated by the random 40 nucleotide region. The 16-mer substrate had two domains, 5 and 10 nucleotides long, that bind the pool, separated by an unpaired guanosine. On the 5′end of the substrate was a biotin attached by a C18 linker. This enabled us to link the substrate to a NeutrAvidin™ resin in a column format. The desired reaction would be cleavage at the unpaired G upon addition of magnesium cofactor followed by dissociation from the column due to instability of the 5 base pair helix. A detailed protocol follows:

[0202] Enzymatic nucleic acid molecule Pool Prep: The initial pool DNA was prepared by converting the following template oligonucleotides into double-stranded DNA by filling in with taq polymerase.

(template=	5′-ACC CTC ACT AAA GGC CGT (N)40 GGT TGC ACA CCT TTC-3′	(SEQ ID NO:1532);
primer 1=	5′- CAC TTA GCA TTA ACC CTC ACT AAA GGC CGT-3′	(SEQ ID NO:1528);
primer 2=	5′-TAA TAC GAC TCA CTA TAG GAA AGG TGT GCA ACC-3′	(SEQ ID NO:1529)].

[0203] All DNA oligonucleotides were synthesized by Operon technologies. Template oligos were purified by denaturing PAGE and Sep-pak chromatography columns (Waters). RNA substrate oligos were using standard solid phase chemistry and purified by denaturing PAGE followed by ethanol precipitation. Substrates for in vitro cleavage assays were 5′-end labeled with gamma-32P-ATP and T4 polynucleotide kinase followed by denaturing PAGE purification and ethanol precipitation.

[0204] 5 nmole of template, 10 nmole of each primer and 250 U taq polymerase were incubated in a 10 ml volume with 1× PCR buffer (10 mM tris-HCl (pH 8.3), 1.5 mM MgCl2, 50 mM KCl) and 0.2 mM each dNTP as follows: 94° C., 4 minutes; (94° C., 1 min; 42° C., 1 min; 72° C., 2 min) through four cycles; and then 72° C., for 10 minutes. The product was analyzed on 2% Separide™ agarose gel for size and then was extracted twice with buffered phenol, then chloroform-isoamyl alcohol, and ethanol precipitated. The initial RNA pool was made by transcription of 500 pmole (3×1014 molecules) of this DNA as follows. Template DNA was added to 40 mM tris-HCl (pH 8.0), 12 mM MgCl2, 5 mM dithiothreitol (DTT), 1 mM spermidine, 0.002% triton X-100, 1 mM LiCl, 4% PEG-8000, 10% methanol, 2 mM ATP, 2 mM GTP, 2 mM 2′-amino-dCTP, 2 mM 2′-amino-dUTP, 5 U/ml inorganic pyrophosphatase, and 5 U/μl T7 RNA polymerase at room temperature for a total volume of 1 ml. A separate reaction contained a trace amount of alpha-32P-GTP for detection. Transcriptions were incubated at 37° C. for 2 hours followed by addition of equal volume STOP buffer (94% formamide, 20 mM EDTA, 0.05% bromophenol blue). The resulting RNA was purified by 6% denaturing PAGE gel, Seppak™ chromatography, and ethanol precipitated.

[0205] INITIAL SELECTION: 2 nmole of 16 mer 5′-biotinylated substrate (Biotin-C18 linker-5′-GCC GUG GGU UGC ACA C-3′ (SEQ ID NO: 1536)) was linked to 200 μl UltraLink Immobilized NeutrAvidin m resin (400 μl slurry, Pierce) in binding buffer (20 mM NaPO4 (pH 7.5), 150 mM NaCl) for 30 minutes at room temperature. The resulting substrate column was washed with 2 ml binding buffer followed by 2 ml column buffer (50 mM tris-HCl (pH 8.5), 100 mM NaCl, 50 mM KCl). The flow was capped off and 1000 pmole of initial pool RNA in 200 μl column buffer was added to the column and incubated 30 minutes at room temperature. The column was uncapped and washed with 2 ml column buffer, then capped off. 200 μl elution buffer (=column buffer +25 mM MgCl2) was added to the column and allowed to incubate 30 minutes at room temperature. The column was uncapped and eluent collected followed by three 200 μl elution buffer washes. The eluent/washes were ethanol precipitated using glycogen as carrier and rehydrated in 50 μl sterile H2O. The eluted RNA was amplified by standard reverse transcription/PCR amplification techniques. 5-31 μl RNA was incubated with 20 pmol of primer 1 in 14 μl volume 90° for 3 min then placed on ice for 1 minute. The following reagent were added (final concentrations noted): 1× PCR buffer, 1 mM each dNTP, 2 U/μl RNase Inhibitor, 10 U/μl SuperScript™ II reverse transcriptase. The reaction was incubated 42° for 1 hour followed by 95° for 5 min in order to inactivate the reverse transcriptase. The volume was then increased to 100 μl by adding water and reagents for PCR: 1×PCR buffer, 20 pmol primer 2, and 2.5 U taq DNA polymerase. The reaction was cycled in a Hybaid thermocycler: 94°, 4 min; (94° C., 30 sec; 54° C., 30 sec; 72° C., 1 min)×25; 72° C., 5 min. Products were analyzed on agarose gel for size and ethanol precipitated. One-third to one-fifth of the PCR DNA was used to transcribe the next generation, in 100 μl volume, as described above. Subsequent rounds used 20 pmol RNA for the column with 40 pmol substrate.

[0206] TWO COLUMN SELECTION: At generation 8 (G8), the column selection was changed to the two column format. 200 pmoles of 22 mer 5′-biotinylated substrate (Biotin-C18 linker-5′-GCC GUG GGU UGC ACA CCU UUC C-3′ (SEQ ID NO: 1568) -C18 linker-thiol modifier C6 S-S-inverted abasic′) was used in the selection column as described above. Elution was in 200 μl elution buffer followed by a 1 ml elution buffer wash. The 1200 μl eluent was passed through a product trap column by gravity. The product trap column was prepared as follows: 200 pmol 16 mer 5′-biotinylated “product” (5′-GGU UGC ACA CCU UUC C-3′(SEQ ID NO: 1569)-C18 linker-biotin′) was linked to the column as described above and the column was equilibrated in elution buffer. Eluent from the product column was precipitated as previously described. The products were amplified as above only with 2.5-fold more volume and 100 pmol each primer. 100 μl of the PCR reaction was used to do a cycle course; the remaining fraction was amplified the minimal number of cycles needed for product. After 3 rounds (G11), there was visible activity in a single turnover cleavage assay. By generation 13, 45% of the substrate was cleaved at 4 hours; kobs of the pool was 0.037 min−1 in 25 mM MgCl2. We subcloned and sequenced generation 13; the pool was still very diverse. Since our goal was a enzymatic nucleic acid molecule that would work in a physiological environment, we decided to change selection pressure rather than exhaustively catalog G13.

[0207] Reselection of the N40 pool was started from G12 DNA. Part of the G12 DNA was subjected to hypermutagenic PCR (Vartanian et al., 1996, Nucleic Acids Research 24, 2627-2631) to introduce a 10% per position mutation frequency and was designated N40H. At round 19, part of the DNA was hypermutagenized again, giving N40M and N40HM (a total of 4 parallel pools). The column substrates remained the same; buffers were changed and temperature of binding and elution was raised to 37° C. Column buffer was replaced by physiological buffer (50 mM tris-HCl (pH 7.5), 140 mM KCl, 10 mM NaCl) and elution buffer was replaced by 1 mM Mg buffer (physiological buffer+1 mM MgCl2). Amount of time allowed for the pool to bind the column was eventually reduced to 10 min and elution time was gradually reduced from 30 min to 20 sec. Between rounds 18 and 23, kobs for the N40 pool stayed relatively constant at 0.035-0.04 min−1. Generation 22 from each of the 4 pools was cloned and sequenced.

[0208] CLONING AND SEQUENCING: Generations 13 and 22 were cloned using Novagen's Perfectly Blunt™ Cloning kit (pT7Blue-3 vector) following the kit protocol. Clones were screened for insert by PCR amplification using vector-specific primers. Positive clones were sequenced using ABI Prism 7700 sequence detection system and vector-specific primer. Sequences were aligned using MacVector software; two-dimensional folding was performed using Mulfold software (Zuker, 1989, Science 244, 48-52; Jaeger et al., 1989, Biochemistry 86, 7706-7710; Jaeger et al., 1989, R. F. Doolittle ed., Methods in Enzymology, 183, 281-306). Individual clone transcription units were constructed by PCR amplification with 50 pmol each primer 1 and primer 2 in 1×PCR buffer, 0.2 mM each dNTP, and 2.5 U of taq polymerase in 100 μl volume cycled as follows: 94° C., 4 min; (94° C., 30 sec; 54° C., 30 sec; 72° C., 1 min)×20; 72° C., 5 min. Transcription units were ethanol precipitated, rehydrated in 30 μl H2O, and 10 μl was transcribed in 100 μl volume and purified as previously described.

[0209] Thirty-six clones from each pool were sequenced and were found to be variations of the same consensus motif. Unique clones were assayed for activity in 1 mM MgCl2 and physiological conditions; nine clones represented the consensus sequence and were used in subsequent experiments. There were no mutations that significantly increased activity; most of the mutations were in regions believed to be duplex, based on the proposed secondary structure. In order to make the motif shorter, we deleted the 3′-terminal 25 nucleotides necessary to bind the primer for amplification. The measured rates of the full length and truncated molecules were both 0.04 min−1; thus we were able reduce the size of the motif from 86 to 61 nucleotides. The molecule was shortened even further by truncating base pairs in the stem loop structures as well as the substrate recognition arms to yield a 48 nucleotide molecule. In addition, many of the ribonucleotides were replaced with 2-O-methyl modified nucleotides to stabilize the molecule. An example of the new motif is given in FIG. 4. Those of ordinary skill in the art will recognize that the molecule is not limited to the chemical modifications shown in the figure and that it represents only one possible chemically modified molecule. KINETIC ANALYSIS

[0210] Single turnover kinetics were performed with trace amounts of 5′-32P-labeled substrate and 10-1000 nM pool of enzymatic nucleic acid molecule. 2×substrate in 1×buffer and 2×pool/enzymatic nucleic acid molecule in 1×buffer were incubated separately 90° for 3 min followed by equilibration to 37° for 3 min. Equal volume of 2×substrate was added to pool/enzymatic nucleic acid molecule at to and the reaction was incubated at 37° C. Time points were quenched in 1.2 vol STOP buffer on ice. Samples were heated to 90° C. for 3 min prior to separation on 15% sequencing gels. Gels were imaged using a Phosphorlmager and quantitated using ImageQuantTM software (Molecular Dynamics). Curves were fit to double-exponential decay in most cases, although some of the curves required linear fits.

[0211] STABILITY: Serum stability assays were performed as previously described (Beigelman et al., 1995, J. Biol. Chem. 270, 25702-25708). 1 μg of 5′-32P-labeled synthetic enzymatic nucleic acid molecule was added to 13 μl cold and assayed for decay in human serum. Gels and quantitation were as described in the kinetics section.

[0212] SUBSTRATE REQUIREMENTS: Table XVII outlines the substrate requirements for Class I motif. Substrates maintained Watson-Crick or wobble base pairing with mutant Class I constructs. Activity in single turnover kinetic assay is shown relative to wild type Class I and 22 mer substrate (50 mM Tris-HCL (pH 7.5), 140 mM KCl, 10 mM NaCl, 1 mM MgCl2, 100 nM ribozyme, 5 nM substrate, 37° C.).

[0213] RANDOM REGION MUTATION ALIGNMENT: Table XVIII outlines the random region alignment of 134 clones from generation 22 (1.×=N40, 2.×=N40M, 3.×=N40H, 4.×=N40HM). The number of copies of each mutant is in parenthesis in the table, deviations from consensus are shown. Mutations that maintain base pair U19:A34 are shown in italic. Activity in single turnover kinetic assay is shown relative to the G22 pool rate (50 mM Tris-HCL pH 7.5, 140 mM KCl, 10 mM NaCl, 1 mM MgCl2, 100 nM ribozyme, trace substrate, 37° C.).

[0214] STEM TRUNCATION AND LOOP REPLACEMENT ANALYSIS: FIG. 16 shows a representation of Class I ribozyme stem truncation and loop replacement analysis. The Krel is compared to a 61 mer Class I ribozyme measured as described above. FIG. 17 shows examples of Class I ribozymes with truncated stem(s) and/or non-nucleotide linker replaced loop structures.

Example 15

Inhibition of HCV Using Class I (Amberzyme) Motif

[0215] During HCV infection, viral RNA is present as a potential target for enzymatic nucleic acid molecule cleavage at several processes: uncoating, translation, RNA replication and packaging. Target RNA can be accessible to enzymatic nucleic acid molecule cleavage at any one of these steps. Although the association between the HCV initial ribosome entry site (IRES) and the translation apparatus is mimicked in the HCV 5′UTR/luciferase reporter system (example 9), these other viral processes are not represented in the OST7 system. The resulting RNA/protein complexes associated with the target viral RNA are also absent. Moreover, these processes could be coupled in an HCV-infected cell, which could further impact target RNA accessibility. Therefore, we tested whether enzymatic nucleic acid molecules designed to cleave the HCV 5′UTR could effect a replicating viral system.

[0216] Recently, Lu and Wimmer characterized an HCV-poliovirus chimera in which the poliovirus IRES was replaced by the IRES from HCV (Lu & Wimmer, 1996, Proc. Natl. Acad. Sci. USA. 93, 1412-1417). Poliovirus (PV) is a positive strand RNA virus like HCV, but unlike HCV is non-enveloped and replicates efficiently in cell culture. The HCV-PV chimera expresses a stable, small plaque phenotype relative to wild type PV.

[0217] The capability of the new enzymatic nucleic acid molecule motifs to inhibit HCV RNA intracellularly was tested using a dual reporter system that utilizes both firefly and Renilla luciferase (FIG. 5). A number of enzymatic nucleic acid molecules having the new class I motif (Amberzyme) were designed and tested (Table XIII). The Amberzyme ribozymes were targeted to the 5′ HCV UTR region, which when cleaved, would prevent the translation of the transcript into luciferase. OST-7 cells were plated at 12,500 cells per well in black walled 96-well plates (Packard) in medium DMEM containing 10% fetal bovine serum, 1% pen/strep, and 1% L-glutamine and incubated at 37° C. overnight. A plasmid containing T7 promoter expressing 5′ HCV UTR and firefly luciferase (T7C1-341 (Wang et al., 1993, J. of Virol. 67, 3338-3344)) was mixed with a pRLSV40 Renilla control plasmid (Promega Corporation) followed by enzymatic nucleic acid molecule, and cationic lipid to make a 5×concentration of the reagents (T7Cl-341 (4 μg/ml), pRLSV40 renilla luciferase control (6 μg/ml), enzymatic nucleic acid molecule (250 nM), transfection reagent (28.5 μg/ml).

[0218] The complex mixture was incubated at 37° C. for 20 minutes. The media was removed from the cells and 120 μl of Opti-mem media was added to the well followed by 30 μl of the 5× complex mixture. 150 μl of Opti-mem was added to the wells holding the untreated cells. The complex mixture was incubated on OST-7 cells for 4 hours, lysed with passive lysis buffer (Promega Corporation) and luminescent signals were quantified using the Dual Luciferase Assay Kit using the manufacturer's protocol (Promega Corporation). The data shown in FIG. 6 is a dose curve of enzymatic nucleic acid molecule targeting site 146 of the HCV RNA and is presented as a ratio between the firefly and Renilla luciferase fluorescence. The enzymatic nucleic acid molecule was able to reduce the quantity of HCV RNA at all enzymatic nucleic acid molecule concentrations yielding an IC 50 of approximately 5 nM. Other sites were also efficacious (FIG. 7), in particular enzymatic nucleic acid molecules targeting sites 133, 209, and 273 were also able to reduce HCV RNA compared to the irrelevant (IRR) controls.

Example 16

Cleavage of Substrates Using Completely Modified class I (Amberzyme) Enzymatic Nucleic Acid Molecule

[0219] The ability of an enzymatic nucleic acid, which is modified at every 2′ position to cleave a target RNA was tested to determine if any ribonucleotide positions are necessary in the Amberzyme motif. Enzymatic nucleic acid molecules were constructed with 2′-O-methyl, and 2′-amino (NH2) nucleotides and included no ribonucleotides (Table XIII; gene name: no ribo) and kinetic analysis was performed as described in example 13. 100 nM enzymatic nucleic acid was mixed with trace amounts of substrate in the presence of 1 mM MgCl2 at physiological conditions (37° C.). The Amberzyme with no ribonucleotide present in it has a Krel of 0.13 compared to the enzymatic nucleic acid with a few ribonucleotides present in the molecule shown in Table XIII (ribo). This shows that Amberzyme enzymatic nucleic acid molecule may not require the presence of 2′-OH groups within the molecule for activity.

Example 17

Substrate Recognition Rules for Class II (zinzyme) Enzymatic Nucleic Acid Molecules

[0220] Class II (zinzyme) ribozymes were tested for their ability to cleave base-paired substrates with all sixteen possible combinations of bases immediately 5′and 3′ proximal to the bulged cleavage site G. Ribozymes were identical in all remaining positions of their 7 base pair binding arns. Activity was assessed at two and twenty-four hour time points under standard reaction conditions [20 mM HEPES pH 7.4, 140 mM KCl, 10 mM NaCl, 1 mM MgCl2, 1 mM CaCl2-370° C.]. FIG. 10 shows the results of this study. Base paired substrate UGG (not shown in the figure) cleaved as poorly as CGG shown in the figure. The figure shows the cleavage site substrate triplet in the 5′-3′ direction and 2 and 24 hour time points are shown top to bottom respectively. The results indicate the cleavage site triplet is most active with a 5′-Y-G-H -3′ (where Y is C or U and H is A, C or U with cleavage between G and H); however activity is detected particularly with the 24 hour time point for most paired substrates. All positions outside of the cleavage triplet were found to tolerate any base pairings (data not shown).

[0221] All possible mispairs immediately 5′ and 3′ proximal to the bulged cleavage site G were tested to a class II ribozyme designed to cleave a 5′-C-G-C -3′. It was observed the 5′ and 3′ proximal sites are as active with G:U wobble pairs, in addition, the 5′proximal site will tolerate a mismatch with only a slight reduction in activity (data not shown).

Example 18

Screening for Novel Enzymatic Nucleic Acid Molecule Motifs (Class II Motifs)

[0222] The selections were initiated with pools of ≧1014 modified RNA's of the following sequence: 5′-GGGAGGAGGAAGUGCCU-3′ (SEQ ID NO: 1537)-(N)35-5′-UGCCGCGCUCGCUCCCAGUCC-3′ (SEQ ID NO: 1538). The RNA was enzymatically generated using the mutant T7 Y639F RNA polymerase prepared by Rui Souza. The following modified NTP's were incorporated: 2′-deoxy-2′-fluoro-adenine triphosphate, 2′-deoxy-2′-fluoro-uridine triphosphate or 2′-deoxy-2′-fluoro-5-[(N-imidazole-4acetyl)propyl amine] uridine triphosphate, and 2′-deoxy-2′-amino-cytidine triphosphate; natural guanidine triphosphate was used in all selections so that alpha -32p-GTP could be used to label pool RNA's. RNA pools were purified by denaturing gel electrophoresus 8% polyacrilamide 7 M Urea.

[0223] The following target RNA (resin A) was synthesized and coupled to Iodoacetyl Ultralink™ resin (Pierce) by the supplier's procedure: 5′-b-L-GGACUGGGAGCGAGCGCGGCGCAGGCACUGAAG-L-S-B-3′ (SEQ ID NO: 1539); where b is biotin (Glenn Research cat# 10-1953-nn), L is polyethylene glycol spacer (Glenn Research cat# 10-1918-nn), S is thiol-modifier C6 S-S (Glenn Research cat# 10-1936-nn), B is a standard inverted deoxy abasic.

[0224] RNA pools were added to 100 μl of 5 uM Resin A in the buffer A (20 mM HEPES pH 7.4, 140 mM KCL, 10 mM NaCl) and incubated at 22° C. for 5 minutes. The temperature was then raised to 37° C. for 10 minutes. The resin was washed with 5 ml buffer A. Reaction was triggered by the addition of buffer B(20 mM HEPES pH 7.4, 140 mM KCL, 10 mM NaCl, 1 mM MgCl2, 1 mM CaCl2). Incubation proceeded for 20 minutes in the first generation and was reduced progressively to 1 minute in the final generations; with 13 total generations. The reaction eluant was collected in 5 M NaCl to give a final concentration of 2 M NaCl. To this was added 100 μl of 50% slurry Ultralink NeutraAvidinTM (Pierce). Binding of cleaved biotin product to the avidin resin was allowed by 20 minute incubation at 22° C. The resin was subsequently washed with 5 ml of 20 mM HEPES pH 7.4, 2 M NaCl. Desired RNA's were removed by a 1.2 ml denaturing wash 1M NaCl, 10 M Urea at 94° C. over 10 minutes. RNA's were double precipitated in 0.3 M sodium acetate to remove Cl− ions inhibitory to reverse transcription. Standard protocols of reverse transcription and PCR amplification were performed. RNA's were again transcribed with the modified NTP's described above. After 13 generations cloning and sequencing provided 14 sequences which were able to cleave the target substrate. Six sequences were characterized to determine secondary structure and kinetic cleavage rates. The structures and kinetic data are given in FIG. 8. The sequences of eight other enzymatic nucleic acid molecule sequences are given in Table XIV. The size, sequence, and chemical compositions of these molecules can be modified as described under example 13 or using other techniques well known in the art.

[0225] Nucleic Acid Catalyst Engineering

[0226] Sequence, chemical and structural variants of Class I and Class II enzymatic nucleic acid molecule can be engineered and re-engineered using the techniques shown in this application and known in the art. For example, the size of class I and class II enzymatic nucleic acid molecules can, be reduced or increased using the techniques known in the art (Zaug et al., 1986 Nature, 324, 429; Ruffner et al., 1990, Biochem., 29, 10695; Beaudry et al., 1990, Biochem., 29, 6534; McCall et al., 1992, Proc. Natl. Acad. Sci., USA., 89, 5710; Long et al., 1994, supra; Hendry et al., 1994, BBA 1219, 405; Benseler et al., 1993, JACS, 115, 8483; Thompson et al., 1996, Nucl. Acids Res., 24, 4401; Michels et al., 1995, Biochem., 34, 2965; Been et al., 1992, Biochem., 31, 11843; Guo et al., 1995, EMBO. J., 14, 368; Pan et al., 1994, Biochem., 33, 9561; Cech, 1992, Curr. Op. Struc. Bio., 2, 605; Sugiyama et al., 1996, FEBS Lett., 392, 215; Beigelman et al., 1994, Bioorg. Med. Chem., 4, 1715; Santoro et al., 1997, PNAS 94, 4262; all are incorporated in their totality by reference herein), to the extent that the overall catalytic activity of the ribozyme is not significantly decreased.

[0227] Further rounds of in vitro selection strategies described herein and variations thereof can be readily used by a person skilled in the art to evolve additional nucleic acid catalysts and such new catalysts are within the scope of the instant invention.

Example 19

Activity of Class II (zinzyme) Nucleic Acid Catalysts to Inhibit HER2 Gene Expression

[0228] HER2 (also known as neu, erbB2 and c-erbB2) is an oncogene that encodes a 185-kDa transmembrane tyrosine kinase receptor. HER2 is a member of the epidermal growth factor receptor (EGFR) family and shares partial homology with other family members. In normal adult tissues HER2 expression is low. However, HER2 is overexpressed in at least 25-30% of breast (McGuire & Greene, 1989) and ovarian cancers (Berchuck, et al., 1990). Furthermore, overexpression of HER2 in malignant breast tumors has been correlated with increased metastasis, chemoresistance and poor survival rates (Slamon et al., 1987 Science 235: 177-182). Because HER2 expression is high in aggressive human breast and ovarian cancers, but low in normal adult tissues, it is an attractive target for ribozyme-mediated therapy (Thompson et al., supra).

[0229] Cell Culture Review

[0230] The greatest HER2 specific effects have been observed in cancer cell lines that express high levels of HER2 protein (as measured by ELISA). Specifically, in one study that treated five human breast cancer cell lines with the HER2 antibody (anti-erbB2-sFv), the greatest inhibition of cell growth was seen in three cell lines (MDA-MB-361, SKBR-3 and BT-474) that express high levels of HER2 protein. No inhibition of cell growth was observed in two cell lines (MDA-MB-231 and MCF-7) that express low levels of HER2 protein (Wright et al., 1997). Another group successfully used SKBR-3 cells to show HER2 antisense oligonucleotide-mediated inhibition of HER2 protein expression and HER2 RNA knockdown (Vaughn et al., 1995). Other groups have also demonstrated a decrease in the levels of HER2 protein, HER2 mRNA and/or cell proliferation in cultured cells using anti-HER2 ribozymes or antisense molecules (Suzuki, T. et al., 1997; Weichen, et al., 1997; Czubayko, F. et al., 1997; Colomer, et al., 1994; Betram et al., 1994). Because cell lines that express higher levels of HER2 have been more sensitive to anti-HER2 agents, we prefer using several medium to high expressing cell lines, including SKBR-3 and T47D, for ribozyme screens in cell culture.

[0231] A variety of endpoints have been used in cell culture models to look at HER2-mediated effects after treatment with anti-HER2 agents. Phenotypic endpoints include inhibition of cell proliferation, apoptosis assays and reduction of HER2 protein expression. Because overexpression of HER2 is directly associated with increased proliferation of breast and ovarian tumor cells, a proliferation endpoint for cell culture assays will preferably be used as the primary screen. There are several methods by which this endpoint can be measured. Following treatment of cells with ribozymes, cells are allowed to grow (typically 5 days) after which either the cell viability, the incorporation of [3H] thymidine into cellular DNA and/or the cell density can be measured. The assay of cell density is very straightforward and can be done in a 96-well format using commercially available fluorescent nucleic acid stains (such as Syto® 13 or CyQuant®). The assay using CyQuant® is described herein and is currently being employed to screen ˜100 ribozymes targeting HER2 (details below).

[0232] As a secondary, confirmatory endpoint a ribozyme-mediated decrease in the level of HER2 protein expression can be evaluated using a HER2-specific ELISA.

[0233] Validation of Cell Lines and Ribozyme Treatment Conditions

[0234] Two human breast cancer cell lines (T47D and SKBR-3) that are known to express medium to high levels of HER2 protein, respectively, were considered for ribozyme screening. In order to validate these cell lines for HER2-mediated sensitivity, both cell lines were treated with the HER2 specific antibody, Herceptin® (Genentech) and its effect on cell proliferation was determined. Herceptin® was added to cells at concentrations ranging from 0-8 μM in medium containing either no serum (OptiMem), 0.1% or 0.5% FBS and efficacy was determined via cell proliferation. Maximal inhibition of proliferation (˜50%) in both cell lines was observed after addition of Herceptin® at 0.5 nM in medium containing 0.1% or no FBS. The fact that both cell lines are sensitive to an anti-HER2 agent (Herceptin®) supports their use in experiments testing anti-HER2 ribozymes.

[0235] Prior to ribozyme screening, the choice of the optimal lipid(s) and conditions for ribozyme delivery was determined empirically for each cell line. Applicant has established a panel of cationic lipids (lipids as described in PCT application WO99/05094) that can be used to deliver ribozymes to cultured cells and are very useful for cell proliferation assays that are typically 3-5 days in length. (Additional description of useful lipids is provided above, and those skilled in the art are also familiar with a variety of lipids that can be used for delivery of oligonucleotide to cells in culture.) Initially, this panel of lipid delivery vehicles was screened in SKBR-3 and T47D cells using previously established control oligonucleotides. Specific lipids and conditions for optimal delivery were selected for each cell line based on these screens. These conditions were used to deliver HER2 specific ribozymes to cells for primary (inhibition of cell proliferation) and secondary (decrease in HER2 protein) efficacy endpoints.

[0236] Primary Screen: Inhibition of Cell Proliferation

[0237] Although optimal ribozyme delivery conditions were determined for two cell lines, the SKBR-3 cell line was used for the initial screen because it has the higher level of HER2 protein, and thus should be most susceptible to a HER2-specific ribozyme. Follow-up studies can be carried out in T47D cells to confirm delivery and activity results as necessary.

[0238] Ribozyme screens were performed using an automated, high throughput 96-well cell proliferation assay. Cell proliferation was measured over a 5-day treatment period using the nucleic acid stain CyQuant® for determining cell density. The growth of cells treated with ribozyme/lipid complexes were compared to both untreated cells and to cells treated with Scrambled-arm Attenuated core Controls (SAC; FIG. 11). SACs can no longer bind to the target site due to the scrambled arm sequence and have nucleotide changes in the core that greatly diminish ribozyme cleavage. These SACs are used to determine non-specific inhibition of cell growth caused by ribozyme chemistry (i.e. multiple 2′ O-Me modified nucleotides, a single 2′C-allyl uridine, 4 phosphorothioates and a 3′ inverted abasic). Lead ribozymes are chosen from the primary screen based on their ability to inhibit cell proliferation in a specific manner. Dose response assays are carried out on these leads and a subset was advanced into a secondary screen using the level of HER2 protein as an endpoint.

[0239] Secondary Screen: Decrease in HER2 Protein and/or RTA

[0240] A secondary screen that measures the effect of anti-HER2 ribozymes on HER2 protein and/or RNA levels was used to affirm preliminary findings. A robust HER2 ELISA for both T47D and SKBR-3 cells has been established and is available for use as an additional endpoint. In addition, a real time RT-PCR assay (TaqMan assay) has been developed to assess HER2 RNA reduction compared to an actin RNA control. Dose response activity of nucleic acid molecules of the instant invention can be used to assess both HER2 protein and RNA reduction endpoints.

[0241] Ribozyme Mechanism Assays

[0242] A TaqMan® assay for measuring the ribozyme-mediated decrease in HER2 RNA has also been established. This assay is based on PCR technology and can measure in real time the production of HER2 mRNA relative to a standard cellular MRNA such as GAPDH. This RNA assay is used to establish proof that lead ribozymes are working through an RNA cleavage mechanism and result in a decrease in the level of HER2 mRNA, thus leading to a decrease in cell surface HER2 protein receptors and a subsequent decrease in tumor cell proliferation.

[0243] Animal Models

[0244] Evaluating the efficacy of anti-HER2 agents in animal models is an important prerequisite to human clinical trials. As in cell culture models, the most HER2 sensitive mouse tumor xenografts are those derived from human breast carcinoma cells that express high levels of HER2 protein. In a recent study, nude mice bearing BT-474 xenografts were sensitive to the anti-HER2 humanized monoclonal antibody Herceptin®, resulting in an 80% inhibition of tumor growth at a 1 mg kg dose (ip, 2×week for 4-5 weeks). Tumor eradication was observed in 3 of 8 mice treated in this manner (Baselga et al., 1998). This same study compared the efficacy of Herceptin® alone or in combination with the commonly used chemotherapeutics, paclitaxel or doxorubicin. Although, all three anti-HER2 agents caused modest inhibition of tumor growth, the greatest antitumor activity was produced by the combination of Herceptin® and paclitaxel (93% inhibition of tumor growth vs 35% with paclitaxel alone). The above studies provide proof that inhibition of HER2 expression by anti-HER2 agents causes inhibition of tumor growth in animals. Lead anti-HER2 ribozymes chosen from in vitro assays were further tested in mouse xenograft models. Ribozymes were first tested alone and then in combination with standard chemotherapies.

[0245] Animal Model Development

[0246] Three human breast tumor cell lines (T47D, SKBR-3 and BT-474) were characterized to establish their growth curves in mice. These three cell lines have been implanted into the mammary papillae of both nude and SCID mice and primary tumor volumes are measured 3 times per week. Growth characteristics of these tumor lines using a Matrigel implantation format can also be established. The use of two other breast cell lines that have been engineered to express high levels of HER2 can also be used in the described studies. The tumor cell line(s) and implantation method that supports the most consistent and reliable tumor growth is used in animal studies testing the lead HER2 ribozyme(s). Ribozymes are administered by daily subcutaneous injection or by continuous subcutaneous infusion from Alzet mini osmotic pumps beginning 3 days after tumor implantation and continuing for the duration of the study. Group sizes of at least 10 animals are employed. Efficacy is determined by statistical comparison of tumor volume of ribozyme-treated animals to a control group of animals treated with saline alone. Because the growth of these tumors is generally slow (45-60 days), an initial endpoint is the time in days it takes to establish an easily measurable primary tumor (i.e. 50-100 mm3) in the presence or absence of ribozyme treatment.

[0247] Clinical Summary

[0248] Overview

[0249] Breast cancer is a common cancer in women and also occurs in men to a lesser degree. The incidence of breast cancer in the United States is ˜180,000 cases per year and ˜46,000 die each year of the disease. In addition, 21,000 new cases of ovarian cancer per year lead to ˜13,000 deaths (data from Hung et al., 1995 and the Surveillance, Epidemiology and End Results Program, NCI). Ovarian cancer is a potential secondary indication for anti-HER2 ribozyme therapy.

[0250] A full review of breast cancer is given in the NCI PDQ for Breast Cancer. A brief overview is given here. Breast cancer is evaluated or “staged” on the basis of tumor size, and whether it has spread to lymph nodes and/or other parts of the body. In Stage I breast cancer, the cancer is no larger than 2 centimeters and has not spread outside of the breast. In Stage II, the patient's tumor is 2-5 centimeters but cancer may have spread to the axillary lymph nodes. By Stage III, metastasis to the lymph nodes is typical, and tumors are ≧5 centimeters. Additional tissue involvement (skin, chest wall, ribs, muscles etc.) may also be noted. Once cancer has spread to additional organs of the body, it is classed as Stage IV.

[0251] Almost all breast cancers (>90%) are detected at Stage I or II, but 31% of these are already lymph node positive. The 5-year survival rate for node negative patients (with standard surgery/radiation/chemotherapy/hormone regimens) is 97%; however, involvement of the lymph nodes reduces the 5-year survival to only 77%. Involvement of other organs (≧Stage III) drastically reduces the overall survival, to 22% at 5 years. Thus, chance of recovery from breast cancer is highly dependent on early detection. Because up to 10% of breast cancers are hereditary, those with a family history are considered to be at high risk for breast cancer and should be monitored very closely.

[0252] Therapy

[0253] Breast cancer is highly treatable and often curable when detected in the early stages. (For a complete review of breast cancer treatments, see the NCI PDQ for Breast Cancer.) Common therapies include surgery, radiation therapy, chemotherapy and hormonal therapy. Depending upon many factors, including the tumor size, lymph node involvement and location of the lesion, surgical removal varies from lumpectomy (removal of the tumor and some surrounding tissue) to mastectomy (removal of the breast, lymph nodes and some or all of the underlying chest muscle). Even with successful surgical resection, as many as 21% of the patients may ultimately relapse (10-20 years). Thus, once local disease is controlled by surgery, adjuvant radiation treatments, chemotherapies and/or hormonal therapies are typically used to reduce the rate of recurrence and improve survival. The therapy regimen employed depends not only on the stage of the cancer at its time of removal, but other variables such the type of cancer (ductal or lobular), whether lymph nodes were involved and removed, age and general health of the patient and if other organs are involved.

[0254] Common chemotherapies include various combinations of cytotoxic drugs to kill the cancer cells. These drugs include paclitaxel (Taxol), docetaxel, cisplatin, methotrexate, cyclophosphamide, doxorubin, fluorouracil etc. Significant toxicities are associated with these cytotoxic therapies. Well-characterized toxicities include nausea and vomiting, myelosuppression, alopecia and mucosity. Serious cardiac problems are also associated with certain of the combinations, e.g. doxorubin and paclitaxel, but are less common.

[0255] Testing for estrogen and progesterone receptors helps to determine whether certain anti-hormone therapies might be helpful in inhibiting tumor growth. If either or both receptors are present, therapies to interfere with the action of the hormone ligands, can be given in combination with chemotherapy and are generally continued for several years. These adjuvant therapies are called SERMs, selective estrogen receptor modulators, and they can give beneficial estrogen-like effects on bone and lipid metabolism while antagonizing estrogen in reproductive tissues. Tamoxifen is one such compound. The primary toxic effect associated with the use of tamoxifen is a 2 to 7-fold increase in the rate of endometrial cancer. Blood clots in the legs and lung and the possibility of stroke are additional side effects. However, tamoxifen has been determined to reduce breast cancer incidence by 49% in high-risk patients and an extensive, somewhat controversial, clinical study is underway to expand the prophylactic use of tamoxifen. Another SERM, raloxifene, was also shown to reduce the incidence of breast cancer in a large clinical trial where it was being used to treat osteoporosis. In additional studies, removal of the ovaries and/or drugs to keep the ovaries from working are being tested.

[0256] Bone marrow transplantation is being studied in clinical trials for breast cancers that have become resistant to traditional chemotherapies or where >3 lymph nodes are involved. Marrow is removed from the patient prior to high-dose chemotherapy to protect it from being destroyed, and then replaced after the chemotherapy. Another type of “transplant” involves the exogenous treatment of peripheral blood stem cells with drugs to kill cancer cells prior to replacing the treated cells in the bloodstream.

[0257] One biological treatment, a humanized monoclonal anti-HER2 antibody, Herceptin® (Genentech) has been approved by the FDA as an additional treatment for HER2 positive tumors. Herceptin® binds with high affinity to the extracellular domain of HER2 and thus blocks its signaling action. Herceptin® can be used alone or in combination with chemotherapeutics (i.e. paclitaxel, docetaxel, cisplatin, etc.) (Pegram, et al., 1998). In Phase III studies, Herceptin® significantly improved the response rate to chemotherapy as well as improving the time to progression (Ross & Fletcher, 1998). The most common side effects attributed to Herceptin® are fever and chills, pain, asthenia, nausea, vomiting, increased cough, diarrhea, headache, dyspnea, infection, rhinitis, and insomnia. Herceptin® in combination with chemotherapy (paclitaxel) can lead to cardiotoxicity (Sparano, 1999), leukopenia, anemia, diarrhea, abdominal pain and infection.

[0258] HER2 Protein Levels for Patient Screening and as a Potential Endpoint

[0259] Because elevated HER2 levels can be detected in at least 30% of breast cancers, breast cancer patients can be pre-screened for elevated HER2 prior to admission to initial clinical trials testing an anti-HER2 ribozyme. Initial HER2 levels can be determined (by ELISA) from tumor biopsies or resected tumor samples.

[0260] During clinical trials, it may be possible to monitor circulating HER2 protein by ELISA (Ross and Fletcher, 1998). Evaluation of serial blood/serum samples over the course of the anti-HER2 ribozyme treatment period could be useful in determining early indications of efficacy. In fact, the clinical course of Stage IV breast cancer was correlated with shed HER2 protein fragment following a dose-intensified paclitaxel monotherapy. In all responders, the HER2 serum level decreased below the detection limit (Luftner et al.).

[0261] Two cancer-associated antigens, CA27.29 and CA15.3, can also be measured in the serum. Both of these glycoproteins have been used as diagnostic markers for breast cancer. CA27.29 levels are higher than CA15.3 in breast cancer patients; the reverse is true in healthy individuals. Of these two markers, CA27.29 was found to better discriminate primary cancer from healthy subjects. In addition, a statistically significant and direct relationship was shown between CA27.29 and large vs small tumors and node postive vs node negative disease (Gion, et al., 1999). Moreover, both cancer antigens were found to be suitable for the detection of possible metastases during follow-up (Rodriguez de Paterna et al., 1999). Thus, blocking breast tumor growth may be reflected in lower CA27.29 and/or CA15.3 levels compared to a control group. FDA submissions for the use of CA27.29 and CA15.3 for monitoring metastatic breast cancer patients have been filed (reviewed in Beveridge, 1999). Fully automated methods for measurement of either of these markers are commercially available.

[0262] References

[0263] Baselga, J., Norton, L. Albanell, J., Kim, Y. M. and Mendelsohn, J. (1998) Recombinant humanized anti-HER2 antibody (Herceptin) enhances the antitumor activity of paclitaxel and doxorubicin against HER2/neu overexpressing human breast cancer xenografts. Cancer Res. 15: 2825-2831.

[0264] Berchuck, A. Kamel, A., Whitaker, R. et al. (1990) Overexpression of her-2/neu is associated with poor survival in advanced epithelial ovarian cancer. Cancer Research 50: 4087-4091.

[0265] Bertram, J. Killian, M., Brysch, W., Schlingensiepen, K.-H., and Kneba, M. (1994) Reduction of erbB2 gene product in mamma carcinoma cell lines by erbB2 mRNA-specific and tyrosine kinase consensus phosphorothioate antisense oligonucleotides. Biochem. BioPhys. Res. Comm. 200: 661-667.

[0266] Beveridge, R. A. (1999) Review of clinical studies of CA27.29 in breast cancer management. Int. J. Biol. Markers 14: 36-39.

[0267] Colomer, R., Lupu, R., Bacus, S. S. and Gelmann, E. P. (1994) erbB-2 antisense oligonucloetides inhibit the proliferation of breast carcinoma cells with erbB-2 oncogene amplification. British J. Cancer 70: 819-825.

[0268] Czubayko, F., Downing, S. G., Hsieh, S. S., Goldstein, D. J., Lu P. Y., Trapnell, B. C. and Wellstein, A. (1997) Adenovirus-mediated transduction of ribozymes abrogates HER-2/neu and pleiotrophin expression and inhibits tumor cell proliferation. Gene Ther. 4: 943-949.

[0269] Gion, M., Mione, R., Leon, A. E. and Dittadi, R. (1999) Comparison of the diagnostic accuracy of CA27.29 and CA15.3 in primary breast cancer. Clin. Chem. 45: 630-637.

[0270] Hung, M.-C., Matin, A., Zhang, Y., Xing, X., Sorgi, F., Huang, L. and Yu, D. (1995) HER-2/neu-targeting gene therapy—a review. Gene 159: 65-71.

[0271] Luftner, D., Schnabel. S. and Possinger, K. (1999) c-erbB-2 in serum of patients receiving fractionated paclitaxel chemotherapy. Int. J. Biol. Markers 14: 55-59.

[0272] McGuire, H. C. and Greene, M. I. (1989) The neu (c-erbB-2) oncogene. Semin. Oncol. 16: 148-155.

[0273] NCI PDQ/Treatment/Health Professionals/Breast Cancer:

[0274] http://cancernet.nci.nih.gov/clinpdq/soa/Breast_cancer_Physician.html

[0275] NCI PDQ/Treatment/Patients/Breast Cancer:

[0276] http://cancernet.nci.nih. gov/clinpdq/pif/Breast _cancer _Patient.html Pegram, M. D., Lipton, A., Hayes, D. F., Weber, B. L., Baselga, J. M., Tripathy, D., Baly, D., Baughman, S. A., Twaddell, T., Glaspy, J. A. and Slamon, D. J. (1998) Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p1 85HER2/neu monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment. J. Clin. Oncol. 16: 2659-2671.

[0277] Rodriguez de Patema, L., Arnaiz, F., Estenoz, J. Ortuno, B. and Lanzos E. (1999) Study of serum tumor markers CEA, CA15.3, CA27.29 as diagnostic parameters in patients with breast carcinoma. Int. J. Biol. Markers 10: 24-29.

[0278] Ross, J. S. and Fletcher, J. A. (1998) The HER-2/neu oncogene in breast cancer: Prognostic factor, predictive factor and target for therapy. Oncologist 3: 1998.

[0279] Slamon, D. J., Clark, G. M., Wong, S. G., Levin, W. J., Ullrich, A. and McGuire, W. L. (1987) Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235: 177-182.

[0280] Sparano, J. A. (1999) Doxorubicin/taxane combinations: Cardiac toxicity and pharmacokinetics. Semin. Oncol. 26: 14-19.

[0281] Surveillance, Epidemiology and End Results Program (SEER) Cancer Statistics Review: http://www.seer.ims.nci.nih.gov/Publications/CSR1973—1996/

[0282] Suzuki T., Curcio, L. D., Tsai, J. and Kashani-Sabet M. (1997) Anti-c-erb-B-2 Ribozyme for Breast Cancer. In Methods in Molecular Medicine, Vol. 11, Therapeutic Applications of Ribozmes, Human Press, Inc., Totowa, N.J.

[0283] Vaughn, J. P., Iglehart, J. D., Demirdji, S., Davis, P., Babiss, L. E., Caruthers, M. H., Marks, J. R. (1995) Antisense DNA downregulation of the ERBB2 oncogene measured by a flow cytometric assay. Proc Natl Acad Sci USA 92: 8338-8342.

[0284] Weichen, K., Zimmer, C. and Dietel, M. (1997) Selection of a high activity c-erbB-2 ribozyme using a fusion gene of c-erbB-2 and the enhanced green fluorescent protein. Cancer Gene Therapy 5: 45-51.

[0285] Wright, M., Grim, J., Deshane, J., Kim, M., Strong, T. V., Siegel, G. P., Curiel, D. T. (1997) An intracellular anti-erbB-2 single-chain antibody is specifically cytotoxic to human breast carcinoma cells overexpressing erbB-2. Gene Therapy 4: 317-322.

[0286] Applicant has designed, synthesized and tested several class II (zinzyme) ribozymes targeted against HER2 RNA (see, for example, Tables XV, XVI, and XIX) in cell proliferation RNA reduction assays described herein.

[0287] Proliferation assay: The model proliferation assay used in the study requires a cell-plating density of 2,000-10,000 cells/well in 96-well plates and at least 2 cell doublings over a 5-day treatment period. Cells used in proliferation studies were either human breast or ovarian cancer cells (SKBR-3 and SKOV-3 cells respectively). To calculate cell density for proliferation assays, the FIPS (fluoro-imaging processing system) method known in the art was used. This method allows for cell density measurements after nucleic acids are stained with CyQuant® dye, and has the advantage of accurately measuring cell densities over a very wide range 1,000-100,000 cells/well in 96-well format.

[0288] Ribozymes (50-200 nM) were delivered in the presence of cationic lipid at 2.0-5.0 μg/mL and inhibition of proliferation was determined on day 5 post-treatment. Two fall ribozyme screens were completed resulting in the selection of 14 ribozymes. Class II (zinzyme) ribozymes against sites, 314 (RPI No. 18653), 443 (RPI No. 18680), 597 (RPI No. 18697), 659 (RPI No. 18682), 878 (RPI Nos. 18683 and 18654), 881 (RPI Nos. 18684 and 18685) 934 (RPI No. 18651), 972 (RPI No. 18656, 19292, 19727, 19728, and 19293), 1292 (RPI No. 18726), 1541 (RPI No. 18687), 2116 (RPI No. 18729), 2932 (RPI No. 18678), 2540 (RPI No. 18715), and 3504 (RPI No. 18710) caused inhibition of proliferation ranging from 25-80% as compared to a scrambled control ribozyme. An example of results from a cell culture assay is shown in FIG. 11. Referring to FIG. 11, Class II ribozymes targeted against HER2 RNA are shown to cause significant inhibition of proliferation of cells. This shows that ribozymes, for instance the Class II (zinzyme) ribozymes are capable of inhibiting HER2 gene expression in mammalian cells.

[0289] RNA assay: RNA was harvested 24 hours post-treatment using the Qiagen RNeasy® 96 procedure. Real time RT-PCR (TaqMan® assay) was performed on purified RNA samples using separate primer/probe sets specific for either target HER2 RNA or control actin RNA (to normalize for differences due to cell plating or sample recovery). Results are shown as the average of triplicate determinations of HER2 to actin RNA levels post-treatment. FIG. 21 shows class II ribozyme (zinzyme) mediated reduction in HER2 RNA targeting site 972 vs a scrambled attenuated control.

[0290] Dose response assays: Active ribozyme was mixed with binding arm-attenuated control (BAC) ribozyme to a final oligonucleotide concentration of either 100, 200 or 400 nM and delivered to cells in the presence of cationic lipid at 5.0 μg/mL. Mixing active and BAC in this manner maintains the lipid to ribozyme charge ratio throughout the dose response curve. HER2 RNA reduction was measured 24 hours post-treatment and inhibition of proliferation was determined on day 5 post-treatment. The dose response anti-proliferation results are summarized in FIG. 22 and the dose-dependent reduction of HER2 RNA results are summarized in FIG. 23. FIG. 24 shows a combined dose response plot of both anti-proliferation and RNA reduction data for a class II ribozyme targeting site 972 of HER2 RNA (RPI 19293), “Herzyme”.

Example 20

Reduction of Ribose Residues in Class II (zinzyme) Nucleic Acid Catalysts

[0291] Class II (zinzyme) nucleic acid catalysts were tested for their activity as a function of ribonucleotide content. A Zinzyme having no ribonucleotide residue (ie., no 2′-OH group at the 2′position of the nucleotide sugar) against the K-Ras site 521 was designed. These molecules were tested utilizing the chemistry shown in FIG. 18a. The in vitro catalytic activity of the zinzyme construct was not significantly effected (the cleavage rate reduced only 10 fold).

[0292] The Kras zinzyme shown in FIG. 18a was tested in physiological buffer with the divalent concentrations as indicated in the legend (high NaCl is an altered monovalent condition shown) of FIG. 19. The 1 mM Ca++ condition yielded a rate of 0.005 min−1 while the 1 mM Mg++ condition yielded a rate of 0.002 min−1. The ribose containing wild type yields a rate of 0.05 min−1 while substrate in the absence of zinzyme demonstrates less than 2% degradation at the longest time point under reaction conditions shown. This illustrates a well-behaved cleavage reaction catalyzed by a non-ribose containing catalyst with only a 10-fold reduced cleavage as compared to ribonucleotide-containing zinzyme and vastly above non-catalyzed degradation.

[0293] A more detailed investigation into the role of ribose positions in the Class II (zinzyme) motif was carried out in the context of the HER2 site 972 (Applicant has further designed a fully modified Zinzyme as shown in FIG. 18b targeting the HER2 RNA site 972). FIG. 20 is a diagram of the alternate formats tested and their relative rates of catalysis. The effect of substitution of ribose G for the 2′-O-methyl C-2′-O-methyl A in the loop of Zinzyme (see FIG. 25) was insignificant when assayed with the Kras target but showed a modest rate enhancement in the HER2 assays. The activity of all Zinzyme motifs, including the fully stabilized “0 ribose” (RPI 19727) are well above background noise level degradation. Zinzyme with only two ribose positions (RPI 19293) are sufficient to restore “wild-type” activity. Motifs containing 3 (RPI 19729), 4 (RPI 19730) or 5 ribose (RPI 19731) positions demonstrated a greater extent of cleavage and profiles almost identical to the 2 ribose motif. Applicant has thus demonstrated that a Zinzyme with no ribonucleotides present at any position can catalyze efficient RNA cleavage activity. Thus, Zinzyme enzymatic nucleic acid molecules do not require the presence of 2′-OH group within the molecule for catalytic activity.

Example 21

Activity of Reduced Ribose Containing Class II (zinzyme) Nucleic Acid Catalysts to Inhibit HER2 Gene Expression

[0294] A cell proliferation assay for testing reduced ribo class II (zinzyme) nucleic acid catalysts (50-400 nM) targeting HER2 site 972 was performed as described in example 19. The results of this study are summarized in FIG. 26. These results indicate significant inhibition of HER2 gene expression using stabilized Class II (zinzyme) motifs, including two ribo (RPI 19293), one ribo (RPI 19728), and non-ribo (RPI 19727) containing nucleic acid catalysts.

Example 22

Activity of Nucleic Acid Catalysts and Chemotherapy in Combination to Inhibit HER2 Gene Expression

[0295] A series of cell culture experiments that combined the anti-HER2 zinzyme nucleic acid targeting site 972 (RPI 19293) “Herzyme” with Paclitaxel (PAX in FIGS. 27 and 30), Doxorubicin (DOX in FIGS. 28 and 31), and Cisplatin (CIS in FIGS. 29 and 32) in HER2 over-expressing cell lines (SK-BR-3 and SK-OV-3) were performed. SK-BR-3 cells were maintained in McCoy's medium (GIBCO/BRL) supplemented with 10% fetal calf serum, L-glutamine (2 mM), bovine insulin (10 μg/mL) and penicillin/streptomycin. SK-OV-3 cells were maintained in EMEM (GIBCO/BRL) supplemented with 10% fetal calf serum and penicillin/streptomycin. SK-BR-3 or SK-OV-3 cells were seeded at densities of 5,000 or 10,000 cells/well respectively in 100 μL of complexing medium and incubated at 37° C. under 5% CO2 for 24 hours. Transfection of zinzymes (50-400 nM) was achieved by the following method: a 5× mixture of zinzyme (250-2000 nM) and cationic lipid (7.5-25 μg/mL) was made in 150 μL of complexing medium (growth medium minus pen/strep). Zinzyme/lipid complexes were allowed to form for 20 min at 37° C. under 5% CO2. A 25 μL aliquot of 5×zinzyme/lipid complexes was then added to treatment wells in triplicate resulting in a 1× final concentration of zinzyme and lipid. Anti-proliferative activity of zinzymes was determined at 24-120 hours post-treatment depending on the assay used (see below). HER2 mRNA reduction was determined at 18, 20 or 24 hours post-treatment using the RT-PCR assay.

[0296] Zinzyme-mediated anti-proliferative activity was determined by measuring cell density at various times post treatment. For initial screens, cell density was determined by nucleic acid staining of live cells with CyQuant (Molecular Probes) 5 days post-treatment. Anti-proliferative activity of lead zinzymes was subsequently measured by the ability of live cells to incorporate BrdU or reduce MTS to formazon (Promega).

[0297] Total RNA was purified from transfected cells using the Qiagen RNeasy 96 procedure including a DNase I treatment at 12, 18, or 24 hours post-treatment. Real time RT-PCR (Taqman assay) was performed on purified RNA samples using separate primer/probe sets for the target HER2 RNA or actin housekeeping RNA. Actin RNA was used to normalize for differences in total RNA samples due to non-specific toxicity associated with the use of a cationic lipid delivery vehicle or differences in sample recovery. A scrambled-arm attenuated core (SAC) zinzyme (RPI 21083) was used as a control. SACs contain scrambled binding arms and changes to the catalytic core and thus, can no longer bind or catalyze cleavage of target HER2 mRNA. Cells were pre-treated with either the active zinzyme (RPI 19293), “Herzyme” or SAC control (RPI 21083) (50-200 nM) for 24 hours. Paclitaxel (0-6 nM), Doxorubicin (0-40 nM), or Cisplatin (0-5 nM) was added to pre-treated cells for an additional 3-4 days. Anti-proliferative activity was determined by the ability of live cells to reduce MTS to formazon (Promega). ANOVA and student's T-test were used to determine statistical analysis of results. Results are summarized in FIGS. 27-32, which demonstrate an additive effect of combined zinzyme treatment with chemotherapy against HER2 expression.

[0298] Applications

[0299] The use of NTP's described in this invention have several research and commercial applications. These modified nucleotide triphosphates can be used for in vitro selection (evolution) of oligonucleotides with novel functions. Examples of in vitro selection protocols are incorporated herein by reference (Joyce, 1989, Gene, 82, 83-87; Beaudry et al., 1992, Science 257, 635-641; Joyce, 1992, Scientific American 267, 90-97; Breaker et al., 1994, TIBTECH 12, 268; Bartel et al.,1993, Science 261:1411-1418; Szostak, 1993, TIBS 17, 89-93; Kumar et al, 1995, FASEB J., 9, 1183; Breaker, 1996, Curr. Op. Biotech., 7, 442).

[0300] Additionally, these modified nucleotide triphosphates can be employed to generate modified oligonucleotide combinatorial chemistry libraries. Several references for this technology exist (Brenner et al., 1992, PNAS 89, 5381-5383, Eaton, 1997, Curr. Opin. Chem. Biol. 1, 10-16) which are all incorporated herein by reference.

[0301] Diagnostic uses

[0302] Enzymatic nucleic acid molecules of this invention can be used as diagnostic tools to examine genetic drift and mutations within diseased cells or to detect the presence of specific RNA in a cell. The close relationship between enzymatic nucleic acid molecule activity and the structure of the target RNA allows the detection of mutations in any region of the molecule which alters the base-pairing and three-dimensional structure of the target RNA. By using multiple enzymatic nucleic acid molecules described in this invention, one can map nucleotide changes that are important to RNA structure and function in vitro, as well as in cells and tissues. Cleavage of target RNAs with enzymatic nucleic acid molecules can be used to inhibit gene expression and define the role (essentially) of specified gene products in the progression of disease. In this manner, other genetic targets can be defined as important mediators of the disease. These experiments can lead to better treatment of the disease progression by affording the possibility of combinational therapies (e.g., multiple enzymatic nucleic acid molecules targeted to different genes, enzymatic nucleic acid molecules coupled with known small molecule inhibitors, radiation or intermittent treatment with combinations of enzymatic nucleic acid molecules and/or other chemical or biological molecules). Other in vitro uses of enzymatic nucleic acid molecules of this invention are well known in the art, and include detection of the presence of mRNAs associated with related conditions. Such RNA is detected by determining the presence of a cleavage product after treatment with a enzymatic nucleic acid molecule using standard methodology.

[0303] In a specific example, enzymatic nucleic acid molecules which cleave only wild-type or mutant forms of the target RNA are used for the assay. The first enzymatic nucleic acid molecule is used to identify wild-type RNA present in the sample and the second enzymatic nucleic acid molecule is used to identify mutant RNA in the sample. As reaction controls, synthetic substrates of both wild-type and mutant RNA are cleaved by both enzymatic nucleic acid molecules to demonstrate the relative enzymatic nucleic acid molecule efficiencies in the reactions and the absence of cleavage of the “non-targeted” RNA species. The cleavage products from the synthetic substrates also serve to generate size markers for the analysis of wild type and mutant RNAs in the sample population. Thus, each analysis involves two enzymatic nucleic acid molecules, two substrates and one unknown sample which is combined into six reactions. The presence of cleavage products is determined using an RNAse protection assay so that full-length and cleavage fragments of each RNA can be analyzed in one lane of a polyacrylamide gel. It is not absolutely required to quantify the results to gain insight into the expression of mutant RNAs and putative risk of the desired phenotypic changes in target cells.

[0304] The expression of mRNA whose protein product is implicated in the development of the phenotype is adequate to establish risk. If probes of comparable specific activity are used for both transcripts, then a qualitative comparison of RNA levels is adequate and will decrease the cost of the initial diagnosis. Higher mutant form to wild-type ratios are correlated with higher risk whether RNA levels are compared qualitatively or quantitatively.

[0305] Additional Uses

[0306] Potential usefulness of sequence-specific enzymatic nucleic acid molecules of the instant invention has many of the same applications for the study of RNA that DNA restriction endonucleases have for the study of DNA (Nathans et al., 1975 Ann. Rev. Biochem. 44:273). For example, the pattern of restriction fragments can be used to establish sequence relationships between two related RNAs, and large RNAs could be specifically cleaved to fragments of a size more useful for study. The ability to engineer sequence specificity of the enzymatic nucleic acid molecule is ideal for cleavage of RNAs of unknown sequence. Applicant has described the use of nucleic acid molecules to down-regulate gene expression of target genes in bacterial, microbial, fungal, viral, and eukaryotic systems including plant, or mammalian cells.

[0307] All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually.

[0308] 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. The methods and compositions described herein as 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.

[0309] 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. Thus, such additional embodiments are within the scope of the present invention and the following claims.

[0310] The invention illustratively described herein suitably can be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. Thus, for example, in each instance herein any of the terms “comprising”, “consisting essentially of” and “consisting of” may be replaced with either of the other two terms. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that 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 preferred embodiments, optional features, modification and variation of the concepts 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 as defined by the description and the appended claims.

[0311] In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group.

[0312] Thus, additional embodiments are within the scope of the invention and within the following claims.

TABLE 1
NUCLEOSIDES USED FOR CHEMICAL SYNTHESIS OF MODIFIED NUCLEOTIDE TRIPHOSPHATES
	NUCLEOTIDES	Abbreviation	CHEMICAL STRUCTURE
1	2′-O-methyl-2,6- diaminopurine riboside	2′-O—Me-DAP	5
2	2′-deoxy-2′amino-2,6- diaminopurine riboside	2′-NH2-DAP	6
3	2′-(N-alanyl)amino-2′- deoxy-uridine	ala-2′-NH2U	7
4	2′-(N- phenylalanyl)amino-2′- deoxy-uridine	phe-2′-NH2-U	8
5	2′-(Nβ-alanyl)amino- 2′-deoxy uridine	2-β-Ala-NH2-U	9
6	2′-Deoxy-2′-(lysyl) amino uridine	2′-L-lys-NH2-U	10
7	2′-C-allyl uridine	2′-C-allyl-U	11
8	2′-O-amino-uridine	2′-I—NH2-U	12
9	2′-O-methylthiomethyl adenosine	2′-O-MTM-A	13
10	2′-O-methylthiomethyl cytidine	2′-O-MTM-C	14
11	2′-O-methylthiomethyl guanosine	2′-O-MTM-G	15
12	2′-O-methylthiomethyl- uridine	2′-O-MTM-U	16
13	2′-(N-histidyl) amino uridine	2′-his-NH2-U	17
14	2′-Deoxy-2′-amino-5- methyl cytidine	5-Me-2′-NH2—C	18
15	2′-(N-β-carboxamidine- β-alanyl)amino-2′- deoxy-uridine	β-ala-CA-NH2-U	19
16	2′-(N-β-alanyl) guanosine	β-Ala-NH2-G	20
17	2′-O-Amino-Uridine	2′-O—NH2-U	21
18	2′-(N-lysyl)amino-2′- deoxy-cytidine	2′-NH2-lys-C	22
19	2′-Deoxy-2′-(L- histidine)amino Cytidine	2′-NH2-his-C	23
20	5-Imidazoleacetic acid 2′-deoxy uridine	5-IAA-U	24
21	5-[3-(N-4- imidazoleacetyl) aminopropynyl]-2′-O- methyl uridine	5-IAA- propynylamino-2′- OMe U	25
22	5-(3-aminopropynyl)-2′- O-methyl uridine	5-aminopropynyl- 2′-OMe U	26
23	5-(3-aminopropyl)-2′-O- methyl uridine	5-aminopropyl-2′- OMe U	27
24	5-[3-(N-4- imidazoleacetyl) aminopropyl]-2′-O- methyl Uridine	5-IAA- propylamino-2′- OMe U	28
25	5-(3-aminopropyl)-2′- deoxy-2-fluoro uridine	5-aminopropyl-2′- F dU	29
26	2′-Deoxy-2′-(β-alanyl-L- histidyl)amino Uridine	2′-amino-β-ALA- HIS dU	30
27	2′-deoxy-2′-β- alaninamido-uridine	2′-β-ALA dU	31
28	3-(2′-deoxy-2′-fluoro-β- D- ribofuranosyl)piperazino [2,3-D]pyrimidine-2-one	2′-F piperazino- pyrimidinone	32
29	5-[3-(N-4- imidazoleacetyl)amino- propyl]-2′-deoxy-2′-fluoro Uridine	5-IAA- propylamino-2′-F dU	33
30	5-[3-(N-4- imidazoleacetyl)amino- propynyl]-2′-deoxy-2′- fluoro uridine	5-IAA- propynylamino-2′- F dU	34
31	5-E-(2-carboxyvinyl-2′- deoxy-2′-fluoro uridine	5-carboxyvinyl-2′- F dU	35
32	5-[3-(N-4- aspartyl)aminopropynyl- 2′-fluoro uridine	5-ASP- aminopropyl-2′-F- dU	36
33	5-(3-aminopropyl)-2′- deoxy-2-fluoro cytidine	5-aminopropyl-2′- F dC	37
34	5-[3-(N-4- succynyl)aminopropyl- 2′-deoxy-2-fluoro cytidine	5-succynylamino- propyl-2′-F dC	38

[0313]

TABLE II
				Wait Time* 2′-O-
Reagent	Equivalents	Amount	Wait Time* DNA	methyl	Wait Time* RNA
A. 2.5 pmol Synthesis Cycle ABI 394 Instrument
Phosphoramidites	6.5	163	μL	45	sec	2.5	min	7.5	min
S-Ethyl Tetrazole	23.8	238	μL	45	sec	2.5	min	7.5	min
Acetic Anhydride	100	233	μL	5	sec	5	sec	5	sec
N-Methyl	186	233	μL	5	sec	5	sec	5	sec
Imidazole
TCA	176	2.3	mL	21	sec	21	sec	21	sec
Iodine	11.2	1.7	mL	45	sec	45	sec	45	sec
Beaucage	12.9	645	μL	100	sec	300	sec	300	sec
Acetonitrile	NA	6.67	mL	NA	NA	NA
B. 0.2 μmol Synthesis Cycle ABI 394 Instrument
Phosphoramidites	15	31	μL	45	sec	233	sec	465	sec
S-Ethyl Tetrazole	38.7	31	μL	45	sec	233	min	465	sec
Acelic Anhydride	655	124	μL	5	sec	5	sec	5	sec
N-Methyl	1245	124	μL	5	sec	5	sec	5	sec
Imidazole
TCA	700	732	μL	10	sec	10	sec	10	sec
Iodine	20.6	244	μL	15	sec	15	sec	15	sec
Beaucage	7.7	232	μL	100	sec	300	sec	300	sec
Acetonitrile	NA	2.64	mL	NA	NA	NA
C. 0.2 μmol Synthesis Cycle 96 well Instrument
	Equivalents:
	DNA/2′-O-	Amount: DNA/2′-O-	Wait Time*	Wait Time* 2′-	Wait Time*
Reagent	methyl/Ribo	methyl/Ribo	DNA	O-methyl	Ribo
Phosphoramidites	22/33/66	40/60/120	μL	60	sec	180	sec	360	sec
S-Ethyl Tetrazole	70/105/210	40/60/120	μL	60	sec	180	min	360	sec
Acetic Anhydride	265/265/265	50/50/50	μL	10	sec	10	sec	10	sec
N-Methyl	502/502/502	50/50/50	μL	10	sec	10	sec	10	sec
Imidazole
TCA	238/475/475	250/500/500	μL	15	sec	15	sec	15	sec
Iodine	6.8/6.8/6.8	80/80/80	μL	30	sec	30	sec	30	sec
Beaucage	34/51/51	80/120/120		100	sec	200	sec	200	sec
Acetonitrile	NA	1150/1150/1150	μL	NA	NA	NA
*Wait time does not include contact time during delivery.

[0314]

TABLE III
PHOSPHORYLATION OF URIDINE IN THE PRESENCE
OF DMAP
	0.2	0.5	1.0
0 equiv. DMAP	equiv. DMAP	equiv. DMAP	equiv. DMAP
Time	Product	Time	Product	Time	Product	Time	Product
(min)	%	(min)	%	(min)	%	(min)	%
0	1	0	0	0	0	0	0
40	7	10	8	20	27	30	74
80	10	50	24	60	46	70	77
120	12	90	33	100	57	110	84
160	14	130	39	140	63	150	83
200	17	170	43	180	63	190	84
240	19	210	47	220	64	230	77
320	20	250	48	260	68	270	79
1130	48	290	49	300	64	310	77
1200	46	1140	68	1150	76	1160	72
		1210	69	1220	76	1230	74

[0315]

TABLE IV
Detailed Description of the NTP Incorporation Reaction Conditions
Condition	TRIS-HCL	MgCl2	DTT	Spermidine	Triton	METHANOL	LiCI	PEG	Temp
No.	(mM)	(mM)	(mM)	(mM)	X-100 (%)	(%)	(mM)	(%)	(° C.)
1	40 (pH 8.0)	20	10	5	0.01	10	1	—	25
2	40 (pH 8.0)	20	10	5	0.01	10	1	4	25
3	40 (pH 8.1)	12	5	1	0.002	—	—	4	25
4	40 (pH 8.1)	12	5	1	0.002	10	—	4	25
5	40 (pH 8.1)	12	5	1	0.002	—	1	4	25
6	40 (pH 8.1)	12	5	1	0.002	10	1	4	25
7	40 (pH 8.0)	20	10	5	0.01	10	1	—	37
8	40 (pH 8.0)	20	10	5	0.01	10	1	4	37
9	40 (pH 8.1)	12	5	1	0.002	—	—	4	37
10	40 (pH 8.1)	12	5	1	0.002	10	—	4	37
11	40 (pH 8.1)	12	5	1	0.002	—	1	4	37
12	40 (pH 8.1)	12	5	1	0.002	10	1	4	37

[0316]

TABLE V
INCORPORATION OF MODIFIED NUCLEOTIDE TRIPHOSPHATES
	COND	COND	COND	COND	COND	COND	COND	COND	COND	COND	COND	COND
Modification	#1	#2	#3	#4	#5	#6	#7	#8	#9	#10	#11	#12
2′-NH2-ATP	1	2	3	5	2	4	1	2	10	11	5	9
2′-NH2-CTP	11	37	45	64	25	70	26	54	292	264	109	244
2′-NH2-GTP	4	7	6	14	5	17	3	16	10	21	9	16
2′-NH2-UTP	14	45	4	100	85	82	48	88	20	418	429	440
2′-dATP	9	3	19	23	9	24	6	3	84	70	28	51
2′-dCTP	1	10	43	46	35	47	27	127	204	212	230	235
2′-dGTP	6	10	9	15	9	12	8	34	38	122	31	46
2′-dTTP	9	9	14	18	13	18	8	15	116	114	59	130
2′-O-Me-ATP	0	0	0	0	0	0	1	1	2	2	2	2
2′-O-Me-CTP	no data compared to ribo; incorporates at low level
2′-O-Me-GTP	4	3	4	4	4	4	2	4	4	5	4	5
2′-O-Me-UTP	55	52	39	38	41	48	55	71	93	103	81	77
2′-O-Me-DAP	4	4	3	4	4	5	4	3	4	5	5	5
2′-NH2-DAP	0	0	1	1	1	1	1	0	0	0	0	0
ala-2′-NH2-UTP	2	2	2	2	3	4	14	18	15	20	13	14
phe-2′-NH2-UTP	8	12	7	7	8	8	4	10	6	6	10	6
2′-βNH2-ala-UTP	65	48	25	17	21	21	220	223	265	300	275	248
2′-F-ATP	227	252	98	103	100	116	288	278	471	198	317	185
2′-F-GTP	39	44	17	30	17	26	172	130	375	447	377	438
2′-C-allyl-UTP	3	2	2	3	3	2	3	3	3	2	3	3
2′-O-NH2-UTP	6	8	5	5	4	5	16	23	24	24	19	24
2′-O-MTM-ATP	0	1	0	0	0	0	1	0	0	0	0	0
2′-O-MTM-CTP	2	2	1	1	1	1	3	4	5	4	5	3
2′-O-MTM-GTP	6	1	1	3	1	2	0	1	1	3	1	4
2′-F-CTP									100
2′-F-UTP									100
2′-F-TTP									50
2′-F-C5-carboxy-									100
vinyl UTP
2′-F-C5-aspartyl-									100
aminopropyl UTP
2′-F-C5-propyl-									100
amine CTP
2′-O-Me CTP									0
2′-O-Me UTP									25
2′-O-Me 5-3-									4
aminopropyl UTP
2′-O-Me 5-3-									10
aminopropyl UTP

[0317]

TABLE VI
INCORPORATION OF MODIFIED NUCLEOTIDE TRIPHOSPHATES
USING WILD TYPE BACTERIOPHAGE T7 POLYMERASE
	Modification	label	% ribo control
	2′-NH2-GTP	ATP	4%
	2′-dGTP	ATP	3%
	2′-O—Me-GTP	ATP	3%
	2′-F-GTP	ATP	4%
	2′-O-MTM-GTP	ATP	3%
	2′-NH2-UTP	ATP	39%
	2′-dTTP	ATP	5%
	2′-O—Me-UTP	ATP	3%
	ala-2′-NH2-UTP	ATP	2%
	phe-2′-NH2-UTP	ATP	1%
	2′-β-ala-NH2UTP	ATP	3%
	2′-C-allyl-UTP	ATP	2%
	2′-O—NH2-UTP	ATP	1%
	2′-O-MTM-UTP	ATP	64%
	2′-NH2-ATP	GTP	1%
	2′-O-MTM-ATP	GTP	1%
	2′-NH2-CTP	GTP	59%
	2′-dCTP	GTP	40%
	2′-F-CTP	GTP	100%
	2′-F-UTP	GTP	100%
	2′-F-TTP	GTP	0%
	2′-F-C5-carboxyvinyl UTP	GTP	100%
	2′-F-C5-aspartyl-aminopropyl UTP	GTP	100%
	2′-F-C5-propylamine CTP	GTP	100%
	2′-O—Me CTP	GTP	0%
	2′-O—Me UTP	GTP	0%
	2′-O—Me 5-3-aminopropyl UTP	GTP	0%
	2′-O—Me 5-3-aminopropyl UTP	GTP	0%

[0318]

TABLE VII a
Incorporation of 2′-his-UTP and Modified CTP′s
	modification	2′-his-UTP	rUTP
	CTP	16.1	100
	2′-amino-CTP	9.5*	232.7
	2′-deoxy-OTP	9.6*	130.1
	2′-OMe-CTP	1.9	6.2
	2′-MTM-CTP	5.9	5.1
	control	1.2

[0319]

TABLE VII b
Incorporation of 2′-his-UTP, 2-amino CTP, and Modified ATP′s
		2′-his-UTP and
	modification	2′amino-CTP	rUTP and rCTP
	ATP	15.7	100
	2′-amino-ATP	2.4	28.9
	2′-deoxy-ATP	2.3	146.3
	2′-OMe-ATP	2.7	15
	2′-F-ATP	4	222.6
	2′-MTM-ATP	4.7	15.3
	2′-OMe-DAP	1.9	5.7
	2′-amino-DAP	8.9*	9.6
	Numbers shown are a percentage of incorporation compared to the all-RNA control
	*Bold number indicates best observed rate of modified nucleotide triphosphate incorporation

[0320]

TABLE VIII
INCORPORATION OF 2′-his-UTP, 2′-NH2-CTP, 2′-NH2-DAP, and rGTP
USING VARIOUS REACTION CONDITIONS
Conditions compared to all rNTP
7          8.7*
8          7*
9          2.3
10         2.7
11         1.6
12         2.5
Numbers shown are a percentage of incorporation compared to the all-RNA control
*Two highest levels of incorporation contained both methanol and LiCl

[0321]

TABLE IX
Selection of Oligonucleotides with Ribozyme Activity
			substrate		Substrate
pool	Generation	time	remaining (%)	time	remaining (%)
N60	0	4 hr	100.00	24 hr	100.98
N60	14	4 hr	99.67	24 hr	97.51
N60	15	4 hr	98.76	24 hr	96.76
N60	16	4 hr	97.09	24 hr	96.60
N60	17	4 hr	79.50	24 hr	64.01
N40	0	4 hr	99.89	24 hr	99.78
N40	10	4 hr	99.74	24 hr	99.42
N40	11	4 hr	97.18	24 hr	90.38
N40	12	4 hr	61.64	24 hr	44.54
N40	13	4 hr	54.28	24 hr	36.46
N20	0	4 hr	99.18	24 hr	100.00
N20	11	4 hr	100.00	24 hr	100.00
N20	12	4 hr	99.51	24 hr	100.00
N20	13	4 hr	90.63	24 hr	84.89
N20	14	4 hr	91.16	24 hr	85.92
N60B	0	4 hr	100.00	24 hr	100.00
N60B	1	4 hr	100.00	24 hr	100.00
N60B	2	4 hr	100.00	24 hr	100.00
N60B	3	4 hr	100.00	24 hr	100.00
N60B	4	4 hr	99.24	24 hr	100.00
N60B	5	4 hr	97.81	24 hr	96.65
N60B	6	4 hr	89.95	24 hr	77.14

[0322]

TSBLE X
Kinetic Activity of Combinatorial Libraries
	Pool	Generation	kobs (min−1)
	N60	17	0.0372
		18	0.0953
		19	0.0827
	N40	12	0.0474
		13	0.037
		14	0.065
		15	0.0254
	N20	13	0.0359
		14	0.0597
		15	0.0549
		16	0.0477
	N60B	6	0.0209
		7	0.0715
		8	0.0379

[0323]

TABLE XL
Kinetic Activity of Clones within N60 and N40 Combinatorial Libraries
	clone	library	activity(min−1)	krel
	G18	N60	0.00226	1.00
	0-2	N60	0.0389	17.21
	0-3	N60	0.000609	0.27
	0-5	N60	0.000673	0.30
	0-7	N60	0.00104	0.46
	0-8	N60	0.000739	0.33
	0-11	N60	0.0106	4.69
	0-12	N60	0.00224	0.99
	0-13	N60	0.0255	11.28
	0-14	N60	0.000878	0.39
	0-15	N60	0.0000686	0.03
	0-21	N60	0.0109	4.82
	0-22	N60	0.000835	0.37
	0-24	N60	0.000658	0.29
	0-28	N40	0.000741	0.33
	0-35	N40	0.00658	2.91
	3-1	N40	0.0264	11.68
	3-3	N40	0.000451	0.20
	3-7	N40	0.000854	0.38
	3-15	N40	0.000832	0.37

[0324]

TABLE XII
Effect of Magnesium Concentration of the Cleavage Rate of N20
[Mg++] kobs(min−1)
25     0.0259
20     0.0223
15     0.0182
10     0.0208
5      0.0121
2      0.00319
2      0.00226

[0325]

TABLE XIII
Class I Enzymatic Nucleic Acid Motifs Targeting HCV
		Seq
		ID		Seq. ID
Pos	Target	No.	Alias	No.	Sequence
6	AUGGGGGCGACACUCC	1	HCV.R1A-6 Amb.Rz-10/5	746	ggagugucgc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cccau B
56	UUCACGCAGAAAGCGU	2	HCV.R1A-56 Amb.Rz-10/5	747	acgcuuucug GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG gugaa B
75	GCCAUGGCGUUAGUAU	3	HCV.R1A-75 Amb.Rz-10/5	748	auacuaacgc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG augyc B
76	CCAUGGCGUUAGUAUG	4	HCV.R1A-76 Amb.Rz-10/5	749	cauacuaacg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG caugg B
95	GUCGUGCAGCCUCCAG	5	HCV.R1A-95 Amb.Rz-10/5	750	cuggaggcug GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG acgac B
138	GGUCUGCGGAACCGGU	6	HCV.R1A-138 Amb.Rz-10/5	751	accgguuccg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG agacc B
146	GAACCGGUGAGUACAC	7	HCV.R1A-146 Amb.Rz-10/5	752	guguacucac GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG gguuc B
158	ACACCGGAAUUGCCAG	8	HCV.R1A-158 Amb.Rz-10/5	753	cuggcaauuc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG ggugu B
164	GAAUUGCCAGGACGAC	9	HCV.R1A-164 Amb.Rz-10/5	754	gucguccugg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG aauuc B
176	CGACCGGGUCCUUUCU	10	HCV.R1A-176 Amb.Rz-10/5	755	agaaaggacc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG ggucg B
177	GACCGGGUCCUUUCUU	11	HCV.R1A-177 Amb.Rz-10/5	756	aagaaaggac GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cgguc B
209	UGCCUGGAGAUUUGCG	12	HCV.R1A-209 Amb.Rz-10/5	757	cccaaaucuc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG aggca B
237	AGACUGCUAGCCGAGU	13	HCV.R1A-237 Amb.Rz-10/5	758	acucggcuag GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG agucu B
254	GUGUUGGGUCGCGAAA	14	HCV.R1A-254 Amb.Rz-10/5	759	uuucgcgacc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG aacac B
255	UGUUGGGUCGCGAAAG	15	HCV.R1A-255 Amb.Rz-10/5	760	cuuucgcgac GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG caaca B
259	GGGUCGCGAAAGGCCU	16	HCV.R1A-259 Amb.Rz-10/5	761	aggccuuucg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG gaccc B
266	GAAAGGCCUUGUGGUA	17	HCV.R1A-266 Amb.Rz-10/5	762	uaccacaagg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cuuuc B
273	CUUGUGGUACUGCCUG	18	HCV.R1A-273 Amb.Rz-10/5	763	caggcaguac GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG acaag B
288	GAUAGGGUGCUUGCGA	19	HCV.R1A-288 Amb.Rz-10/5	764	ucgcaagcac GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cuauc B
291	AGGGUGCUUGCGAGUG	20	HCV.R1A-291 Amb.Rz-10/5	765	cacucgcaag GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG acccu B
7	UGGGGGCGACACUCCA	21	HCV.R1A-7 Amb.Rz-10/5	766	uggagugucg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cccca B
119	CUCCCGGGAGAGCCAU	22	HCV.R1A-119 Amb.Rz-10/5	767	auggcucucc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG gggag B
120	UCCCGGGAGAGCCAUA	23	HCV.R1A-120 Amb.Rz-10/5	768	uauggcucuc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cggga B
133	AUAGUGGUCUGCGGAA	24	HCV.R1A-133 Amb.Rz-10/5	769	uuccgcagac GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG acuau B
140	UCUGCGGAACCGGUGA	25	HCV.R1A-140 Amb.Rz-10/5	770	ucaccgguuc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG gcaga B
188	UUCUUGGAUAACCCCG	26	HCV.R1A-188 Amb.RZ-10/5	771	cgggguuauc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG aagaa B
198	ACCCCGCUCAAUGCCU	27	HCV.R1A-198 Amb.Rz-10/5	772	aggcauugag GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG ggggu B
205	UCAAUGCCUGGAGAUU	28	HCV.R1A-205 Amb.Rz-10/5	773	aaucuccagg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG auuga B
217	GAUUUGGGCGUGCCCC	29	HCV.R1A-217 Amb.Rz-10/5	774	ggggcacgcc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG aaauc B
218	AUUUGGGCGUGCCCCC	30	HCV.R1A-218 Amb.Rz-10/5	775	gggggcacgc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG caaau B
219	UUUGGGCGUGCCCCCG	31	HCV.R1A-219 Amb.Rz-10/5	776	cgggggcacg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG ccaaa B
223	GGCGUGCCCCCGCAAG	32	HCV.R1A-223 Amb.Rz-10/5	777	cuugcggggg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG acgcc B
229	CCCCCGCAAGACUGCU	33	HCV.R1A-229 Amb.Rz-10/5	778	agcagucuug GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG ggggg B
279	GUACUGCCUGAUAGGG	34	HCV.R1A-279 Amb.Rz-10/5	779	cccuaucagg Ggag9aaacucC CU
					UC AAGGACAUCGUCCGGG aguac B
295	UGCUUGCGAGUGCCCC	35	HCV.R1A-295 Amb.Rz-10/5	780	ggggcacucg cgaggaaacucC CU
					UC AAGGACAUCGUCCGGG aagca B
301	CGAGUGCCCCGGGAGG	36	HCV.R1A-301 Amb.Rz-10/5	781	ccucccgggg GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG acucg B
306	GCCCCGGGAGGUCUCG	37	HCV.R1A-306 Amb.Rz-10/5	782	cgagaccucc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG ggggc B
307	CCCCGGGAGGUCUCGU	38	HCV.R1A-307 Amb.Rz-10/5	783	acgagaccuc GgaggaaacucC CU
					UC AAGGACAUCGUCCGGG cgggg B
No Ribo				784	Ggaaaggugugcaaccggagucauca
					uaauggcuucCCUUCaaggaCaUCgCCg
					ggacggcB
Ribo				785	GGAAAGGUGUGCAACCGGAGUCAUCA
					UAAUGGCUCCCUUCAAGGACAUCGUCCG
					GGACGGCB
lower case=2′-O-methyl
U,C=2′ -deoxy-2′-amino U,=2′-deoxy-2′-amino C
G,A=ribo G,A
B=inverted deoxyabasic

[0326]

TABLE XIV
Additional Class II enzymatic nucleic acid Motifs
Class II			Kinetic
Motif ID	Sequence	Seq ID No.	Rate
A2	GGGAGGAGGAAGUGCCUGGUCAGUCACACCGAGACUGGCAGACGCUGAAACC	786	UNK
	GCCGCGCUCGCUCCCAGUCC
A12	GGGAGGAGGAAGUGCCUGGUAGUAAUAUAAUCGUUACUACGAGUGCAAGGUC	787	UNK
	GCCGCGCUCGCUCCCAGUCC
A11	GGGAGGAGGAAGUGCCUGGUAGUUGCCCGAACUGUGACUACGAGUGAGGUC	788	UNK
	GCCGCGCUCGCUCCCAGUCC
B14	GGGAGGAGGAAGUGCCUGGCGAUCAGAUGAGAUGAUGGCAGACGCAGAGACC	789	UNK
	GCCGCGCUCGCUCCCAGUCC
B10	GGGAGGAGGAAGUGCCUGGCGACUGAUACGAAAAGUCGCAGUUUCGAAACC	790	UNK
	GCCGCGCUCGCUCCCAGUCC
B21	GGGAGGAGGAAGUGCCUGGCGACUGAUACGAAAAGUCGCAGGUUUCGAAACC	791	UNK
	GCCGCGCUCGCUCCCAGUCC
B7	GGGAGGAGGAAGUGCCUUGGCUCAGCAUAAGUGAGCAGAUUGCGACACC	792	UNK
	GCCGCGCUCGCUCCCAGUCC
C8	GGGAGGAGGAAGUGCCUUGGUCAUUAGGAUGACAAACGUAUACUGAACACU	793	0.01
	GCCGCGCUCGCUCCCAGUCC		MIN−1

[0327]

TABLE XV
Human Her2 Class II Ribozyme and Target Sequence
			Seq		Seq.
			ID		ID
RPI#	NT Pos	Substrate	No.	Ribozyme Alias	No.	Ribozyme Sequence
18722	180	CAUGGA G CUGGCC	39	erbB2-180	794	c s g s c s c s ag GccgaaagGCGaGucaaGGuCu uccaug B
				Zin.Rz-6		s s s s
				amino stabl
18835	184	CAGCUG G CGGCCU	40	erbB2-184	795	asgsgscscg GccgaaagGCaGucaaGGuCcagcuc B
				Zin.Rz-6		s s s s
				amino stabl
18828	276	AGCUGCG CUCCCUG	41	erbB2-276	796	csasgsgsgag GccgaaagGCaGucaaGGuCcgcagcu B
				Zin.Rz-7		s s s s
				amino stabl
18653	314	UGCUCC G CCACCU	42	erbB2-314	797	asgsgsusgg GccgaaaggCGaGucaaGGuCggagca B
				Zin.Rz-6		s s s s
				amino stabl
18825	314	AUGCUCC G CCACCUC	43	erbB2-314	798	gsasgsgsugg GccgaaagGCaGucaaGGuCggagcau B
				Zin.Rz-7		s s s s
				amino stabl
18831	379	ACCAAU G CCAGCC	44	erbB2-379	799	gsgscsusgg GccgaaagGCaGUcaaGGUCU auuggu B
				Zin.Rz-6		s s s s
				amino stabl
18680	433	GCUCAUC G CUCACAA	742	erbB2-433	800	ususgsusgag GccgaaagGCaGucaaGGuCgaugagc B
				Zin.Rz-7		s s s s
				amino stabl
18711	594	GGAGCU G CAGCUU	45	erbB2-594	801	asasgscsug GccgaaagGCaGucaaGGuCagcucc B
				Zin.Rz-6		s s s s
				amino stabl
18681	594	GGGAGCU G CAGCUUC	46	erbB2-594	802	gsasasgscug CccgaaagGCaGucaaGGuCagcuccc B
				Zin.Rz-7		s s s s
				amino stabl
18697	597	GCUGCA G CUUCCA	47	erbB2-597	803	uscsgsasag GccgaaagGCaGucaaGGuCugcagc B
				Zin.Rz-6		s s s s
				amino stabl
18665	597	AGCUGCA G CUUCGAA	48	erbB2-597	804	ususcsgsaag GccgaaagGCaGucaaGGuCugcagcu B
				Zin.Rz-7		s s s s
				amino stabl
18712	659	AGCUCU G CUACCA	49	erbB2-659	805	usgsgsusag GccgaaagGCaGucaaGGuCagagcu B
				Zin.Rz-6		s s s s
				amino stabl
18682	659	CAGCUCU G CUACCAG	50	erbB2-659	806	cguggsgsuag GcegaaagGCaGucaaGGuCagagcug B
				Zin.Rz-7		s s s s
				amino stabl
18683	878	CUGACU G CUGCCA	51	erbB2-878	807	usgsgscsag GccgaaagGCaGucaaGGuCagucag B
				Zin.Rz-6		s s s s
				amino stabl
18654	878	ACUGACU G CUGCCAU	52	erbB2-878	808	asusgsgscag GccgaaagGCaGucaaGGuCagucagu B
				Zin.Rz-7		s s s s
				amino stabl
18685	881	ACUGCU G CCAUGA	53	erbB2-881	809	uscsasusgg GccgaaagGCaGucaaGGuCagcagu B
				Zin.Rz-6		s s s s
				amino stabl
18684	881	GACUGCU G CCAUGAG	54	erbB2-881	810	csuscsasugg GccgaaagGCaGucaaGGuCagcaguc B
				Zin.Rz-7		s s s s
				amino stabl
18723	888	GCCAUGA G CAGUGUG	55	erbB2-888	811	csascsascug GccgaaagGCaGucaaGGuCucauggc B
				Zin.Rz-7		s s s s
				amino stabl
18686	929	CUGACU G CCUGCC	56	erbB2-929	812	gscscsasgg GccgaaagGCaGucaaGGuCagucag B
				Zin.Rz-6		s s s s
				amino stabl
18648	929	UCUGACU G CCUGGCC	57	erbB2-929	813	gsgscscsagg GccgaaagGCaGucaaGGuCagucaga B
				Zin.Rz-7		s s s s
				amino stabl
18888	934	UGCCUG G CCUGCC	58	erbB2-934	814	gsgscsasgg GccgaaagGCaGucaaGGuCcaggca B
				Zin.Rz-6		s s s s
				amino stabl
18651	934	CUGCCUG G CCUGCCU	743	erbB2-934	815	asgsgscsagg GccgaaagCCGaGucaaCCuCcaggcag B
				Zin.Rz-7		s s s s
				amino stabl
18655	938	UGGCCU G CCUCCA	59	erbB2-938	816	usgsgsasgg GccgaaagGCaCucaaCCuCaggcca B
				Zin.Rz-6		s s s s
				amino stabl
18649	938	CUGGCCU G CCUCCAC	60	erbB2-938	817	gsusgsgsagg GccgaaagGCaGucaaCCuCaggccag B
				Zin.Rz-7		s s s s
				amino stabl
18887	969	CUGUGA G CUGCAC	61	erbB2-969	818	gsusgscsag GccgaaagGCaGucaaGGuCucacag B
				Zin.Rz-6		s s s s
				amino stabl
18888	969	UCUGUGA G CUGCACU	62	erbB2-969	819	asgsusgscag GccgaaagGCaGucaaGGuCucacaga B
				Zin.Rz-7		s s s s
				amino stabl
18656	972	UGAGCU G CACUGC	744	erbB2-972	820	gscsasgsug GccgaaagGCaGucaaGGuCagcuca B
				Zin.Rz-6		s s s s
				amino stabl
18657	972	GUGAGCU G CACUGCC	63	erbB2-972	821	gsgscsasgug GccgaaagGCaGucaaGGuCagcucac B
				Zin.RZ-7		s s s s
				amino stabl
19294	972	UGAGCU G CACUGC	744	erbB2-972	822	gscsasgsug GccaauuugugGCaGucaaGGuCagcuca B
				Zin.Rz-6		s s s s
				amino stabl
19295	972	UGAGCU G CACUGC	744	erbB2-972	823	gscsasgsug GccAAuuuGuGGCaGucaaGGuCagcuca B
				Zin.Rz-6		s s s s
				amino stabl
19293	972	UGAGCU G CACUGC	744	erbB2-972	824	gscsasgsug GccgaaagGCaGuGaGGuCagcoca B
				Zin.Rz-6		s s s s
				amino stabl
19292	972	UGAGCU G CACUGC	744	erbB2-972	824	gscsasgsug GccgaaagGCaGuGaGGuCagcuca B
				Zin.Rz-6		s s s s
				amino stabl
19296	972	UGAGCU G CACUGC	744	erbB2-972	825	gscsasgsug GccacAAuuuGuGGcagGCaGucaaGGuCagcuca
				Zin.Rz-6		s s s s
				amino stabl
19727	972	UGAGCU G CACUGC	744	erbB2-972	826	gscsasgsug gccgaaaggCgagugagguCagcuca B
				Zin.Rz-6		s s s s
				amino stabl
19728	972	UGAGCU G CACUGC	744	erbB2-972	827	gscsasgsug gccgaaaggCgagugagGuCagcuca B
				Zin.Rz-6		s s s s
				amino stabl
18659	1199	GAGUGU G CUAUGG	64	erbB2-1199	828	cscsasusag GccgaaagGCaGucaaGGuCacacuc B
				Zin.Rz-6		s s s s
				amino stabl
18658	1199	CGAGUGU G CUAUGGU	65	erbB2-1199	829	ascscsasuag GccgaaagGCaGucaaGGuCacacucg B
				Zin.Rz-7		s s s s
				amino stabl
18724	1205	GCUAUG G UCUGGG	66	erbB2-1205	830	cscscsasga CccgaaagGCaGucaaGGuCcauagc B
				Zin.Rz-6		s s s s
				amino stabl
18669	1205	UGCUAUG G UCUGGGC	67	erbB2-1205	831	gscscscsaga GccgaaagGCaGucaaGGuCcauagca B
				Zin.Rz-7		s s s s
				amino stabl
18725	1211	GUCUGG G CAUGGA	68	erbB2-1211	832	uscscsasug CccgaaagGCaGucaaGGuCccagac B
				Zin.Rz-6		s s s s
				amino stabl
18726	1292	UUGGGA G CCUGGC	745	erbB2-1292	833	gscscsasgg GccgaaagGCaGucaaGGuCucccaa B
				Zin.Rz-6		s s s s
				amino stabl
18698	1292	UUUGGGA G CCUGGCA	69	erbB2-1292	834	usgscscsagg GccgaaagGCaGucaaGGuCucccaaa B
				Zin.RZ-7		s s s s
				amino stabl
18727	1313	CCGGAGA G CUUUGAU	70	erbB2-1313	835	asuscsasaag GccgaaagGCaGucaaGGucu ucuccgg B
				Zin.Rz-7		s s s s
				amino stabl
18699	1397	UCACAG G UUACCU	71	erbB2-1397	836	asgsgsusaa CccgaaagGCaGucaaGGuCcuguga B
				Zin.Bz-6		s s s s
				amino stabl
18728	1414	AUCUCA G CAUGGC	72	erbB2-1414	837	gscscsasug CccgaaagGCaGuCaaGGUCu ugagau B
				Zin.Rz-6		s s s s
				amino stabl
18670	1414	CAUCUCA G CAUGGCC	73	erbB2-1414	838	gsgscscsaug GccgaaagGCaGucaaGGuCugagaug B
				Zin.Bz-7		s s s s
				amino stabl
18671	1536	GCUGGG G CUGCGC	74	erbB2-1536	839	gscsgscsag CccgaaagGCaGucaaGGuCcccagc B
				Zin.Rz-6		s s s s
				amino stabl
18687	1541	GGCUGC G CUCACU	75	erbB2-1541	840	asgsusgsag GccgaaagGCaGucaaGGuCgcagcc B
				Zin.Rz-6		s s s s
				amino stabl
18829	1562	CUGGGCA G UGGACUG	76	erbB2-1562	841	csasgsuscca CccgaaagGCaGucaaGGuCugcccag B
				Zin.Rz-7		s s s s
				amino stabl
18830	1626	GGGACCA G CUCUUUC	77	erbB2-1626	842	gsasasasgag CccgaaagGCaGucaaGGuCugguccc B
				Zin.Rz-7		s s s s
				amino stabl
18700	1755	CACCCA G UGUGUC	78	erbB2-1755	843	gsascsasca CccgaaagGCaGucaaGGuCugggug B
				Zin.Rz-6		s s s s
				amino stabl
18672	1755	CCACCCA G UGUGUCA	79	erbB2-1755	844	usgsascsaca CccgaaagGCaGucaaGGuCugggugg B
				Zin.Rz-7		s s s s
				amino stabl
18688	1757	CCCAGU G UGUCAA	80	erbB2-1757	845	ususgsasca GccgaaagGCaGucaaGGuCacuggg B
				Zin.Rz-6		s s s s
				amino stabl
18660	1757	ACCCAGU G UGUCAAC	81	erbB2-1757	846	gsususgsaca GccgaaagGCaGucaaGGuCacugggu B
				Zin.Rz-7		s s s s
				amino stabl
18689	1759	CAGUGU G UCAACUG	82	erbB2-1759	847	asgsususga GccgaaagGCaGucaaGGuCacacug B
				Zin.Rz-6		s s s s
				amino stabl
18690	1759	CCAGUGU G UCAACUG	83	erbB2-1759	848	csasgsusuga GccgaaagGCaGucaaGGuCacacugg B
				Zin.Rz-7		s s s s
				amino stabl
18701	1784	UUCGGG G CCAGGA	84	erbB2-1784	849	uscscsusgg GcogaaagGCaGucaaGGuCcccgaa B
				Zin.Rz-6		s s s s
				amino stabl
18673	1784	CUUCGGG G CCAGGAG	85	erbB2-1764	850	csuscscsugg GccgaaagGCaGucaaGGuCcccgaag B
				Zin.Rz-7		s s s s
				amino stabl
18691	2063	UCAACU G CACCCA	86	erbB2-2063	851	usgsgsgsug GccgaaagGCaGucaaGGuCaguuga B
				Zin.Rz-6		s s s s
				amino stabl
18661	2063	AUCAACU G CACCCAC	87	erbB2-2083	852	gsusgsgsgug GccgaaagGCaGucaaGGuCaguugau B
				Zin.Rz-7		s s s s
				amino stabl
18692	2075	ACUCCU G UGUGGA	88	erbB2-2075	853	uscscsasca GccgaaagGCaGucaaGGuCaggagu B
				Zin.Rz-6		s s s s
				amino stabl
18729	2116	CAGAGA G CCAGCC	89	erbB2-2116	854	gsgscsusgg GccgaaagGCaGucaaGGuCucucug B
				Zin.Rz-6		s s s s
				amino stabl
18832	2247	GACUGCU G CAGGAAA	93	erbB2-2247	855	usususcscug GccgaaagGCaGucaaGGuCagcaguc B
				Zin.Rz-7		s s s s
				amino stabl
18833	2271	UGGAGCC G CUGACAC	91	erbB2-2271	856	gsusgsuscag GccgaaagGCaGucaaGGuCggcucca B
				Zin.Rz-7		s s s s
				amino stabl
18702	2341	AGGAAG G UGAAGG	92	erbB2-2341	857	cscsususca GccgaaagGCaGucaaGGuCcuuccu B
				Zin.Rz-6		s s s s
				amino stabl
18730	2347	GUGAAG G UGCUUG	93	erbB2-2347	858	csasasgsca GccgaaagGCaGucaaGGuCcuucac B
				Zin.Rz-6		s s s s
				amino stabl
18674	2347	GGUGAAG G UGCUUGG	94	erbB2-2347	859	cscsasasgca GccgaaagGCaGucaaGGuCcuucacc B
				Zin.Rz-7		s s s s
				amino stabl
18713	2349	GAAGGU G CUUGGA	95	erbB2-2349	860	uscscsasag GccgaaagGCaGucaaGGuCaccuuc B
				Zin.Rz-6		s s s s
				amino stabl
18693	2349	UGAAGGU G CUUGGAU	96	erbB2-2349	861	asuscscsaag GccgaaagGCaGucaaGGuCaccuuca B
				Zin.Rz-7		s s s s
				amino stabl
18731	2384	UACAAGG G CAUCUGG	97	erbB2-2384	862	cscsasgsaug GccgaaagGCaGucaaGGuCccuugua B
				Zin.Rz-7		s s s s
				amino stabl
18714	2410	GGAGAAU G UGAAAAU	98	erbB2-2410	863	asusususuca GccgaaagGCaGucaaGGuCauucucc B
				Zin.Rz-7		s s s s
				amino stabl
18732	2497	GUGAUG G CUGGUG	99	erbB2-2497	864	csascscsag GccgaaagGCaGucaaGGuCcaucac B
				Zin.Rz-6		s s s s
				amino stabl
18703	2501	UGGCUG G UGUGGG	100	erb82-2501	865	cscscsasca GccgaaagGCaGucaaGGuCcagcca B
				Zin.Rz-6		s s s s
				amino stabl
18715	2540	GCAUCU G CCUGAC	101	erbB2-2540	866	gsuscsasgg GccgaaagGCaGucaaGGuCagaugc B
				Zin.Rz-6		s s s s
				amino stabl
18733	2563	CAGCUG G UGACAC	102	erbB2-2563	867	gsusgsusca GccgaaagGCaGucaaGGuCcagcug B
				Zin.Rz-6		s s s s
				amino stabl
18734	2571	GACACA G CUUAUG	103	erbB2-2571	868	csasusasag GccgaaagGCaGucaaGGuCuguguc B
				Zin.Rz-6		s s s s
				amino stabl
18675	2571	UGACACA G CUUAUGC	104	erbB2-2571	869	gscsasusaag GccgaaagGCaGucaaGGuCuguguca B
				Zin.Rz-7		s s s s
				amino stabl
18716	2662	CAGAUU G CCAAGG	105	erbB2-2682	870	cscsususgg GccgaaagGCaGucaaGGuCaaucug B
				Zin.Rz-6		s s s s
				amino stabl
18704	2675	GGAUGA G CUACCU	106	erb62-2675	871	asgsgsusag GccgaaagGCaGucaaGGuCucaucc B
				Zin.Rz-6		s s s s
				amino stabl
18676	2675	GGGAUGA G CUACCUG	107	erb62-2875	872	csasgsgsuag GccgaaagGCaGucaaGGuCucauccc B
				Zin.Rz-7		s s s s
				amino stabl
18735	2738	GUCAAGA G UCCCAAC	108	erb62-2738	873	gsususgsgga GccgaaagGCaGucaaGGuCucuugac B
				Zin.Rz-7		s s s s
				amino stabl
18705	2773	GGGCUG G CUCGGC	109	erbB2-2773	874	gscscsgsag GccgaaagGCaGucaaGGuCcagccc B
				Zin.Rz-6		s s s s
				amino stabl
18836	2778	UGGCUCG G CUGCUGG	110	erbB2-2778	875	cscsasgscag GccgaaagGCaGucaaGGuCcgagcca B
				Zin.Rz-7		s s s s
				amino stabl
18694	2781	UCGGCU G CUGGAC	111	erbB2-2781	876	gsuscscsag GccgaaagGCaGucaaGGuCagccga B
				Zin.Rz-6		s s s s
				amino stabl
18662	2781	CUCGGCU G CUGGACA	112	erbB2-2781	877	usgsuscscag Gcc9aaagGCaGucaaGGuCagocqag B
				Zin.Rz-7		s s s s
				amino stabl
18737	2802	GACAGA G UACCAU	113	erbB2-2802	878	asusgsgsua GccgaaagGCaGucaaGGuCucuguc B
				Zin.Rz-6		s s s s
				amino stabl
18736	2802	AGACAGA G UACCAUG	114	erbB2-2802	879	csasusgsgua GccgaaagGCaGucaaGGuCucuguco B
				Zin.Rz-7		s s s s
				amino stabl
18717	2809	GUACCAU G CAGAUGG	115	erbB2-2809	880	cscsasuscug GccgaaagGCaGucaaGGuCauggoac B
				Zin.Rz-7		s s s s
				amino stabl
18738	2819	AUGGGG G CAAGGU	116	erbB2-2819	881	ascscsusug GccgaaagGCaGucaaoCucu ccccau B
				Zin.Rz-6		s s s s
				amino stabl
18706	2819	GAUGGGG G CAAGGG	117	erbB2-2819	882	csascscsuug GccgaaagGCaGucaaGGuCccccauc B
				Zin.Rz-7		s s s s
				amino stabl
18695	2887	GAGUGAU G UGUGGAG	118	erbB2-2887	883	csuscscsaca GccgaaagGCaGucaaGGuCaucacuc B
				Zin.Rz-7		s s s s
				amino stabl
18663	2908	GUGACU G UGUGGG	119	erbB2-2908	884	cscscsasca GccgaaagGCaGucaaGGuCagucac B
				Zin.Rz-6		s s s s
				amino stabl
18826	2908	UGUGACU G UGUGGGA	120	erbB2-2998	885	uscscscsaca GccgaaagGCaGucaaGGuCagucaca B
				Zin.Rz-7		s s s s
				amino stabl
18864	2810	GACUGU G UGGUAG	121	erbB2-2910	886	csuscscsca GccgaaagGCaGucaaGGuCacaguc B
				Zin.Rz-6		s s s s
				amino stabl
18650	2910	UGACUGU G UGGGAGC	122	erbB2-2910	887	gscsuscscca GccgaaagGCaGucaaGGuCacaguca B
				Zin.Rz-7		s s s s
				amino stabl
18677	2916	GUGGGA G CUGAUG	123	erbB2-2916	888	csasuscsag GccgaaagGCaGucaaGGuCucccac B
				Zin.Rz-6		s s s s
				amino stabl
18652	2916	UGUGGGA G CUGAUGA	124	erbB2-2916	889	uscsasuscag GccgaaagGCaGucaaGCuCucccaca B
				Zin.Rz-7		s s s s
				amino stabl
18707	2932	UUUGGG G CCAAAC	125	erbB2-2932	890	gsusususgg GccgaaagGCaGucaaGGuCcccaaa B
				Zin.Rz-6		s s s s
				amino stabl
18678	2932	UUUUGGG G CCAAACC	126	erbB2-2932	891	gsgsususugg GccgaaagGCaGucaaGGuCcccaaaa B
				Zin.Rz-7		s s s s
				amino stabl
18719	3025	AUUGAU G UCUACA	127	erbB2-3025	892	usgsusasga GccgaaagGCaGucaaGGuCaucsau B
				Zin.Rz-6		s s s s
				amino stabl
18718	3025	CAUUGAU G UCUACAU	128	erbB2-3025	893	asusgsusaga GccgaaagGCaGucaaGGuCaucaaug B
				Zin.Rz-7		s s s s
				amino stabl
18720	3047	UCAAAU G UUGGAU	129	erbB2-3047	894	asuscscsaa GccgaaagGCaGucaaGGuCauuuga B
				Zin.Rz-6		s s s s
				amino stabl
18696	3047	GUCAAAU G UUGGAUG	130	erbB2-3047	895	csasuscscaa GccgaaagGCaGucaaCGuCauuugac B
				Zin.Rz-7		s s s s
				amino stabl
18739	3087	CCGGGA G UUGGUG	131	erbB2-3087	896	csascscsaa GccgaaagGCaGucaaGGuCucccgg B
				Zin.Rz-6		s s s s
				amino stabl
18708	3087	UCCGGGA G UUGGUGU	132	erbB2-3087	897	ascsascscaa GccgaaagGCaGucaaGGuCucccgga B
				Zin.Rz-7		s s s s
				amino stabl
18740	3415	GAAGGG G CUGGCU	133	erbB2-3415	898	asgscscsag GccgaaagGCaGucaaGGuCcccuuc B
				Zin.Rz-6		s s s s
				amino stabl
18741	3419	GGGCUG G CUCCGA	134	erbB2-3419	899	uscsgsgsag GccgaaagGCaGucaaGGuCcagccc B
				Zin.Rz-6		s s s s
				amino stabl
18837	3419	GGGGCUG G CUCCGAU	135	erbB2-3419	900	asuscsgsgag GccgaaagGCaCucaaGGuCcagcccc B
				Zin.Rz-7		s s s s
				amino stabl
18709	3437	UUGAUG G UGACCU	136	erbB2-3437	901	asgsgsusca GccgaaagGCaGucaaGGuCcaucaa B
				Zin.Rz-6		s s s s
				amino stabl
18679	3437	UUUGAUG G UGACCUG	137	erbB2-3437	902	csasgsgsuca GccgaaagGCaGucaaGGuCcaucama B
				Zin.Rz-7		s s s s
				amino stabl
18823	3504	UCUACA G CGGUAC	138	erbB2-3504	903	gsusascscg GccgaaagGCaGucaaGGuCuguaga B
				Zin.Rz-6		s s s s
				amino stabl
18710	3504	CUCUACA G CGGUACA	139	erbB2-3504	904	usgsusasccg GccgaaagGCaGucaaGGuCuguagag B
				Zin.Rz-7		s s s s
				amino stabl
18721	3724	CAAAGAC G UUUUUGC	140	erbB2-3724	905	gscsasasaaa GccgaaagGCaGucaaGGuGu gucuuug B
				Zin.Rz-7		s s s s
				amino stabl
18834	3808	CCUCCU G CCUUCA	141	erbB2-3808	906	usgsasasgg GccgaaagGCaGucaaCGuCaggagg B
				Zin.Rz-6		s s s s
				amino stabl
18827	3608	UCCUCCU G CCUUCAG	142	erbB2-3808	907	csusgsasagg GccgaaagGCaGucaaCGuCaggagg B
				Zin.Rz-7		s s s s
				amino stabl
18824	3996	GGCAAG G CCUGAC	143	erbB2-3996	908	gsuscsasgg GccgaaagGCaGucaaCGuCcuuccc B
				Zin.Rz-6		s s s s
				amino stabl
UPPER CASE = RIBO
Lower case = 2′-O-methyl
C  = 2′-deoxy-2′-amino Cytidine
s = phosphorothioate
B = inverted deoxyabasic

[0328]

TABLE XVI
Human HER2 Class II (zinzyme) Ribozyme and Target Sequence
	Seq. ID		Seq. ID
Pos	No.	Substrate	No.	Ribozyme
46	144	GGGCAGCC G CGCGCCCC	909	GGGGCGCG GCCGAAAGGCGAGUCAAGGUCU GGCUGCCC
48	145	GCAGCCGC G CGCCCCUU	910	AAGGGGCG GCCGAAAGGCGAGUCAAGGUCU GCGGCUGC
50	146	AGCCGCGC G CCCCUUCC	911	GGAAGGGG GCCGAAAGGCGAGUCAAGGUCU GCGCGGCU
75	147	CCUUUACU G CGCCGCGC	912	GCGCGGCG GCCGAAAGGCGAGUCAAGGUCU AGUAAAGG
77	148	UUUACUGC G CCGCGCGC	913	GCGCGCGG GCCGAAAGGCGAGUCAAGGUCU GCAGUAAA
80	149	ACUGCGCC G CGCGCCCG	914	CGGGCGCG GCCGAAAGGCGAGUCAAGGUCU GGCGCAGU
82	150	UGCGCCGC G CGCCCGGC	915	GCCGGGCG GCCGAAAGGCGAGUCAAGGUCU GCGGCGCA
84	151	CGCCGCGC G CCCGGCCC	916	GGGCCGGG GCCGAAAGGCGAGUCAAGGUCU GCGCGGCG
102	152	CACCCCUC G CAGCACCC	917	GGGUGCUG GCCGAAAGGCGAGUCAAGGUCU GAGGGGUG
112	153	AGCACCCC G CGCCCCGC	918	GCGGGGCG GCCGAAAGGCGAGUCAAGGUCU GGGGUGCU
114	154	CACCCCGC G CCCCGCGC	919	GCGCGGGG GCCGAAAGGCGAGUCAAGGUCU GCGGGGUG
119	155	CGCGCCCC G CGCCCUCC	920	GGAGGGCG GCCGAAAGGCGAGUCAAGGUCU GGGGCGCG
121	156	CGCCCCGC G CCCUCCCA	921	UGGGAGGG GCCGAAAGGCGAGUCAAGGUCU GCGGGGCG
163	157	CCGGAGCC G CAGUGAGC	922	GCUCACUG GCCGAAAGGCGAGUCAAGGUCU GGCUCCGG
194	158	GGCCUUGU G CCGCUGGG	923	CCCAGCGG GCCGAAAGGCGAGUCAAGGUCU ACAAGGCC
197	159	CUUGUGCC G CUGGGGGC	924	GCCCCCAG GCCGAAAGGCGAGUCAAGGUCU GGCACAAG
214	160	UCCUCCUC G CCCUCUUG	925	CAAGAGGG GCCGAAAGGCGAGUCAAGGUCU GAGGAGGA
222	161	GCCCUCUU G CCCCCCGG	926	CCGGGGGG GCCGAAAGGCGAGUCAAGGUCU AAGAGGGC
235	162	CCGGAGCC G CGAGCACC	927	GGUGCUCG GCCGAAAGGCGAGUCAAGGUCU GGCUCCGG
251	163	CCAAGUGU G CACCGGCA	928	UGCCGGUG GCCGAAAGGCGAGUCAAGGUCU ACACUUGG
273	164	AUGAAGCU G CGGCUCCC	929	GGGAGCCG GCCGAAAGGCGAGUCAAGGUCU AGCUUCAU
283	165	GGCUCCCU G CCAGUCCC	930	GGGACUGG GCCGAAAGGCGAGUCAAGGUCU AGGGAGCC
309	166	CUGGACAU G CUCCGCCA	931	UGGCGGAG GCCGAAAGGCGAGUCAAGGUCU AUGUCCAG
314	167	CAUGCUCC G CCACCUCU	932	AGAGGUGG GCCGAAAGGCGAGUCAAGGUCU GGAGCAUG
332	168	CCAGGGCU G CCAGGUGG	933	CCACCUGG GCCGAAAGGCGAGUCAAGGUCU AGCCCUGG
342	169	CAGGUGGU G CAGGGAAA	934	UUUCCCUG GCCGAAAGGCGAGUCAAGGUCU ACCACCUG
369	170	ACCUACCU G CCCACCAA	935	UUGGUGGG GCCGAAAGGCGAGUCAAGGUCU AGGUAGGU
379	171	CCACCAAU G CCAGCCUG	936	CAGGCUGG GCCGAAAGGCGAGUCAAGGUCU AUUGGUGG
396	172	UCCUUCCU G CAGGAUAU	937	AUAUCCUG GCCGAAAGGCGAGUCAAGGUCU AGGAAGGA
414	173	CAGGAGGU G CAGGGGUA	938	UAGCCCUG GCCGAAAGGCGAGUCAAGGUCU ACCUCCUG
426	174	GGCUACGU G CUCAUCGC	939	GCGAUGAG GCCGAAAGGCGAGUCAAGGUCU ACGUAGCC
433	175	UGCUCAUC G CUCACAAC	940	GUUGUGAG GCCGAAAGGCGAGUCAAGGUCU GAUGAGGA
462	176	GUCCCACU G CAGAGGCU	941	AGCCUCUG GCCGAAAGGCGAGUCAAGGUCU AGUGGGAC
471	177	CAGAGGCU G CGGAUUGU	942	ACAAUCCG GCCGAAAGGCGAGUCAAGGUCU AGCCUCUG
480	178	CGGAUUGU G CGAGGCAC	943	GUGCCUCG GCCGAAAGGCGAGUCAAGGUCU ACAAUCCG
511	179	ACAACUAU G CCCUGGCC	944	GGCCAGGG GCCGAAAGGCGAGUCAAGGUCU AUAGUUGU
522	180	CUGGCCGU G CUAGACAA	945	UUGUCUAG GCCGAAAGGCGAGUCAAGGUCU ACGGCCAG
540	181	GGAGACCC G CUGAACAA	946	UUGUUCAG GCCGAAAGGCGAGUCAAGGUCU GGGUCUCC
585	182	GGAGGCCU G CGGGAGCU	947	AGCUCCCG GCCGAAAGGCGAGUCAAGGUCU AGGCCUCC
594	183	CGGGAGCU G CAGCUUCG	948	CGAAGCUG GCCGAAAGGCGAGUCAAGGUCU AGCUCCCG
659	184	CCAGCUCU G CUACCAGG	949	CCUGGUAG GCCGAAAGGCGAGUCAAGGUCU AGAGCUGG
737	185	CACCAACC G CUCUCGGG	950	CCCGAGAG GCCGAAAGGCGAGUCAAGGUCU GGUUGGUG
749	186	UCGGGCCU G CCACCCCU	951	AGGGGUGG GCCGAAAGGCGAGUCAAGGUCU AGGCCCGA
782	187	GGGCUCCC G CUGCUGGG	952	CCCAGCAG GCCGAAAGGCGAGUCAAGGUCU GGGAGCCC
785	188	CUCCCGCU G CUGGGGAC	953	CUCCCCAG GCCGAAAGGCGAGUCAAGGUCU AGCGGGAC
822	189	AGCCUGAC G CGCACUGU	954	ACAGUGCG GCCGAAAGGCGAGUCAAGGUCU GUCAGGCU
824	190	CCUGACGC G CACUGUCU	955	AGACAGUG GCCGAAAGGCGAGUCAAGGUCU GCGUCAGG
835	191	CUGUCUGU G CCGGUGGC	956	GCCACCGG GCCGAAAGGCGAGUCAAGGUCU ACAGACAG
847	192	GUGGCUGU G CCCGCUGC	957	GCAGCGGG GCCGAAAGGCGAGUCAAGGUCU ACAGCCAC
851	193	CUGUGCCC G CUGCAAGG	958	CCUUGCAG GCCGAAAGGCGAGUCAAGGUCU GGGCACAG
854	194	UGCCCGCU G CAAGGGGC	959	GCCCCUUG GCCGAAAGGCGAGUCAAGGUCU AGCGGGCA
867	195	GGGCCACU G CCCACUGA	960	UCAGUGGG GCCGAAAGGCGAGUCAAGGUCU AGUGGCCC
878	196	CACUGACU G CUGCCAUG	961	CAUGGCAG GCCGAAAGGCGAGUCAAGGUCU AGUCAGUG
881	197	UGACUGCU G CCAUGAGC	962	GCUCAUGG GCCGAAAGGCGAGUCAAGGUCU AGCAGUCA
895	198	AGCAGUGU G CUGCCGGC	963	GCCGGCAG GCCGAAAGGCGAGUCAAGGUCU ACACUGCU
898	199	AGUGUGCU G CCGGCUGC	964	GCAGCCGG GCCGAAAGGCGAGUCAAGGUCU AGCACACU
905	200	UGCCGGCU G CACGGGCC	965	GGCCCGUG GCCGAAAGGCGAGUCAAGGUCU AGCCGGCA
929	201	CUCUGACU G CCUGGCCU	966	AGGCCAGG GCCGAAAGGCGAGUCAAGGUCU AGUCAGAG
938	202	CCUGGCCU G CCUCCACU	967	AGUGGAGG GCCGAAAGGCGAGUCAAGGUCU AGGCCAGG
972	203	UGUGAGCU G CACUGCCC	968	GGGCAGUG GCCGAAAGGCGAGUCAAGGUCU AGCUCACA
977	204	GCUGCACU G CCCAGCCC	969	GGGCUGGG GCCGAAAGGCGAGUCAAGGUCU AGUGCAGC
1020	205	GAGUCCAU G CCCAAUCC	970	GGAUUGGG GCCGAAAGGCGAGUCAAGGUCU AUGGACUC
1051	206	CAUUCGGC G CCAGCUGU	971	ACAGCUGG GCCGAAAGGCGAGUCAAGGUCU GCCGAAUG
1066	207	GUGUGACU G CCUGUCCC	972	GGGACAGG GCCGAAAGGCGAGUCAAGGUCU AGUCACAC
1106	208	GGGAUCCU G CACCCUCG	973	CGAGGGUG GCCGAAAGGCGAGUCAAGGUCU AGGAUCCC
1118	209	CCUCGUCU G CCCCCUGC	974	GCAGGGGG GCCGAAAGGCGAGUCAAGGUCU AGACGAGG
1125	210	UGCCCCCU G CACAACCA	975	UGGUUGUG GCCGAAAGGCGAGUCAAGGUCU AGGGGGCA
1175	211	UGAGAAGU G CAGCAAGC	976	GCUUGCUG GCCGAAAGGCGAGUCAAGGUCU ACUCCUCA
1189	212	AGCCCUGU G CCCGAGUG	977	CACUCGGG GCCGAAAGGCGAGUCAAGGUCU ACAGGGCU
1199	213	CCGAGUGU G CUAUGGUC	978	GACCAUAG GCCGAAAGGCGAGUCAAGGUCU ACACUCGG
1224	214	GAGCACUC G CGAGAGGU	979	ACCUCUCG GCCGAAAGGCGAGUCAAGGUCU AAGUGCUC
1249	215	UUACCAGU G CCAAUAUC	980	GAUAUUGG GCCGAAAGGCGAGUCAAGGUCU ACUGGUAA
1267	216	AGGAGUUU G CUGGCUGC	981	GCAGCCAG GCCGAAAGGCGAGUCAAGGUCU AAACUCCU
1274	217	UGCUGGCU G CAAGAACA	982	UCUUCUUC GCCGAAAGGCGAGUCAAGGUCU AGCCAGCA
1305	218	GCAUUUCU G CCGGAGAG	983	CUCUCCGG GCCGAAAGGCGAGUCAAGGUCU AGAAAUGC
1342	219	CCAACACU G CCCCGCUC	984	GAGCGGGG GCCGAAAGGCGAGUCAAGGUCU AGUGUUGG
1347	220	ACUGCCCC G CUCCAGCC	985	GGCUGGAG GCCGAAAGGCGAGUCAAGGUCU GGGGCAGU
1431	221	GACAGCCU G CCUGACCU	986	AGGUCAGG GCCGAAAGGCGAGUCAAGGUCU AGGCUGUC
1458	222	CAGAACCU G CAAGUAAU	987	AUUACUUG GCCGAAAGGCGAGUCAAGGUCU AGGUCCUG
1482	223	CGAAUUCU G CACAAUGG	988	CCAUUGUG GCCGAAAGGCGAGUCAAGGUCU AGAAUUCG
1492	224	ACAAUGGC G CCUACUCG	989	CGAGUAGG GCCGAAAGGCGAGUCAAGGUCU GCCAUUGU
1500	225	GCCUACUC G CUCACCCU	990	AGGGUCAG GCCGAAAGGCGAGUCAAGGUCU GAGUAGGC
1509	226	CUGACCCU G CAAGGGCU	991	AGCCCUUG GCCGAAAGGCGAGUCAAGGUCU AGGGUCAG
1539	227	CUGGGGCU G CGCUCACU	992	AGUGAGCG GCCGAAAGGCGAGUCAAGGUCU AGCCCCAG
1541	228	GGGGCUGC G CUCACUGA	993	UCAGUGAG GCCGAAAGGCGAGUCAAGGUCU GCAGCCCC
1598	229	CCACCUCU G CUUCGUGC	994	GCACGAAG GCCGAAAGGCGAGUCAAGGUCU AGAGGUGG
1605	230	UGCUUCGU G CACACGGU	995	ACCGUGUG GCCGAAAGGCGAGUCAAGGUCU ACGAAGCA
1614	231	CACACGGU G CCCUGGGA	996	UCCCAGGG GCCGAAAGGCGAGUCAAGGUCU ACCGUGUG
1641	232	CGGAACCC G CACCAAGC	997	GCUUGGUG GCCGAAAGGCGAGUCAAGGUCU GGGUUCCG
1653	233	CAAGCUCU G CUCCACAC	998	GUGUGGAG GCCGAAAGGCGAGUCAAGGUCU AGAGCUUG
1663	234	UCCACACU G CCAACCGG	999	CCGGUUGG GCCGAAAGGCGAGUCAAGGUCU AGUGUGGA
1706	235	CCUGGCCU G CCACCAGC	1000	GCUGGUGG GCCGAAAGGCGAGUCAAGGUCU AGGCCAGG
1718	236	CCAGCUGU G CGCCCGAG	1001	CUCGGGCG GCCGAAAGGCGAGUCAAGGUCU ACAGCUGG
1720	237	AGCUGUGC G CCCGAGGG	1002	CCCUCGGG GCCGAAAGGCGAGUCAAGGUCU GCACAGCU
1733	238	AGGGCACU G CUGGGGUC	1003	GACCCCAG GCCGAAAGGCGAGUCAAGGUCU AGUGCCCU
1766	239	UGUCAACU G CAGCCAGU	1004	ACUGGCUG GCCGAAAGGCGAGUCAAGGUCU AGUUGACA
1793	240	CCAGGAGU G CGUGGAGG	1005	CCUCCACG GCCGAAAGGCGAGUCAAGGUCU ACUCCUGG
1805	241	GGAGGAAU G CCGAGUAC	1006	GUACUCGG GCCGAAAGGCGAGUCAAGGUCU AUUCCUCC
1815	242	CGAGUACU G CAGGGGCU	1007	AGCCCCUG GCCGAAAGGCGAGUCAAGGUCU AGUACUCG
1843	243	AUGUGAAU G CCAGGCAC	1008	GUGCCUGG GCCGAAAGGCGAGUCAAGGUCU AUUCACAU
1857	244	CACUGUUU G CCGUGCCA	1009	UGGCACGG GCCGAAAGGCGAGUCAAGGUCU AAACAGUG
1862	245	UUUGCCGU G CCACCCUG	1010	CAGGGUGG GCCGAAAGGCGAGUCAAGGUCU ACGGCAAA
1936	246	UGGCCUGU G CCCACUAU	1011	AUAGUGGG GCCGAAAGGCGAGUCAAGGUCU ACAGGCCA
1961	247	UCCCUUCU G CGUGGCCC	1012	GGGCCACG GCCGAAAGGCGAGUCAAGGUCU AGAAGGGA
1970	248	CGUGGCCC G CUGCCCCA	1013	UGGGGCAG GCCGAAAGGCGAGUCAAGGUCU GGGCCACG
1973	249	GGCCCGCU G CCCCAGCG	1014	CGCUGGGG GCCGAAAGGCGAGUCAAGGUCU AGCGGGCC
2007	250	UCCUACAU G CCCAUCUG	1015	CAGAUGGG GCCGAAAGGCGAGUCAAGGUCU AUGUAGGA
2038	251	AGGAGGGC G CAUGCCAG	1016	CUGGCAUG GCCGAAAGGCGAGUCAAGGUCU GCCCUCCU
2042	252	GGGCGCAU G CCAGCCUU	1017	AAGGCUGG GCCGAAAGGCGAGUCAAGGUCU AUGCGCCC
2051	253	CCAGCCUU G CCCCAUCA	1018	UGAUGGGG GCCGAAAGGCGAGUCAAGGUCU AAGGCUGG
2063	254	CAUCAACU G CACCCACU	1019	AGUGGGUG GCCGAAAGGCGAGUCAAGGUCU AGUUGAUG
2099	255	CAAGGGCU G CCCCGCCG	1020	CGGCGGGG GCCGAAAGGCGAGUCAAGGUCU AGCCCUUG
2104	256	GCUGCCCC G CCGAGCAG	1021	CUGCUCGG GCCGAAAGGCGAGUCAAGGUCU GGGGCAGC
2143	257	UCAUCUCU G CGGUGGUU	1022	AACCACCG GCCGAAAGGCGAGUCAAGGUCU AGAGAUGA
2160	258	GGCAUUCU G CUGGUCGU	1023	ACGACCAG GCCGAAAGGCGAGUCAAGGUCU AGAAUGCC
2235	259	UACACGAU G CGGAGACU	1024	AGUCUCCG GCCGAAAGGCGAGUCAAGGUCU AUCGUGUA
2244	260	CGGAGACU G CUGCAGGA	1025	UCCUGCAG GCCGAAAGGCGAGUCAAGGUCU AGUCUCCG
2247	261	AGACUGCU G CAGGAAAC	1026	GUUUCCUG GCCGAAAGGCGAGUCAAGGUCU AGCAGUCU
2271	262	GUGGAGCC G CUGACACC	1027	GGUGUCAG GCCGAAAGGCGAGUCAAGGUCU GGCUCCAC
2292	263	GGAGCGAU G CCCAACCA	1028	UGGUUGGG GCCGAAAGGCGAGUCAAGGUCU AUCGCUCC
2304	264	AACCAGGC G CAGAUGCG	1029	CGCAUCUG GCCGAAAGGCGAGUCAAGGUCU GCCUGGUU
2310	265	GCGCAGAU G CGGAUCCU	1030	AGGAUCCG GCCGAAAGGCGAGUCAAGGUCU AUCUGCGC
2349	266	GUGAAGGU G CUUGGAUC	1031	GAUCCAAG GCCGAAAGGCGAGUCAAGGUCU ACCUUCAC
2362	267	GAUCUGGC G CUUUUGGC	1032	GCCAAAAG GCCGAAAGGCGAGUCAAGGUCU GCCAGAUC
2525	268	UGUCUCCC G CCUUCUGG	1033	CCAGAAGG GCCGAAAGGCGAGUCAAGGUCU GGGAGACA
2540	269	GGGCAUCU G CCUGACAU	1034	AUGUCAGG GCCGAAAGGCGAGUCAAGGUCU AGAUGCCC
2556	270	UCCACGGU G CAGCUGGU	1035	ACCAGCUG GCCGAAAGGCGAGUCAAGGUCU ACCGUGGA
2577	271	CAGCUUAU G CCCUAUGG	1036	CCAUAGGG GCCGAAAGGCGAGUCAAGGUCU AUAAGCUG
2588	272	CUAUGGCU G CCUCUUAG	1037	CUAAGAGG GCCGAAAGGCGAGUCAAGGUCU AGCCAUAG
2615	273	GGAAAACC G CGGACGCC	1038	GGCGUCCG GCCGAAAGGCGAGUCAAGGUCU GGUUUUCC
2621	274	CCGCGGAC G CCUGGGCU	1039	AGCCCAGG GCCGAAAGGCGAGUCAAGGUCU GUCCGCGG
2640	275	CAGGACCU G CUGAACUG	1040	CAGUUCAG GCCGAAAGGCGAGUCAAGGUCU AGGUCCUG
2655	276	UGGUGUAG G CAGAUUGC	1041	GCAAUCUG GCCGAAAGGCGAGUCAAGGUCU AUACACCA
2662	277	UGCAGAUU G CCAAGGGG	1042	CCCCUUGG GCCGAAAGGCGAGUCAAGGUCU AAUCUGCA
2691	278	GAGGAUGU G CGGCUCGU	1043	ACGAGCCG GCCGAAAGGCGAGUCAAGGUCU ACAUCCUC
2716	279	ACUUGGCC G CUCGGAAC	1044	GUUCCGAG GCCGAAAGGCGAGUCAAGGUCU GGCCAAGU
2727	280	CGGAACGU G CUGGUCAA	1045	UUGACCAG GCCGAAAGGCGAGUCAAGGUCU ACGUUCCG
2781	281	GCUCGGCU G CUGGACAU	1046	AUGUCCAG GCCGAAAGGCGAGUCAAGGUCU AGCCGAGC
2809	282	AGUACCAU G CAGAUGGG	1047	CCCAUCUG GCCGAAAGGCGAGUCAAGGUCU AUGGUACU
2826	283	GGCAAGGU G CCCAUCAA	1048	UUGAUGGG GCCGAAAGGCGAGUCAAGGUCU ACCUUGCC
2844	284	UGGAUGGC G CUGGAGUC	1049	GACUCCAG GCCGAAAGGCGAGUCAAGGUCU GCCAUCCA
2861	285	CAUUCUCC G CCGGCGGU	1050	ACCGCCGG GCCGAAAGGCGAGUCAAGGUCU GGAGAAUG
2976	286	CCUGACCU G CUGGAAAA	1051	UUUUCCAG GCCGAAAGGCGAGUCAAGGUCU AGGUCAGG
2997	287	GAGCGGCU G CCCCAGCC	1052	GGCUGGGG GCCGAAAGGCGAGUCAAGGUCU AGCCGCUC
3014	288	CCCCAUCU G CACCAUUG	1053	CAAUGGUG GCCGAAAGGCGAGUCAAGGUCU AGAUGGGG
3107	289	AUUCUCCC G CAUGGCCA	1054	UGGCCAUG GCCGAAAGGCGAGUCAAGGUCU GGGAGAAU
3128	290	CCCCCAGC G CUUUGUGG	1055	CCACAAAG GCCGAAAGGCGAGUCAAGGUCU GCUGGGGG
3191	291	CUUCUACC G CUCACUGC	1056	GCAGUGAG GCCGAAAGGCGAGUCAAGGUCU GGUAGAAG
3198	292	CGCUCACU G CUGGAGGA	1057	UCCUCCAG GCCGAAAGGCGAGUCAAGGUCU AGUGAGCG
3232	293	UGGUGGAU G CUGAGGAG	1058	CUCCUCAG GCCGAAAGGCGAGUCAAGGUCU AUCCACCA
3280	294	CAGACCCU G CCCCGGGC	1059	GCCCGGGG GCCGAAAGGCGAGUCAAGGUCU AGGGUCUG
3289	295	CCCCGGGC G CUGGGGGC	1060	GCCCCCAG GCCGAAAGGCGAGUCAAGGUCU GCCCGGGG
3317	296	CAGGCACC G CAGCUCAU	1061	AUGAGCUG GCCGAAAGGCGAGUCAAGGUCU GGUGCCUG
3468	297	AAGGGGCU G CAAAGCCU	1062	AGGCUUUG GCCGAAAGGCGAGUCAAGGUCU AGCCCCUU
3534	298	GUACCCCU G CCCUCUGA	1063	UCAGAGGG GCCGAAAGGCGAGUCAAGGUCU AGGGGUAC
3559	299	GCUACGUU G CCCCCCUG	1064	CAGUGGGG GCCGAAAGGCGAGUCAAGGUCU AACGUAGC
3572	300	CCUGACCU G CAGCCCCC	1065	GGGGGCUG GCCGAAAGGCGAGUCAAGGUCU AGGUCAGG
3627	301	CCCCCUUC G CCCCGAGA	1066	UCUCGGGG GCCGAAAGGCGAGUCAAGGUCU GAAGGGGG
3645	302	GGCCCUCU G CCUGCUGC	1067	GCAGCAGG GCCGAAAGGCGAGUCAAGGUCU AGAGGGCC
3649	303	CUCUGCCU G CUGCCCGA	1068	UCGGGCAG GCCGAAAGGCGAGUCAAGGUCU AGGCAGAG
3652	304	UGCCUGCU G CCCGACCU	1069	AGGUCGGG GCCGAAAGGCGAGUCAAGGUCU AGCAGGCA
3661	305	CCCGACCU G CUGGUGCC	1070	GGCACCAG GCCGAAAGGCGAGUCAAGGUCU AGGUCGGG
3667	306	CUGCUGGU G CCACUCUG	1071	CAGAGUGG GCCGAAAGGCGAGUCAAGGUCU ACCAGCAG
3730	307	ACGUUUUU G CCUUUGGG	1072	CCCAAAGG GCCGAAAGGCGAGUCAAGGUCU AAAAACGU
3742	308	UUGGGGGU G CCGUGGAG	1073	CUCCACGG GCCGAAAGGCGAGUCAAGGUCU ACCCCCAA
3784	309	GAGGAGCU G CCCCUCAG	1074	CUGAGGGG GCCGAAAGGCGAGUCAAGGUCU AGCUCCUC
3808	310	CUCCUCCU G CCUUCAGC	1075	GCUGAAGG GCCGAAAGGCGAGUCAAGGUCU AGGAGGAG
3933	311	CUGGACGU G CCAGUGUG	1076	CACACUGG GCCGAAAGGCGAGUCAAGGUCU ACGUCCAG
3960	312	CCAAGUCC G CAGAAGCC	1077	GGCUUCUG GCCGAAAGGCGAGUCAAGGUCU GGACUUGG
4007	313	UGACUUCU G CUGGCAUC	1078	GAUGCCAG GCCGAAAGGCGAGUCAAGGUCU AGAAGUCA
4056	314	GGGAACCU G CCAUGCCA	1079	UGGCAUGG GCCGAAAGGCGAGUCAAGGUCU AGGUUCCC
4061	315	CCUGCCAU G CCAGGAAC	1080	GUUCCUGG GCCGAAAGGCGAGUCAAGGUCU AUGGCAGG
4094	316	UCCUUCCU G CUUGAGUU	1081	AACUCAAG GCCGAAAGGCGAGUCAAGGUCU AGGAAGGA
4179	317	GAGGCCCU G CCCAAUGA	1082	UCAUUGGG GCCGAAAGGCGAGUCAAGGUCU AGGGCCUC
4208	318	CAGUGGAU G CCACAGCC	1083	GGCUGUGG GCCGAAAGGCGAGUCAAGGUCU AUCCACUG
4351	319	CUAGUACU G CCCCCCAU	1084	AUGGGGGG GCCGAAAGGCGAGUCAAGGUCU AGUACUAG
4406	320	UACAGAGU G CUUUUCUG	1085	CAGAAAAG GCCGAAAGGCGAGUCAAGGUCU ACUCUGUA
192	321	GCGGCCUU G UGCCGCUG	1086	CAGCGGCA GCCGAAAGGCGAGUCAAGGUCU AAGGCCGC
249	322	ACCCAAGU G UGCACCGG	1087	CCGGUGCA GCCGAAAGGCGAGUCAAGGUCU ACUUGGGU
387	323	GCCAGCCU G UCCUUCCU	1088	AGGAAGGA GCCGAAAGGCGAGUCAAGGUCU AGGCUGGC
478	324	UGCGGAUU G UGCGAGGC	1089	GCCUCGCA GCCGAAAGGCGAGUCAAGGUCU AAUCCGCA
559	325	CCACCCCU G UCACACGG	1090	CCCUGUGA GCCGAAAGGCGAGUCAAGGUCU AGGGGUGG
678	326	ACGAUUUU G UGGAAGGA	1091	UCCUUCCA GCCGAAAGGCGAGUCAAGGUCU AAAAUCGU
758	327	CCACCCCU G UUCUCCGA	1092	UCGGAGAA GCCGAAAGGCGAGUCAAGGUCU AGGGGUGG
768	328	UCUCCCAU G UGUAAGGG	1093	CCCUUACA GCCGAAAGGCGAGUCAAGGUCU AUCGGAGA
770	329	UCCGAUGU G UAAGGGCU	1094	AGCCCUUA GCCGAAAGGCGAGUCAAGGUCU ACAUCGGA
809	330	UGAGGAUU G UCAGAGCC	1095	GGCUCUGA GCCGAAAGGCGAGUCAAGGUCU AAUCCUCA
829	331	CCCGCACU G UCUGUGCC	1096	GGCACAGA GCCGAAAGGCGAGUCAAGGUCU AGUGCGCG
833	332	CACUGUCU G UGCCCGUG	1097	CACCGGCA GCCGAAAGGCGAGUCAAGGUCU AGACAGUG
845	333	CGGUCGCU G UGCCCGCU	1098	AGCGGGCA GCCGAAAGGCGAGUCAAGGUCU AGCCACCG
893	334	UCAGCAGU G UGCUGCCG	1099	CGGCAGCA GCCGAAAGGCGAGUCAAGGUCU ACUGCUCA
965	335	UGGCAUCU G UGAGCUGC	1100	GCAGCUCA GCCGAAAGGCGAGUCAAGGUCU ACAUGCCA
1058	336	CGCCAGCU G UGUGACUG	1101	CAGUCACA GCCGAAAGGCGAGUCAAGGUCU AGCUGGCG
1060	337	CCACCUCU G UGACUGCC	1102	GGCAGUCA GCCGAAAGGCGAGUCAAGGUCU ACAGCUGG
1070	338	GACUGCCU G UCCCUACA	1103	UGUACGGA GCCGAAAGGCGAGUCAAGGUCU AGGCAGUC
1166	339	ACAGCCGU G UGAGAAGU	1104	ACUUCUCA GCCGAAAGGCGAGUCAAGGUCU ACCGCUGU
1187	340	CAAGCCCU G UGCCCGAG	1105	CUCGGGCA GCCGAAAGGCGAGUCAAGGUCU AGGGCUUG
1197	341	GCCCGACU G UGCUAUGG	1106	CCAUAGCA GCCGAAAGGCGAGUCAAGGUCU ACUCGGGC
1371	342	CUCCAAGU G UUUGAGAC	1107	GUCUCAAA GCCGAAAGGCGAGUCAAGGUCU ACUUGGAC
1685	343	CGACGAGU G UGUGGGCG	1108	CGCCCACA GCCGAAAGGCGAGUCAAGGUCU ACUCGUCC
1687	344	ACGAGUGU G UGGGCGAG	1109	CUCGCCCA GCCGAAAGGCGAGUCAAGGUCU ACACUCGU
1716	345	CACCAGCU G UGCGCCCG	1110	CGGGCGCA GCCGAAAGGCGAGUCAAGGUCU AGCUGGUG
1757	346	CACCCACU G UGUCAACU	1111	AGUUGACA GCCGAAAGGCGAGUCAAGGUCU ACUGGGUG
1759	347	CCCACUGU G UCAACUGC	1112	GCAGUUGA GCCGAAAGGCGAGUCAAGGUCU ACACUGGG
1837	348	GGGAGUAU G UGAAUGCC	1113	GGCAUUCA GCCGAAAGGCGAGUCAAGGUCU AUACUCCC
1853	349	CAGGCACU G UUUGCCGU	1114	ACGGCAAA GCCGAAAGGCGAGUCAAGGUCU AGUGCCUG
1874	350	CCCUGAGU G UCAGCCCC	1115	GGGGCUGA GCCGAAAGGCGAGUCAAGGUCU ACUCAGGG
1901	351	AGUGACCU G UCUUGGAC	1116	GUCCAAAA GCCGAAAGGCGAGUCAAGGUCU AGGUCACU
1925	352	UCACCACU G UGUGGCCU	1117	ACGGCACA GCCGAAAGGCGAGUCAAGGUCU ACUGGUCA
1927	353	ACCACUCU G UGGCCUGU	1118	ACAGGCCA GCCGAAAGGCGAGUCAAGGUCU ACACUGGU
1934	354	UGUGGCCU G UGCCCACU	1119	AGUGGGCA GCCGAAAGGCGAGUCAAGGUCU AGGCCACA
1984	355	CCAGCGCU G UGAAACCU	1120	AGGUUUCA GCCGAAAGGCGAGUCAAGGUCU ACCGCUGG
2075	356	CCACUCCU G UGUGGACC	1121	GGUCCACA GCCGAAAGGCGAGUCAAGGUCU AGGAGUGG
2077	357	ACUCCUGU G UGGACCUG	1122	CAGGUCCA GCCGAAAGGCGAGUCAAGGUCU ACAGGAGU
2410	358	GGGAGAAU G UGAAAAUU	1123	AAUUUUCA GCCGAAAGGCGAGUCAAGGUCU AUUCUCCC
2436	359	AUCAAAGU G UUGAGGGA	1124	UCCCUCAA GCCGAAAGGCGAGUCAAGGUCU ACUUUGAU
2503	360	UGGCUGGU G UGGGCUCC	1125	GGAGCCCA GCCGAAAGGCGAGUCAAGGUCU ACCAGCCA
2518	361	CCCCAUAU G UCUCCCGC	1126	GCGGGAGA GCCGAAAGGCGAGUCAAGGUCU AUAUGGGG
2602	362	UAGACCAU G UCCGGGAA	1127	UUCCCGGA GCCGAAAGGCGAGUCAAGGUCU AUGGUCUA
2651	363	GAACUGGU G UAUGCAGA	1128	UCUGCAUA GCCGAAAGGCGAGUCAAGGUCU ACCAGUUC
2689	364	UGGAGGAU G UGCGGGUC	1129	GAGCCGCA GCCGAAAGGCGAGUCAAGGUCU AUCCUCCA
2749	365	CCAACCAU G UCAAAAUU	1130	AAUUUUGA GCCGAAAGGCGAGUCAAGGUCU AUGGUUGG
2887	366	AGAGUGAU G UGUGGAGU	1131	ACUCCACA GCCGAAAGGCGAGUCAAGGUCU AUCACUCU
2889	367	AGUGAUGU G UGGAGUUA	1132	UAACUCCA GCCGAAAGGCGAGUCAAGGUCU ACAUCACU
2902	368	GUUAUGGU G UGACUGUG	1133	CACAGUCA GCCGAAAGGCGAGUCAAGGUCU AGCAUAAC
2908	369	GUGUGACU G UGUGGGAG	1134	CUCCCACA GCCGAAAGGCGAGUCAAGGUCU AGUCACAC
2910	370	GUGACUCU G UGGGAGCU	1135	AGCUCCCA GCCGAAAGGCGAGUCAAGGUCU ACAGUCAC
3025	371	CCAUUGAU G UCUACAUG	1136	CAUGUAGA GCCGAAAGGCGAGUCAAGGUCU AUCAAUGG
3047	372	GGUCAAAU G UUGGAUGA	1137	UCAUCCAA GCCGAAAGGCGAGUCAAGGUCU AUUUGACC
3068	373	CUCUGAAU G UCGGCCAA	1138	UUGGCCGA GCCGAAAGGCGAGUCAAGGUCU AUUCAGAG
3093	374	GAGUUGGU G UCUGAAUU	1139	AAUUCAGA GCCGAAAGGCGAGUCAAGGUCU ACCAACUC
3133	375	AGCGCUUU G UGGUCAUC	1140	GAUGACCA GCCGAAAGGCGAGUCAAGGUCU AAACCGCU
3269	376	CUUCUUCU G UCCAGACC	1141	GGUCUGGA GCCGAAAGGCGAGUCAAGGUCU AGAAGAAG
3427	377	CCUCCGAU G UAUUUGAU	1142	AUCAAAUA GCCGAAAGGCGAGUCAAGGUCU AUCGGAGC
3592	378	CUGAAUAU G UGAACCAG	1143	CUGGUUCA GCCGAAAGGCGAGUCAAGGUCU AUAUUCAG
3607	379	AGCCAGAU G UUCGGCCC	1144	GGGCCGAA GCCGAAAGGCGAGUCAAGGUCU AUCUGGCU
3939	380	GUGCCAGU G UGAACCAG	1145	CUGGUUCA GCCGAAAGGCGAGUCAAGGUCU ACUGGCAC
3974	381	GCCCUGAU G UGUCCUCA	1146	UGAGGACA GCCGAAAGGCGAGUCAAGGUCU AUCAGGGC
3976	382	CCUGAUGU G UCCUCAGG	1147	CCUGAGGA GCCGAAAGGCGAGUCAAGGUCU ACAUCAGG
4072	383	AGGAACCU G UCCUAAGG	1148	CCUUAGGA GCCGAAAGGCGAGUCAAGGUCU AGGUUCCU
4162	384	GAGUCUUU G UGGAUUCU	1149	AGAAUCCA GCCGAAAGGCGAGUCAAGGUCU AAAGACUC
4300	385	AAGGGAGU G UCUAAGAA	1150	UUCUUAGA GCCGAAAGGCGAGUCAAGGUCU ACUCCCUU
4332	386	CAGAGACU G UCCCUGAA	1151	UUCAGGGA GCCGAAAGGCGAGUCAAGGUCU AGUCUCUG
4380	387	GCAAUGGU G UCAGUAUC	1152	GAUACUGA GCCGAAAGGCGAGUCAAGGUCU ACCAUUGC
4397	388	CAGGCUUU G UACAGAGU	1153	ACUCUGUA GCCGAAAGGCGAGUCAAGGUCU AAAGCCUG
4414	389	GCUUUUCU G UUUAGUUU	1154	AAACUAAA GCCGAAAGGCGAGUCAAGGUCU AGAAAAGC
4434	390	CUUUUUUU G UUUUGUUU	1155	AAACAAAA GCCGAAAGGCGAGUCAAGGUCU AAAAAAAG
4439	391	UUUGUUUU G UUUUUUUA	1156	UAAAAAAA GCCGAAAGGCGAGUCAAGGUCU AAAACAAA
9	392	AAGGGGAG G UAACCCUG	1157	CAGGGUUA GCCGAAAGGCGAGUCAAGGUCU CUCCCCUU
18	393	UAACCCUG G CCCCUUUG	1158	CAAAGGGG GCCGAAAGGCGAGUCAAGGUCU CAGGGUUA
27	394	CCCCUUUG G UCGGGGCC	1159	GGCCCCGA GCCGAAAGGCGAGUCAAGGUCU CAAAGGGG
33	395	UGGUCGGG G CCCCGGGC	1160	GCCCGGGG GCCGAAAGGCGAGUCAAGGUCU CCCGACCA
40	396	GGCCCCGG G CAGCCGCG	1161	CGCGGCUG GCCGAAAGGCGAGUCAAGGUCU CCGGGGCC
43	397	CCCGGGCA G CCGCGCGC	1162	GCGCGCGG GCCGAAAGGCGAGUCAAGGUCU UGCCCGGG
65	398	CCCACGGG G CCCUUUAC	1163	GUAAAGGG GCCGAAAGGCGAGUCAAGGUCU CCCGUGGG
89	399	CGCGCCCG G CCCCCACC	1164	GGUGGGGG GCCGAAAGGCGAGUCAAGGUCU CGGGCGCG
105	400	CCCUCGCA G CACCCCGC	1165	GCGGGGUG GCCGAAAGGCGAGUCAAGGUCU UGCGAGGG
130	401	CCCUCCCA G CCGGGUCC	1166	GGACCCGG GCCGAAAGGCGAGUCAAGGUCU UGGGAGGG
135	402	CCAGCCGG G UCCAGCCG	1167	CGGCUGGA GCCGAAAGGCGAGUCAAGGUCU CCGGCUGG
140	403	CGGGUCCA G CCGGAGCC	1168	GGCUCCGG GCCGAAAGGCGAGUCAAGGUCU UGGACCCG
146	404	CAGCCGGA G CCAUGGGG	1169	CCCCAUGG GCCGAAAGGCGAGUCAAGGUCU UCCGGCUG
154	405	GCCAUGGG G CCGGAGCC	1170	GGCUCCGG GCCGAAAGGCGAGUCAAGGUCU CCCAUGGC
160	406	GGGCCGGA G CCGCAGUG	1171	CACUCCGG GCCGAAAGGCGAGUCAAGGUCU UCCCGCCC
166	407	GAGCCGCA G UGAGCACC	1172	GGUGCUCA GCCGAAAGGCGAGUCAAGGUCU UGCGGCUC
170	408	CGCAGUGA G CACCAUGG	1173	CCAUGGUG GCCGAAAGGCGAGUCAAGGUCU UCACUGCG
180	409	ACCAUGGA G CUGGCGGC	1174	GCCGCCAG GCCGAAAGGCGAGUCAAGGUCU UCCAUGGU
184	410	UGGAGCUG G CGGCCUUG	1175	CAAGGCCG GCCGAAAGGCGAGUCAAGGUCU CAGCUCCA
187	411	AGCUGGCG G CCUUGUGC	1176	GCACAAGG GCCGAAAGGCGAGUCAAGGUCU CGCCAGCU
204	412	CGCUGGGG G CUCCUCCU	1177	AGGAGGAG GCCGAAAGGCGAGUCAAGGUCU CCCCAGCG
232	413	CCCCCGGA G CCGCGAGC	1178	GCUCGCGG GCCGAAAGGCGAGUCAAGGUCU UCCGGGGG
239	414	AGCCGCGA G CACCCAAG	1179	CUUGGGUG GCCGAAAGGCGAGUCAAGGUCU UCGCGGCU
247	415	GCACCCAA G UGUGCACC	1180	GGUGCACA GCCGAAAGGCGAGUCAAGGUCU UUGGGUGC
257	416	GUGCACCG G CACAGACA	1181	UGUCUGUG GCCGAAAGGCGAGUCAAGGUCU CGGUGCAC
270	417	GACAUGAA G CUGCGGCU	1182	AGCCGCAG GCCGAAAGGCGAGUCAAGGUCU UUCAUGUC
276	418	AAGCUGCG G CUCCCUGC	1183	GCAGGGAG GCCGAAAGGCGAGUCAAGGUCU CGCAGCUU
287	419	CCCUGCCA G UCCCGAGA	1184	UCUCGGGA GCCGAAAGGCGAGUCAAGGUCU UGGCAGGG
329	420	CUACCAGG G CUGCCAGG	1185	CCUGGCAG GCCGAAAGGCGAGUCAAGGUCU CCUGGUAG
337	421	GCUGCCAG G UGGUGCAG	1186	CUGCACCA GCCGAAAGGCGAGUCAAGGUCU CUGGCAGC
340	422	GCCAGGUG G UGCAGGGA	1187	UCCCUGCA GCCGAAAGGCGAGUCAAGGUCU CACCUGGC
383	423	CAAUGCCA G CCUGUCCU	1188	AGGACAGG GCCGAAAGGCGAGUCAAGGUCU UGGCAUUG
412	424	UCCAGGAG G UGCAGGGC	1189	GCCCUGCA GCCGAAAGGCGAGUCAAGGUCU CUCCUGGA
419	425	GGUGCAGG G CUACGUGC	1190	GCACGUAG GCCGAAAGGCGAGUCAAGGUCU CCUGCACC
424	426	AGGGCUAC G UGCUCAUC	1191	GAUGAGCA GCCGAAAGGCGAGUCAAGGUCU GUAGCCCU
445	427	ACAACCAA G UGAGGCAG	1192	CUGCCUCA GCCGAAAGGCGAGUCAAGGUCU UUGGUUGU
450	428	CAAGUGAG G CAGGUCCC	1193	GGGACCUG GCCGAAAGGCGAGUCAAGGUCU CUCACUUG
454	429	UGAGGCAG G UCCCACUG	1194	CAGUGGGA GCCGAAAGGCGAGUCAAGGUCU CUGCCUCA
468	430	CUGCAGAG G CUGCGGAU	1195	AUCCGCAG GCCGAAAGGCGAGUCAAGGUCU CUCUGCAG
485	431	UGUGCGAG G CACCCAGC	1196	GCUGGGUG GCCGAAAGGCGAGUCAAGGUCU CUCGCACA
492	432	GGCACCCA G CUCUUUGA	1197	UCAAAGAG GCCGAAAGGCGAGUCAAGGUCU UGGGUGCC
517	433	AUGCCCUG G CCGUGCUA	1198	UAGCACGG GCCGAAAGGCGAGUCAAGGUCU CAGGGCAU
520	434	CCCUGGCC G UGCUAGAC	1199	GUCUAGCA GCCGAAAGGCGAGUCAAGGUCU GGCCAGGG
568	435	UCACAGGG G CCUCCCCA	1200	UGGGGAGG GCCGAAAGGCGAGUCAAGGUCU CCCUGUGA
581	436	CCCAGGAG G CCUGCGGG	1201	CCCGCAGG GCCGAAAGGCGAGUCAAGGUCU CUCCUGGG
591	437	CUGCGGGA G CUGCAGCU	1202	AGCUGCAG GCCGAAAGGCGAGUCAAGGUCU UCCCGCAG
597	438	GAGCUGCA G CUUCGAAG	1203	CUUCGAAG GCCGAAAGGCGAGUCAAGGUCU UGCAGCUC
605	439	GCUUCGAA G CCUCACAG	1204	CUGUGAGG GCCGAAAGGCGAGUCAAGGUCU UUCGAAGC
631	440	AAGGAGGG G UCUUGAUC	1205	GAUCAAGA GCCGAAAGGCGAGUCAAGGUCU CCCUCCUU
642	441	UGGAUCCA G CGGAACCC	1206	GGGUUCCG GCCGAAAGGCGAGUCAAGGUCU UGGAUCAA
654	442	AACCCCCA G CUCUGCUA	1207	UAGCAGAG GCCGAAAGGCGAGUCAAGGUCU UGGGGGUU
708	443	AACAACCA G CUGGCUCU	1208	AGAGCCAG GCCGAAAGGCGAGUCAAGGUCU UGGUUGUU
712	444	ACCAGCUG G CUCUCACA	1209	UGUGAGAG GCCGAAAGGCGAGUCAAGGUCU CAGCUGGU
745	445	GCUCUCGG G CCUGCCAC	1210	GUGGCAGG GCCGAAAGGCGAGUCAAGGUCU CCGAGAGC
776	446	GUGUAAGG G CUCCCGCU	1211	AGCGGGAG GCCGAAAGGCGAGUCAAGGUCU CCUUACAC
797	447	GGGAGAGA G UUCUGAGG	1212	CCUCAGAA GCCGAAAGGCGAGUCAAGGUCU UCUCUCCC
815	448	UUGUCAGA G CCUGACGC	1213	GCGUCAGG GCCGAAAGGCGAGUCAAGGUCU UCUGACAA
839	449	CUGUGCCG G UGGCUGUG	1214	CACAGCCA GCCGAAAGGCGAGUCAAGGUCU CGGCACAG
842	450	UGCCGGUG G CUGUGCCC	1215	GGGCACAG GCCGAAAGGCGAGUCAAGGUCU CACCGGCA
861	451	UGCAAGGG G CCACUGCC	1216	GGCAGUGG GCCGAAAGGCGAGUCAAGGUCU CCCUUGCA
888	452	GOCCAUGA G CAGUGUGC	1217	GCACACUG GCCGAAAGGCGAGUCAAGGUCU UCAUGGCA
891	453	CAUGAGCA G UGUGCUGC	1218	GCAGCACA GCCGAAAGGCGAGUCAAGGUCU UGCUCAUG
902	454	UGCUGCCG G CUGCACGG	1219	CCGUGCAG GCCGAAAGGCGAGUCAAGGUCU CGGCAGCA
911	455	CUGCACGG G CCCCAAGC	1220	GCUUGGGG GCCGAAAGGCGAGUCAAGGUCU CCGUGCAG
918	456	GGCCCCAA G CACUCUGA	1221	UCAGAGUG GCCGAAAGGCGAGUCAAGGUCU UUGGGGCC
934	457	ACUGCCUG G CCUGCCUC	1222	GAGGCAGG GCCGAAAGGCGAGUCAAGGUCU CAGGCAGU
956	458	CAACCACA G UGGCAUCU	1223	AGAUGCCA GCCGAAAGGCGAGUCAAGGUCU UGUGGUUG
959	459	CCACAGUG G CAUCUGUG	1224	CACAGAUG GCCGAAAGGCGAGUCAAGGUCU CACUGUGG
969	460	AUCUGUGA G CUGCACUG	1225	CAGUGCAG GCCGAAAGGCGAGUCAAGGUCU UCACAGAU
982	461	ACUGCCCA G CCCUGGUC	1226	GACCAGGG GCCGAAAGGCGAGUCAAGGUCU UGGGCAGU
988	462	CAGCCCUG G UCACCUAC	1227	GUAGGUGA GCCGAAAGGCGAGUCAAGGUCU CAGGGCUG
1008	463	ACAGACAC G UUUGAGUC	1228	GACUCAAA GCCGAAAGGCGAGUCAAGGUCU GUGUCUGU
1014	464	ACGUUUGA G UCCAUGCC	1229	GGCAUGGA GCCGAAAGGCGAGUCAAGGUCU UCAAACGU
1034	465	UCCCGAGG G CCGGUAUA	1230	UAUACCGG GCCGAAAGGCGAGUCAAGGUCU CCUCGGGA
1038	466	GAGGGCCG G UAUACAUU	1231	AAUGUAUA GCCGAAAGGCGAGUCAAGGUCU CGGCCCUC
1049	467	UACAUUCG G CGCCAGCU	1232	AGCUGGCG GCCGAAAGGCGAGUCAAGGUCU CGAAUGUA
1055	468	CGGCGCCA G CUGUGUGA	1233	UCACACAG GCCGAAAGGCGAGUCAAGGUCU UGGCGCCG
1096	469	CUACGGAC G UGGGAUCC	1234	GGAUCCCA GCCGAAAGGCGAGUCAAGGUCU GUCCGUAG
1114	470	GCACCCUC G UCUGCCCC	1235	GGGGCAGA GCCGAAAGGCGAGUCAAGGUCU GAGGGUGC
1138	471	ACCAAGAG G UGACAGCA	1236	UGCUGUCA GCCGAAAGGCGAGUCAAGGUCU CUCUUGGU
1144	472	AGGUGACA G CAGAGGAU	1237	AUCCUCUG GCCGAAAGGCGAGUCAAGGUCU UGUCACCU
1161	473	GGAACACA G CGGUGUGA	1238	UCACACCG GCCGAAAGGCGAGUCAAGGUCU UGUGUUCC
1164	474	ACACAGCG G UGUGAGAA	1239	UUCUCACA GCCGAAAGGCGAGUCAAGGUCU CGCUGUGU
1173	475	UGUGAGAA G UGCAGCAA	1240	UUGCUGCA GCCGAAAGGCGAGUCAAGGUCU UUCUCACA
1178	476	GAAGUGCA G CAAGCCCU	1241	AGGGCUUG GCCGAAAGGCGAGUCAAGGUCU UGCACUUC
1182	477	UGCAGCAA G CCCUGUGC	1242	GCACAGGG GCCGAAAGGCGAGUCAAGGUCU UUGCUGCA
1195	478	GUGCCCGA G UGUGCUAU	1243	AUAGCACA GCCGAAAGGCGAGUCAAGGUCU UCGGGCAC
1205	479	GUGCUAUG G UCUGGGCA	1244	UGCCCAGA GCCGAAAGGCGAGUCAAGGUCU CAUAGCAC
1211	480	UGGUCUGG G CAUGGAGC	1245	GCUCCAUG GCCGAAAGGCGAGUCAAGGUCU CCAGACCA
1218	481	GGCAUGGA G CACUUGCG	1246	CGCAAGUG GCCGAAAGGCGAGUCAAGGUCU UCCAUGCC
1231	482	UGCGAGAG G UGAGGGCA	1247	UGCCCUCA GCCGAAAGGCGAGUCAAGGUCU CUCUCGCA
1237	483	AGGUGAGG G CAGUUACC	1248	GGUAACUG GCCGAAAGGCGAGUCAAGGUCU CCUCACCU
1240	484	UGAGGGCA G UUACCAGU	1249	ACUGGUAA GCCGAAAGGCGAGUCAAGGUCU UGCCCUCA
1247	485	AGUCACCA G UGCCAAUA	1250	UAUUGGCA GCCGAAAGGCGAGUCAAGGUCU UGGUAACU
1263	486	AUCCAGGA G UUUGCUGC	1251	CCAGCAAA GCCGAAAGGCGAGUCAAGGUCU UCCUGGAU
1271	487	GUUUGCUG G CUGCAAGA	1252	UCUUGCAG GCCGAAAGGCGAGUCAAGGUCU CAGCAAAC
1292	488	CUUUGGGA G CCUGGCAU	1253	AUGCCAGG GCCGAAAGGCGAGUCAAGGUCU UCCCAAAG
1297	489	GGAGCCUC G CAUUUCUG	1254	CAGAAAUG GCCGAAAGGCGAGUCAAGGUCU CAGGCUCC
1313	490	GCCGGAGA G CUUUGAUG	1255	CAUCAAAG GCCGAAAGGCGAGUCAAGGUCU UCUCCGGC
1330	491	GGGACCCA G CCUCCAAC	1256	GUUGGAGG GCCGAAAGGCGAGUCAAGGUCU UGGGUCCC
1353	492	CCGCUCCA G CCAGAGCA	1257	UGCUCUGG GCCGAAAGGCGAGUCAAGGUCU UGGAGCGG
1359	493	CAGCCAGA G CAGCUCCA	1258	UGGAGCUG GCCGAAAGGCGAGUCAAGGUCU UCUGGCUG
1362	494	CCAGAGCA G CUCCAAGU	1259	ACUUGGAG GCCGAAAGGCGAGUCAAGGUCU UGCUCUGG
1369	495	AGCUCCAA G UGUUUGAG	1260	CUCAAACA GCCGAAAGGCGAGUCAAGGUCU UUGGAGCU
1397	496	GAUCACAG G UUACCUAU	1261	AUAGGUAA GCCGAAAGGCGAGUCAAGGUCU CUGUGAUC
1414	497	ACAUCUCA G CAUCGCCG	1262	CGGCCAUG GCCGAAAGGCGAGUCAAGGUCU UGAGAUGU
1419	498	UCAGCAUG G CCGGACAG	1263	CUCUCCGG GCCGAAAGGCGAGUCAAGGUCU CAUGCUGA
1427	499	GCCGGACA G CCUGCCUG	1264	CAGGCAGG GCCGAAAGGCGAGUCAAGGUCU UGUCCGGC
1442	500	UGACCUCA G CGUCUUCC	1265	GGAAGACG GCCGAAAGGCGAGUCAAGGUCU UGAGGUCA
1444	501	ACCUGACC G UCUUCCAG	1266	CUGGAAGA GCCGAAAGGCGAGUCAAGGUCU GCUGAGGU
1462	502	ACCUGCAA G UAAUCCGG	1267	CCGGAUUA GCCGAAAGGCGAGUCAAGGUCU UUGCAGGU
1490	503	GCACAAUG G CGCCUACU	1268	AGUAGGCG GCCGAAAGGCGAGUCAAGGUCU CAUUGUGC
1515	504	CUGCAAGG G CUGGGCAU	1269	AUGCCCAG GCCGAAAGGCGAGUCAAGGUCU CCUUGCAG
1520	505	AGGGCUGG G CAUCACGU	1270	AGCUGAUG GCCGAAAGGCGAGUCAAGGUCU CCAGCCCU
1526	506	GGGCAUCA G CUGGCUGG	1271	CCAGCCAG GCCGAAAGGCGAGUCAAGGUCU UGAUGCCC
1530	507	AUCAGCUG G CUGGGGCU	1272	AGCCCCAG GCCGAAAGGCGAGUCAAGGUCU CAGCUGAU
1536	508	UGGCUGGG G CUGCGCUC	1273	GAGCGCAG GCCGAAAGGCGAGUCAAGGUCU CCCAGCCA
1559	509	GGAACUGG G CAGUGGAC	1274	GUCCACUG GCCGAAAGGCGAGUCAAGGUCU CCAGUUCC
1562	510	ACUGGGCA G UGGACUGG	1275	CCAGUCCA GCCGAAAGGCGAGUCAAGGUCU UGCCCAGU
1570	511	GUGGACUG G CCCUCAUC	1276	GAUGAGGG GCCGAAAGGCGAGUCAAGGUCU CAGUCCAC
1603	512	UCUGCUUC G UGCACACG	1277	CGUGUGCA GCCGAAAGGCGAGUCAAGGUCU GAAGCAGA
1612	513	UGCACACG G UGCCCUGG	1278	CCAGGGCA GCCGAAAGGCGAGUCAAGGUCU CGUGUGCA
1626	514	UGGGACCA G CUCUUUCG	1279	CGAAAGAG GCCGAAAGGCGAGUCAAGGUCU UGGUCCCA
1648	515	CGCACCAA G CUCUGCUC	1280	GAGCAGAG GCCGAAAGGCGAGUCAAGGUCU UUGGUGCG
1671	516	GCCAACCG G CCAGAGGA	1281	UCCUCUGG GCCGAAAGGCGAGUCAAGGUCU CGGUUGGC
1683	517	GAGGACGA G UGUGUGGG	1282	CCCACACA GCCGAAAGGCGAGUCAAGGUCU UCGUCCUC
1691	518	GUGUGUGG G CGAGGGCC	1283	GGCCCUCG GCCGAAAGGCGAGUCAAGGUCU CCACACAC
1697	519	GGGCGAGG G CCUGGCCU	1284	AGGCCAGG GCCGAAAGGCGAGUCAAGGUCU CCUCGCCC
1702	520	AGGGCCUG G CCUGCCAC	1285	GUGGCAGG GCCGAAAGGCGAGUCAAGGUCU CAGGCCCU
1713	521	UGCCACCA G CUGUGCGC	1286	GCGCACAG GCCGAAAGGCGAGUCAAGGUCU UGGUGGCA
1728	522	GCCCGAGG G CACUGCUG	1287	CAGCAGUG GCCGAAAGGCGAGUCAAGGUCU CCUCGGGC
1739	523	CUGCUGGG G UCCAGGGC	1288	GCCCUGGA GCCGAAAGGCGAGUCAAGGUCU CCCAGCAG
1746	524	GGUCCAGG G CCCACCCA	1289	UGGGUGGG GCCGAAAGGCGAGUCAAGGUCU CCUGGACC
1755	525	CCCACCCA G UGUGUCAA	1290	UUGACACA GCCGAAAGGCGAGUCAAGGUCU UGGGUGGG
1769	526	CAACUGCA G CCAGUUCC	1291	GGAACUGG GCCGAAAGGCGAGUCAAGGUCU UGCAGUUG
1773	527	UGCAGCCA G UUCCUUCG	1292	CGAAGGAA GCCGAAAGGCGAGUCAAGGUCU UGGCUGCA
1784	528	CCUUCGGG G CCAGGAGU	1293	ACUCCUGG GCCGAAAGGCGAGUCAAGGUCU CCCGAAGG
1791	529	GGCCAGGA G UGCGUGGA	1294	UCCACGCA GCCGAAAGGCGAGUCAAGGUCU UCCUGGCC
1795	530	AGGAGUGC G UGGAGGAA	1295	UUCCUCCA GCCGAAAGGCGAGUCAAGGUCU GCACUCCU
1810	531	AAUGCCGA G UACUGCAG	1296	CUGCAGUA GCCGAAAGGCGAGUCAAGGUCU UCGGCAUU
1821	532	CUGCAGGG G CUCCCCAG	1297	CUGGGGAG GCCGAAAGGCGAGUCAAGGUCU CCCUGCAG
1833	533	CCCAGGGA G UAUGUGAA	1298	UUCACAUA GCCGAAAGGCGAGUCAAGGUCU UCCCUGGG
1848	534	AAUGCCAG G CACUGUUU	1299	AAACAGUG GCCGAAAGGCGAGUCAAGGUCU CUGGCAUU
1860	535	UGUUUGCC G UGCCACCC	1300	GGGUGGCA GCCGAAAGGCGAGUCAAGGUCU GGCAAACA
1872	536	CACCCUGA G UGUCAGCC	1301	GGCUGACA GCCGAAAGGCGAGUCAAGGUCU UCAGGGUG
1878	537	GAGUGUCA G CCCCAGAA	1302	UUCUGGGG GCCGAAAGGCGAGUCAAGGUCU UGACACUC
1889	538	CCAGAAUG G CUCAGUGA	1303	UCACUGAG GCCGAAAGGCGAGUCAAGGUCU CAUUCUGG
1894	539	AUGGCUCA G UGACCUGU	1304	ACAGGUCA GCCGAAAGGCGAGUCAAGGUCU UGAGCCAU
1915	540	GACCGGAG G CUGACCAG	1305	CUGGUCAG GCCGAAAGGCGAGUCAAGGUCU CUCCGGUC
1923	541	GCUGACCA G UGUGUGGC	1306	GCCACACA GCCGAAAGGCGAGUCAAGGUCU UGGUCAGC
1930	542	AGUGUGUG G CCUGUGCC	1307	GGCACAGG GCCGAAAGGCGAGUCAAGGUCU CACACACU
1963	543	CCUUCUGC G UGGCCCGC	1308	GCGGGCCA GCCGAAAGGCGAGUCAAGGUCU GCAGAAGG
1966	544	UCUGCGUG G CCCGCUGC	1309	GCAGCGGG GCCGAAAGGCGAGUCAAGGUCU CACGCAGA
1979	545	CUGCCCCA G CGGUGUGA	1310	UCACACCG GCCGAAAGGCGAGUCAAGGUCU UGGGGCAG
1982	546	CCCCAGCG G UGUGAAAC	1311	GUUUCACA GCCGAAAGGCGAGUCAAGGUCU CGCUGGGG
2019	547	AUCUGGAA G UUUCCAGA	1312	UCUGGAAA GCCGAAAGGCGAGUCAAGGUCU UUCCAGAU
2036	548	UGAGGAGG G CGCAUGCC	1313	GGCAUGCG GCCGAAAGGCGAGUCAAGGUCU CCUCCUCA
2046	549	GCAUGCCA G CCUUGCCC	1314	GGGCAAGG GCCGAAAGGCGAGUCAAGGUCU UGGCAUGC
2096	550	UGACAAGG G CUGCCCCG	1315	CGGGGCAG GCCGAAAGGCGAGUCAAGGUCU CCUUGUCA
2109	551	CCCGCCGA G CAGAGAGC	1316	GCUCUCUG GCCGAAAGGCGAGUCAAGGUCU UCGGCGGG
2116	552	AGCAGAGA G CCAGCCCU	1317	AGGGCUGG GCCGAAAGGCGAGUCAAGGUCU UCUCUGCU
2120	553	GAGAGCCA G CCCUCUGA	1318	UCAGAGGG GCCGAAAGGCGAGUCAAGGUCU UGGCUCUC
2130	554	CCUCUGAC G UCCAUCAU	1319	AUGAUGGA GCCGAAAGGCGAGUCAAGGUCU GUCAGAGG
2146	555	UCUCUGCG G UGGUUGGC	1320	GCCAACCA GCCGAAAGGCGAGUCAAGGUCU CGCAGAGA
2149	556	CUGCGGUG G UUGGCAUU	1321	AAUGCCAA GCCGAAAGGCGAGUCAAGGUCU CACCGCAG
2153	557	GGUGGUUG G CAUUCUGC	1322	GCAGAAUG GCCGAAAGGCGAGUCAAGGUCU CAACCACC
2164	558	UUCUGCUG G UCGUGGUC	1323	GACCACGA GCCGAAAGGCGAGUCAAGGUCU CAGCAGAA
2167	559	UGCUGGUC G UGGUCUUG	1324	CAAGACCA GCCGAAAGGCGAGUCAAGGUCU GACCAGCA
2170	560	UGGUCGUG G UCUUGGGG	1325	CCCCAAGA GCCGAAAGGCGAGUCAAGGUCU CACGACCA
2179	561	UCUUGGGG G UGGUCUUU	1326	AAAGACCA GCCGAAAGGCGAGUCAAGGUCU CCCCAAGA
2182	562	UGGGGGUG G UCUUUGGG	1327	CCCAAAGA GCCGAAAGGCGAGUCAAGGUCU CACCCCCA
2202	563	CUCAUCAA G CGACGGCA	1328	UGCCGUCG GCCGAAAGGCGAGUCAAGGUCU UUGAUGAG
2208	564	AAGCGACG G CAGCAGAA	1329	UUCUGCUG GCCGAAAGGCGAGUCAAGGUCU CGUCGCUU
2211	565	CGACGGCA G CAGAAGAU	1330	AUCUUCUG GCCGAAAGGCGAGUCAAGGUCU UGCCGUCG
2226	566	AUCCGGAA G UACACGAU	1331	AUCGUGUA GCCGAAAGGCGAGUCAAGGUCU UUCCGGAU
2259	567	GAAACGGA G CUGGUGGA	1332	UCCACCAG GCCGAAAGGCGAGUCAAGGUCU UCCGUUUC
2263	568	CGGAGCUG G UGGAGCCG	1333	CGGCUCCA GCCGAAAGGCGAGUCAAGGUCU CAGCUCCG
2268	569	CUGGUGGA G CCGCUGAC	1334	GUCAGCGG GCCGAAAGGCGAGUCAAGGUCU UCCACCAG
2282	570	GACACCUA G CGGAGCGA	1335	UCGCUCCG GCCGAAAGGCGAGUCAAGGUCU UAGGUGUC
2287	571	CUAGCGGA G CGAUGCCC	1336	GGGCAUCG GCCGAAAGGCGAGUCAAGGUCU UCCGCUAG
2302	572	CCAACCAG G CGCAGAUG	1337	CAUCUGCG GCCGAAAGGCGAGUCAAGGUCU CUGGUUGG
2331	573	GAGACGGA G CUGAGGAA	1338	UUCCUCAG GCCGAAAGGCGAGUCAAGGUCU UCCGUCUC
2341	574	UGAGGAAG G UGAAGGUG	1339	CACCUUCA GCCGAAAGGCGAGUCAAGGUCU CUUCCUCA
2347	575	AGGUGAAG G UGCUUGGA	1340	UCCAAGCA GCCGAAAGGCGAGUCAAGGUCU CUUCACCU
2360	576	UGGAUCUG G CGCUUUUG	1341	CAAAAGCG GCCGAAAGGCGAGUCAAGGUCU CAGAUCCA
2369	577	CGCUUUUG G CACAGUCU	1342	AGACUGUG GCCGAAAGGCGAGUCAAGGUCU CAAAAGCG
2374	578	UUGGCACA G UCUACAAG	1343	CUUGUAGA GCCGAAAGGCGAGUCAAGGUCU UGUGCCAA
2384	579	CUACAAGG G CAUCUGGA	1344	UCCAGAUG GCCGAAAGGCGAGUCAAGGUCU CCUUGUAG
2422	580	AAAUUCCA G UGGCCAUC	1345	GAUGGCCA GCCGAAAGGCGAGUCAAGGUCU UGGAAUUU
2425	581	UUCCAGUG G CCAUCAAA	1346	UUUGAUGG GCCGAAAGGCGAGUCAAGGUCU CACUGGAA
2434	582	CCAUCAAA G UGUUGAGG	1347	CCUCAACA GCCGAAAGGCGAGUCAAGGUCU UUUGAUGG
2461	583	CCCCCAAA G CCAACAAA	1348	UUUGUUGG GCCGAAAGGCGAGUCAAGGUCU UUUGGGGG
2485	584	UAGACGAA G CAUACGUG	1349	CACGUAUG GCCGAAAGGCGAGUCAAGGUCU UUCGUCUA
2491	585	AAGCAUAC G UGAUGGCU	1350	AGCCAUCA GCCGAAAGGCGAGUCAAGGUCU GUAUGCUU
2497	586	ACGUGAUG G CUGGUGUG	1351	CACACCAG GCCGAAAGGCGAGUCAAGGUCU CAUCACGU
2501	587	GAUGGCUG G UGUGGGCU	1352	AGCCCACA GCCGAAAGGCGAGUCAAGGUCU CAGCCAUC
2507	588	UGGUGUGG G CUCCCCAU	1353	AUGGGGAG GCCGAAAGGCGAGUCAAGGUCU CCACACCA
2534	589	CCUUCUGG G CAUCUGCC	1354	GGCAGAUG GCCGAAAGGCGAGUCAAGGUCU CCAGAAGG
2554	590	CAUCCACG G UGCAGCUG	1355	CAGCUGCA GCCGAAAGGCGAGUCAAGGUCU CGUGGAUG
2559	591	ACGGUGCA G CUGGUGAC	1356	GUCACCAG GCCGAAAGGCGAGUCAAGGUCU UGCACCGU
2563	592	UGCAGCUG G UGACACAG	1357	CUGUGUCA GCCGAAAGGCGAGUCAAGGUCU CAGCUGCA
2571	593	GUGACACA G CUUAUGCC	1358	GGCAUAAG GCCGAAAGGCGAGUCAAGGUCU UGUGUCAC
2585	594	GCCCUAUG G CUGCCUCU	1359	AGAGGCAG GCCGAAAGGCGAGUCAAGGUCU CAUAGGGC
2627	595	ACGCCUGG G CUCCCAGG	1360	CCUGGGAG GCCGAAAGGCGAGUCAAGGUCU CCAGGCGU
2649	596	CUGAACUG G UGUAUGCA	1361	UGCAUACA GCCGAAAGGCGAGUCAAGGUCU CAGUUCAG
2675	597	GGGGAUGA G CUACCUGG	1362	CCAGGUAG GCCGAAAGGCGAGUCAAGGUCU UCAUCCCC
2694	598	GAUGUGCG G CUCGUACA	1363	UGUACGAG GCCGAAAGGCGAGUCAAGGUCU CGCACAUC
2698	599	UGCGGCUC G UACACAGG	1364	CCUGUGUA GCCGAAAGGCGAGUCAAGGUCU GAGCCGCA
2713	600	GGGACUUG G CCGCUCGG	1365	CCGAGCGG GCCGAAAGGCGAGUCAAGGUCU CAAGUCCC
2725	601	CUCGGAAC G UGCUGGUC	1366	GACCAGCA GCCGAAAGGCGAGUCAAGGUCU GUUCCGAG
2731	602	ACGUGCUG G UCAAGAGU	1367	ACUCUUGA GCCGAAAGGCGAGUCAAGGUCU CAGCACGU
2738	603	GGUCAAGA G UCCCAACC	1368	GGUUGGGA GCCGAAAGGCGAGUCAAGGUCU UCUUGACC
2769	604	GACUUCGG G CUGGCUCG	1369	CGAGCCAG GCCGAAAGGCGAGUCAAGGUCU CCGAAGUC
2773	605	UCGGGCUG G CUCGGCUG	1370	CAGCCGAG GCCGAAAGGCGAGUCAAGGUCU CAGCCCGA
2778	606	CUGGCUCG G CUGCUGGA	1371	UCCAGCAG GCCGAAAGGCGAGUCAAGGUCU CGAGCCAG
2802	607	GAGACAGA G UACCAUGC	1372	GCAUGGUA GCCGAAAGGCGAGUCAAGGUCU UCUGUCUC
2819	608	AGAUGGGG G CAAGGUGC	1373	GCACCUUG GCCGAAAGGCGAGUCAAGGUCU CCCCAUCU
2824	609	GGGGCAAG G UGCCCAUC	1374	GAUGGGCA GCCGAAAGGCGAGUCAAGGUCU CUUGCCCC
2835	610	CCCAUCAA G UGGAUGGC	1375	GCCAUCCA GCCGAAAGGCGAGUCAAGGUCU UUGAUGGG
2842	611	AGUGGAUG G CGCUGGAG	1376	CUCCAGCG GCCGAAAGGCGAGUCAAGGUCU CAUCCACU
2850	612	GCGCUGGA G UCCAUUCU	1377	AGAAUGGA GCCGAAAGGCGAGUCAAGGUCU UCCAGCGC
2865	613	CUCCGCCG G CGGUUCAC	1378	GUGAACCG GCCGAAAGGCGAGUCAAGGUCU CGGCGGAG
2868	614	CGCCGGCG G UUCACCCA	1379	UGGGUGAA GCCGAAAGGCGAGUCAAGGUCU CGCCGGCG
2882	615	CCACCAGA G UGAUGUGU	1380	ACACAUCA GCCGAAAGGCGAGUCAAGGUCU UCUGGUGG
2894	616	UGUGUGGA G UUAUGGUG	1381	CACCAUAA GCCGAAAGGCGAGUCAAGGUCU UCCACACA
2900	617	GAGUUAUG G UGUGACUG	1382	CAGUCACA GCCGAAAGGCGAGUCAAGGUCU CAUAACUC
2916	618	GUGUGGGA G CUGAUGAC	1383	GUCAUCAG GCCGAAAGGCGAGUCAAGGUCU UCCCACAC
2932	619	CUUUUGGG G CCAAACCU	1384	AGGUUUGG GCCGAAAGGCGAGUCAAGGUCU CCCAAAAG
2956	620	GGAUCCCA G CCCGGGAG	1385	CUCCCGGG GCCGAAAGGCGAGUCAAGGUCU UGGGAUCC
2991	621	AAGGGGGA G CGGCUGCC	1386	GGCAGCCG GCCGAAAGGCGAGUCAAGGUCU UCCCCCUU
2994	622	GGGGAGCG G CUGCCCCA	1387	UGGGGCAG GCCGAAAGGCGAGUCAAGGUCU CGCUCCCC
3003	623	CUGCCCCA G CCCCCCAU	1388	AUGGGGGG GCCGAAAGGCGAGUCAAGGUCU UGGGGCAG
3040	624	UGAUCAUG G UCAAAUGU	1389	ACAUUUGA GCCGAAAGGCGAGUCAAGGUCU CAUGAUCA
3072	625	GAAUGUCG G CCAAGAUU	1390	AAUCUUGG GCCGAAAGGCGAGUCAAGGUCU CGACAUUC
3087	626	UUCCGGGA G UUGGUGUC	1391	GACACCAA GCCGAAAGGCGAGUCAAGGUCU UCCCGGAA
3091	627	GGGAGUUG G UGUCUGAA	1392	UUCAGACA GCCGAAAGGCGAGUCAAGGUCU CAACUCCC
3112	628	CCCGCAUG G CCAGGGAC	1393	CUCCCUGG GCCGAAAGGCGAGUCAAGGUCU CAUGCGGG
3126	629	GACCCCCA G CGCUUUGU	1394	ACAAAGCG GCCGAAAGGCGAGUCAAGGUCU UGGGGGUC
3136	630	GCUUUGUG G UCAUCCAG	1395	CUGGAUGA GCCGAAAGGCGAGUCAAGGUCU CACAAAGC
3158	631	GGACUUGG G CCCAGCCA	1396	UGGCUGGG GCCGAAAGGCGAGUCAAGGUCU CCAAGUCC
3163	632	UGGGCCCA G CCAGUCCC	1397	GGCACUGC GCCGAAAGGCGAGUCAAGGUCU UGGGCCCA
3167	633	CCCAGCCA G UCCCUUGG	1398	CCAAGGGA GCCGAAAGGCGAGUCAAGGUCU UGGCUGGG
3179	634	CUUGGACA G CACCUUCU	1399	AGAAGGUG GCCGAAAGGCGAGUCAAGGUCU UGUCCAAG
3226	635	GGGACCUG G UGGAUGCU	1400	AGCAUCCA GCCGAAAGGCGAGUCAAGGUCU CAGGUCCC
3240	636	GCUGAGGA G UAUCUGGU	1401	ACCAGAUA GCCGAAAGGCGAGUCAAGGUCU UCCUCAGC
3247	637	AGUAUCUG G UACCCCAG	1402	CUGGGGUA GCCGAAAGGCGAGUCAAGGUCU CAGAUACU
3255	638	GUACCCCA G CAGGGCUU	1403	AAGCCCUG GCCGAAAGGCGAGUCAAGGUCU UGGGGUAC
3260	639	CCAGCAGG G CUUCUUCU	1404	AGAAGAAG GCCGAAAGGCGAGUCAAGGUCU CCUGCUGG
3287	640	UGCCCCGG G CGCUGGGG	1405	CCCCAGCG GCCGAAAGGCGAGUCAAGGUCU CCGGGGCA
3296	641	CGCUGGGG G CAUGGUCC	1406	GGACCAUG GCCGAAAGGCGAGUCAAGGUCU CCCCAGCG
3301	642	GGGGCAUG G UCCACCAC	1407	GUGGUGGA GCCGAAAGGCGAGUCAAGGUCU CAUGCCCC
3312	643	CACCACAG G CACCGCAG	1408	CUGCGGUG GCCGAAAGGCGAGUCAAGGUCU CUGUGGUG
3320	644	GCACCGCA G CUCAUCUA	1409	UAGAUGAG GCCGAAAGGCGAGUCAAGGUCU UGCGGUGC
3335	645	UACCAGGA G UGGCGGUG	1410	CACCGCCA GCCGAAAGGCGAGUCAAGGUCU UCCUGGUA
3338	646	CAGGAGUG G CGGUGGGG	1411	CCCCACCG GCCGAAAGGCGAGUCAAGGUCU CACUCCUG
3341	647	GAGUGGCG G UGGGGACC	1412	GGUCCCCA GCCGAAAGGCGAGUCAAGGUCU CGCCACUC
3360	648	ACACUAGG G CUGGAGCC	1413	GGCUCCAG GCCGAAAGGCGAGUCAAGGUCU CCUAGUGU
3366	649	GGGCUGGA G CCCUCUGA	1414	UCAGAGGG GCCGAAAGGCGAGUCAAGGUCU UCCACGCC
3382	650	AAGAGGAG G CCCCCAGG	1415	CCUGGGGG GCCGAAAGGCGAGUCAAGGUCU CUCCUCUU
3390	651	GCCCCCAG G UCUCCACU	1416	AGUGGAGA GCCGAAAGGCGAGUCAAGGUCU CUGGGGGC
3400	652	CUCCACUG G CACCCUCC	1417	GGAGGGUG GCCGAAAGGCGAGUCAAGGUCU CAGUGGAG
3415	653	CCGAAGGG G CUGGCUCC	1418	GGAGCCAG GCCGAAAGGCGAGUCAAGGUCU CCCUUCGG
3419	654	AGGGGCUG G CUCCCAUG	1419	CAUCGGAG GCCGAAAGGCGAGUCAAGGUCU CAGCCCCU
3437	655	AUUUGAUG G UGACCUGG	1420	CCAGGUCA GCCGAAAGGCGAGUCAAGGUCU CAUCAAAU
3454	656	GAAUGGGG G CAGCCAAG	1421	CUUGGCUG GCCGAAAGGCGAGUCAAGGUCU CCCCAUUC
3457	657	UGGGGGCA G CCAAGGGG	1422	CCCCUUGG GCCGAAAGGCGAGUCAAGGUCU UGCCCCCA
3465	658	GCCAAGGG G CUGCAAAG	1423	CUUUGCAG GCCGAAAGGCGAGUCAAGGUCU CCCUUGGC
3473	659	GCUGCAAA G CCUCCCCA	1424	UGGGGAGG GCCGAAAGGCGAGUCAAGGUCU UUUGCAGC
3494	660	UGACCCCA G CCCUCUAC	1425	GUAGAGGG GCCGAAAGGCGAGUCAAGGUCU UGGGGUCA
3504	661	CCUCUACA G CGGUACAG	1426	CUGUACCG GCCGAAAGGCGAGUCAAGGUCU UGUAGAGG
3507	662	CUACAGCG G UACAGUGA	1427	UCACUGUA GCCGAAAGGCGAGUCAAGGUCU CGCUGUAG
3512	663	GCGGUACA G UGAGGACC	1428	GGUCCUCA GCCGAAAGGCGAGUCAAGGUCU UGUACCGC
3526	664	ACCCCACA G UACCCCUG	1429	CAGGGGUA GCCGAAAGGCGAGUCAAGGUCU UGUGGGGU
3551	665	GACUGAUG G CUACGUUG	1430	CAACGUAG GCCGAAAGGCGAGUCAAGGUCU CAUCAGUC
3556	666	AUGGCUAC G UUGCCCCC	1431	GGGGGCAA GCCGAAAGGCGAGUCAAGGUCU GUAGCCAU
3575	667	GACCUGCA G CCCCCAGC	1432	GCUGGGGG GCCGAAAGGCGAGUCAAGGUCU UGCAGGUC
3582	668	AGCCCCCA G CCUGAAUA	1433	UAUUCAGG GCCGAAAGGCGAGUCAAGGUCU UGGGGGCU
3600	669	GUGAACCA G CCAGAUGU	1434	ACAUCUGG GCCGAAAGGCGAGUCAAGGUCU UGGUUCAC
3612	670	GAUGUUCG G CCCCAGCC	1435	GGCUGGGG GCCGAAAGGCGAGUCAAGGUCU CGAACAUC
3618	671	CGGCCCCA G CCCCCUUC	1436	GAAGGGGG GCCGAAAGGCGAGUCAAGGUCU UGGGGCCG
3638	672	CCGAGAGG G CCCUCUGC	1437	GCAGAGGG GCCGAAAGGCGAGUCAAGGUCU CCUCUCGG
3665	673	ACCUGCUG G UGCCACUC	1438	GAGUGGCA GCCGAAAGGCGAGUCAAGGUCU CAGCAGGU
3681	674	CUGGAAAG G CCCAAGAC	1439	GUCUUGGG GCCGAAAGGCGAGUCAAGGUCU CUUUCCAG
3712	675	AGAAUGGG G UCGUCAAA	1440	UUUGACGA GCCGAAAGGCGAGUCAAGGUCU CCCAUUCU
3715	676	AUGGGGUC G UCAAAGAC	1441	GUCUUUGA GCCGAAAGGCGAGUCAAGGUCU GACCCCAU
3724	677	UCAAAGAC G UUUUUGCC	1442	GGCAAAAA GCCGAAAGGCGAGUCAAGGUCU GUCUUUGA
3740	678	CUUUGGGG G UGCCGUGG	1443	CCACGGCA GCCGAAAGGCGAGUCAAGGUCU CCCCAAAG
3745	679	GGGGUGCC G UGGAGAAC	1444	GUUCUCCA GCCGAAAGGCGAGUCAAGGUCU GGCACCCC
3759	680	AACCCCGA G UACUUGAC	1445	GUCAAGUA GCCGAAAGGCGAGUCAAGGUCU UCGGGGUU
3781	681	AGGGAGGA G CUGCCCCU	1446	AGGGGCAG GCCGAAAGGCGAGUCAAGGUCU UCCUCCCU
3792	682	GCCCCUCA G CCCCACCC	1447	GGGUGGGG GCCGAAAGGCGAGUCAAGGUCU UGAGGGGC
3815	683	UGCCUUCA G CCCAGCCU	1448	AGGCUGGG GCCGAAAGGCGAGUCAAGGUCU UGAAGGCA
3820	684	UCAGCCCA G CCUUCGAC	1449	GUCGAAGG GCCGAAAGGCGAGUCAAGGUCU UGGGCUGA
3861	685	CCACCAGA G CGGGGGGC	1450	GCCCCCCG GCCGAAAGGCGAGUCAAGGUCU UCUGGUGG
3868	686	AGCGGGGG G CUCCACCC	1451	GGGUGGAG GCCGAAAGGCGAGUCAAGGUCU CCCCCGCU
3878	687	UCCACCCA G CACCUUCA	1452	UGAAGGUG GCCGAAAGGCGAGUCAAGGUCU UGGGUGGA
3901	688	CACCUACG G CAGAGAAC	1453	GUUCUCUG GCCGAAAGGCGAGUCAAGGUCU CGUAGGUG
3915	689	AACCCAGA G UACCUGGG	1454	CCCAGGUA GCCGAAAGGCGAGUCAAGGUCU UCUGGGUU
3923	690	GUACCUGG G UCUGGACG	1455	CGUCCAGA GCCGAAAGGCGAGUCAAGGUCU CCAGCUAC
3931	691	GUCUGGAC G UGCCAGUG	1456	CACUGGCA GCCGAAAGGCGAGUCAAGGUCU GUCCAGAC
3937	692	ACGUGCCA G UGUGAACC	1457	GGUUCACA GCCGAAAGGCGAGUCAAGGUCU UGGCACGU
3951	693	ACCAGAAG G CCAAGUCC	1458	GGACUUGG GCCGAAAGGCGAGUCAAGGUCU CUUCUGGU
3956	694	AAGGCCAA G UCCGCAGA	1459	UCUGCGGA GCCGAAAGGCGAGUCAAGGUCU UUGGCCUU
3966	695	CCGCAGAA G CCCUGAUG	1460	CAUCAGGG GCCGAAAGGCGAGUCAAGGUCU UUCUGCGG
3987	696	CUCAGGGA G CAGGGAAG	1461	CUUCCCUG GCCGAAAGGCGAGUCAAGGUCU UCCCUGAG
3996	697	CAGGGAAG G CCUGACUU	1462	AAGUCAGG GCCGAAAGGCGAGUCAAGGUCU CUUCCCUG
4011	698	UUCUGCUC G CAUCAAGA	1463	UCUUGAUG GCCGAAAGGCGAGUCAAGGUCU CAGCAGAA
4021	699	AUCAAGAG G UGGGAGGG	1464	CCCUCCCA GCCGAAAGGCGAGUCAAGGUCU CUCUUGAU
4029	700	GUGGGAGG G CCCUCCGA	1465	UCGGAGGG GCCGAAAGGCGAGUCAAGGUCU CCUCCCAC
4100	701	CUGCUUGA G UUCCCAGA	1466	UCUGGGAA GCCGAAAGGCGAGUCAAGGUCU UCAAGCAG
4111	702	CCCAGAUG G CUGGAAGG	1467	CCUUCCAG GCCGAAAGGCGAGUCAAGGUCU CAUCUGGG
4121	703	UGGAAGGG G UCCAGCCU	1468	AGGCUGGA GCCGAAAGGCGAGUCAAGGUCU CCCUUCCA
4126	704	GGGGUCCA G CCUCGUUG	1469	CAACGAGG GCCGAAAGGCGAGUCAAGGUCU UGGACCCC
4131	705	CCAGCCUC G UUGGAAGA	1470	UCUUCCAA GCCGAAAGGCGAGUCAAGGUCU GAGGCUGG
4146	706	GAGGAACA G CACUGGGG	1471	CCCCAGUG GCCGAAAGGCGAGUCAAGGUCU UGGUCCUC
4156	707	ACUGGGGA G UCUUUGUG	1472	CACAAAGA GCCGAAAGGCGAGUCAAGGUCU UCCCCAGU
4174	708	AUCCUGAG G CCCUGCCC	1473	GGGCAGGG GCCGAAAGGCGAGUCAAGGUCU CUCAGAAU
4197	709	ACUCUAGG G UCCAGUGG	1474	CCACUGGA GCCGAAAGGCGAGUCAAGGUCU CCUAGAGU
4202	710	AGGGUCCA G UGGAUGCC	1475	GGCAUCCA GCCGAAAGGCGAGUCAAGGUCU UGGACCCU
4214	711	AUUCCACA G CCCAGCUU	1476	AAGCUGGG GCCGAAAGGCGAGUCAAGGUCU UGUGGCAU
4219	712	ACAGCCCA G CUUGGCCC	1477	GGGCCAAG GCCGAAAGGCGAGUCAAGGUCU UGGGCUGU
4224	713	CCAGCUUG G CCCUUUCC	1478	GGAAAGGG GCCGAAAGGCGAGUCAAGGUCU CAACCUGG
4246	714	GAUCCUGG G UACUGAAA	1479	UUUCAGUA GCCGAAAGGCGAGUCAAGGUCU CCAGGAUC
4255	715	UACUGAAA G CCUUAGGG	1480	CCCUAAGG GCCGAAAGGCGAGUCAAGGUCU UUUCAGUA
4266	716	UUAGGGAA G CUGGCCUG	1481	CAGGCCAG GCCGAAAGGCGAGUCAAGGUCU UUCCCUAA
4270	717	GGAAGCUG G CCUGAGAG	1482	CUCUCAGG GCCGAAAGGCGAGUCAAGGUCU CAGCUUCC
4284	718	GAGGGGAA G CGGCCCUA	1483	UAGGGCCG GCCGAAAGGCGAGUCAAGGUCU UUCCCCUC
4287	719	GGGAAGCG G CCCUAAGG	1484	CCUUAGGG GCCGAAAGGCGAGUCAAGGUCU CGCUUCCC
4298	720	CUAAGGGA G UGUCUAAG	1485	CUUAGACA GCCGAAAGGCGAGUCAAGGUCU UCCCUUAG
4314	721	GAACAAAA G CGACCCAU	1486	AUGGGUCG GCCGAAAGGCGAGUCAAGGUCU UUUUGUUC
4346	722	GAAACCUA G UACUGCCC	1487	GGGCAGUA GCCGAAAGGCGAGUCAAGGUCU UAGGUUUC
4372	723	AAGGAACA G CAUUGGUG	1488	CACCAUUG GCCGAAAGGCGAGUCAAGGUCU UGUUCCUU
4378	724	CAGCAAUG G UGUCAGUA	1489	UACUGACA GCCGAAAGGCGAGUCAAGGUCU CAUUGCUG
4384	725	UGGUGUCA G UAUCCAGG	1490	CCUGGAUA GCCGAAAGGCGAGUCAAGGUCU UGACACCA
4392	726	GUAUCCAG G CUUUGUAC	1491	GUACAAAG GCCGAAAGGCGAGUCAAGGUCU CUGGAUAC
4404	727	UGUACAGA G UGCUUUUC	1492	GAAAAGCA GCCGAAAGGCGAGUCAAGGUCU UCUGUACA
4419	728	UCUGUUUA G UUUUUACU	1493	AGUAAAAA GCCGAAAGGCGAGUCAAGGUCU UAAACAGA
Input Sequence = HSERB2R. Cut Site = G/Y
Stem Length = 8 . Core Sequence = GCcgaaagGCGaGuCaaGGuCu
HSERB2R (Human c-erb-B-2 mRNA; 4473 bp)

[0329]

TABLE XVII
Substrate Specificity for Class I Ribozymes
Substrate sequence	SEQ ID NO	1-9t mutation	krel
5′-GCCGU G GGUUGCAC ACCUUUCC-3′	729	w.t.	1.00
5′-GCCGUG GGUUGCAC ACCUUUCC-3′	729	A57G	2.5
5′-GCCGAG GGUUGCAC ACCUUUCC-3′	730	A57U	0.24
5′-GCCGCG GGUUGCAC ACCUUUCC-3′	731	A57G	0.66
5′-GCCGGG GGUUGCAC ACCUUUCC-3′	732	A57C	0.57
5′-GCCGU U GGUUGCAC ACCUUUCC-3′	733	w.t.	0.17
5′-GCCGU A GGUUGCAC ACCUUUCC-3′	734	w.t.	n.d.
5′-GCCGU C GGUUGCAC ACCUUUCC-3′	735	w.t.	n.d.
5′-GCCGU G GGUUGCAC ACCUUUCC-3′	729	C16U	0.98
5′-GCCGU G UGUUGCAC ACCUUUCC-3′	736	C16G	n.d.
5′-GCCGU G UGUUGCAC ACCUUUCC-3′	736	Cl6A	0.65
5′-GCCGU G AGUUGCAC ACCUUUCC-3′	737	C16U	0.45
5′-GCCGU G CGUUGCAC ACCUUUCC-3′	738	C16G	0.73
5′-GCCGU G GGUUGCAC ACCUUU-3′	739	w.t.	0.89
5′-GCCGU G GGUUGCAC ACCU3′	740	w.t.	1.0
5′-GCCGU G GGUUGCAC AC-3′	741	w.t.	0.67

[0330]

TABLE XVIII

Random region alignments/mutations for Class I ribozyme

Random region alignments/mutations

position

1

2

3

4

5

5

clone(#'s)

7

0

0

0

0

6

Krel

1-9 motif(42)

G

G

U

G

U

C

A

U

C

A

U

A

A

U

G

G

C

A

C

C

C

U

U

C

A

A

G

G

A

C

A

U

C

G

U

C

C

G

G

G

1.01

1.1 (39)

A

U

0.89

1.6

A

1.06

1.27

A

C

U

0.95

1.14(8)

A

0.82

1.16(5)

A

C

U

0.66

1.20.

A

A

U

A

0.61

1.24

U

G

0.75

1.30.

A

U

U

0.81

2.1

C

C

0.24

2.13

A

U

G

0.19

2.18(3)

A

A

0.02

2.34

A

A

0.62

0.25

2.21

C

A

C

0.25

2.23(2)

U

0.9

2.27

A

C

G

U

0.78

2.31

U

1.1

2.35

A

C

C

U

0.84

2.36

A

U

A

0.31

2.38(2)

A

G

U

0.81

2.45(2)

A

C

U

0.36

3.3

C

G

0.6

3.6

A

A

1.11

3.7

A

C

A

U

0.98

3.9

U

0.86

3.26

A

C

U

1.51

3.27(2)

U

0.22

3.28(2)

G

1.1

4.13(3)

A

A

U

0.95

4.19

A

0.44

4.34(2)

A

U

C

0.27

4.383)

C

0.97

mutation maintains base pair

[0331]

TABLE XIX
Human Her2 Class II Ribozyme and Target Sequence
		Seq. ID		Seq ID
RPI #	NT Pos	#	Substrate	#	Ribozyme Sequence
19952	433	742	GCUCAUC G CUCACAA	1494	ususgsusgag gccgaaaggCgagugagguCu gaugagc B
19953	433	742	GCUCAUC G CUCACAA	1495	ususgsusgag gccgaaaggCGagugaGGuCu gaugagc B
19950	934	743	CUGCCUG C CCUGCCU	1496	asgsgscsagg gccgaaaggCgagugagguCu caggcag B
19951	934	743	CUGCCUG G CCUGCCU	1497	asgsgscsagg gccgaaaggCGagugaGGuCu caggcag B
19729	972	744	UGAGCU G CACUGC	1498	gscsasgsug gccgaaaggCGagugaGGuCu agcuca B
19730	972	744	UGAGCU G CACUGC	1499	gscsasgsug gccgaaagGCGagugaGGuCu agcuca B
19731	972	744	UGAGCU G CACUGC	1500	gscsasgsug gccgaaagGCGaGugaGGuCu agcuca B
20315	972	744	UGAGCU G CACUGC	1501	gscsasgsuaag gccgaaaggCgagugaGGuCu agcucaug B
20668	972	744	UGAGCU G CACUGC	1502	gscsasgsuu uua ggc cga aag gCgagu gaG GuC uag cuc aug uuB
20695	972	744	UGAGCU G CACUGC	1503	gscsasgsusususua agg ccg aaa gGC gag uga GGu Cua gcu cau guu uB
20696	972	744	UGAGCU G CACUGC	1504	gscsasgsususususua aaggcc gaa aggCgagugaGG uCu agc uca uga uuu B
20719	972	744	UGAGCU G CACUGC	1505	gscsasgsug gccgaaaggCgagugaGguCu agcuca B
20720	972	744	UGAGCU G CACUGC	1506	gscsasgsug gcc P ggCgagugaGguCu agcuca B
20721	972	744	UGAGCU G CACUGC	1507	gscsasgsug gc P gCgagugaGguCu agcuca B
20770	972	744	UGAGCU G CACUGC	1508	gscsasgsususususasasag gcc gaa agg Cga gug aGG uCu agc uca uga uuu B
20771	972	744	UGAGCU G CACUGC	1509	gscsasgsususususasasasgsgcc gaa agg Cga gug aGG uCu agc uca uga uuu B
20868	972	744	UGAGCU G CACUGC	1510	gscsasgsug gccguuaggCagugaGGuCu agcuca B
20869	972	744	UGAGCU G CACUGC	824	gscsasgsug GccgaaagGCGaGuGaGGuCu agcuca B
20870	972	744	UGAGCU G CACUGC	824	gscsasgsug GccgaaagGCGaGuGaGGuCu agcuoa B
20871	972	744	UGAGCU G CACUGC	824	gscsasgsug GccgaaagGCGaGuGaGGuCu agcuca B
20872	972	744	UGAGCU G CACUGC	1511	gscsasgsug gccgaaaggCgagugaGGuCu agcuca B
20873	972	744	UGAGCU G CACUGC	1511	gscsasgsug gccgaaaggCgagugaGGuCu agcuca B
20874	972	744	UGAGCU G CACUGC	1511	gscsasgsug gccgaaaggCgagugaGGuCu agcuca B
20875	972	744	UGAGCU G CACUGC	1511	gscsasgsug gccgaaaggCgagugaGGuCu agcuca B
21448	972	744	UGAGCU G CACUGC	1512	gscsasgsug g caccCgagugaGGuCu agcuca B
21449	972	744	UGAGCU G CACUGC	1513	gscsasgsug g uuuuCgagugaGGuCu agcuoa B
21450	972	744	UGAGCU G CACUGC	1514	gscsasgsug g uuaa CgagugaGGuCu agcuca B
21451	972	744	UGAGCU G CACUGC	1515	gscsasgsug g ucca CgagugaGGuCu agcuca B
21452	972	744	UGAGCU G CACUGC	1516	gscsasgsug g ucua CgagugaGGuCu agcuca B
21453	972	744	UGAGCU G CACUGC	1517	gscsasgsug g guaa CgagugaGGuCu agcuca B
21454	972	744	UGAGCU G CACUGC	1518	gscsasgsug g aau CgagugaGGuCu agcuca B
21455	972	744	UGAGCU G CACUGC	1519	gscsasgsug g aag CgagugaGGuCu agcuca B
21456	972	744	UGAGCU G CACUGC	1520	gscsasgsug g c aag g CgagugaGGuCu agcuca B
21457	972	744	UGAGGU G CACUGC	1521	gscsasgsug g cc aag gg CgagugaGGuCu agcuca B
21458	972	744	UGAGCU G CACUGC	1510	gscsasgsug g ccguua gg CgagugaGGuCu agcuca B
21459	972	744	UGAGCU G CACUGC	1522	gscsasgsug g cc guua gg CagugaGGuCu agcuca B
19954	1292	745	UUGGGA G CCUGGC	1523	gscscsasgg gccgaaaggCgagugagguCu ucccaa B
20628	1292	745	UUGGGA G CCUGGC	1524	gscscsasgg GccgaaagGCGaGuGaGGuCu ucccaa B
21083				1525	gsgsascsguugCacaugguacacguaCgacgaGGgg B
lower case = 2′-O-methyl
C = 2′-deoxy-2′-amino U, = 2′-deoxy-.2′-amino C
G,A = ribo G,A
B = inverted deoxyabasic
s = phosphorothioate internucleotide linkage
P = polyethylene glycol 18 (PEG 18) linker

Claims

1. A method of inhibiting expression of HER2 in a cell, comprising the step of contacting the cell with a chemotherapeutic agent and an enzymatic nucleic acid molecule having a formula III:

2. The method of claim 1, wherein the “q” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 4, 5, 6, 7, 8 9, 10, 11, 12, and 15.

3. The method of claim 1, wherein the “n” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 2, 3, 4, 5, 6, and 7.

4. The method of claim 1, wherein the “o” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

5. The method of claim 1, wherein said “q1” and “o” in said enzymatic nucleic acid molecule are of the same length.

6. The method of claim 1, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of different length.

7. The method of claim 1, wherein said chemical linkages in the enzymatic nucleic acid molecule are selected from the group consisting of phosphate ester, amide, phosphorothioate, and phosphorodithioate linkages.

8. The method of claim 1, wherein said C in the enzymatic nucleic acid molecule is 2′-deoxy-2′-NH2 or 2′-deoxy-2′-O—NH2.

9. The method of claim 1, wherein said enzymatic nucleic acid molecule is chemically synthesized.

10. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one ribonucleotide.

11. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises no ribonucleotide residues.

12. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one 2′-amino modification.

13. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises at least three phosphorothioate modifications.

14. The method of claim 13, wherein the phosphorothioate modification is at the 5′-end of said enzymatic nucleic acid molecule.

15. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises a 5′-cap, a 3′-cap, or both a 5′-cap and a 3′-cap.

16. The method of claim 15, wherein said 5′-cap is phosphorothioate modification.

17. The method of claim 15, wherein said 3′-cap is an inverted abasic moiety.

18. The method of claim 1, wherein said chemotherapeutic agent is selected from the group consisting of Paclitaxel, Doxorubicin, Cisplatin, and Herceptin.

19. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one sugar modification.

20. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one nucleic acid base modification.

21. The method of claim 1, wherein said enzymatic nucleic acid molecule comprises at least one phosphate backbone modification.

22. The method of claim 19, wherein said sugar modification is a 2′-O-methyl modification.

23. The method of claim 1, wherein said cell is a cancer cell.

24. A method of treatment of a patient having a condition associated with the level of HER2, wherein said patient is administered a chemotherapeutic agent and an enzymatic nucleic acid molecule having a formula III:

25. The method of claim 24, wherein the “q” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

26. The method of claim 24, wherein the “n” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 2, 3, 4, 5, 6. and 7.

27. The method of claim 24, wherein the “o” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

28. The method of claim 24, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of the same length.

29. The method of claim 24, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of different length.

30. The method of claim 24, wherein said chemical linkages in the enzymatic nucleic acid molecule are selected from the group consisting of phosphate ester, amide, phosphorothioate, and phosphorodithioate linkages.

31. The method of claim 24, wherein said C in the enzymatic nucleic acid molecule is 2′-deoxy-2′-NH2 or 2′-deoxy-2′-O—NH2.

32. The method of claim 24, wherein said enzymatic nucleic acid molecule is chemically synthesized.

33. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises at least one ribonucleotide.

34. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises no ribonucleotide residues.

35. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises at least one 2′-amino modification.

36. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises at least three phosphorothioate modifications.

37. The method of claim 36, wherein the phosphorothioate modification is at the 5′-end of said enzymatic nucleic acid molecule.

38. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises a 5′-cap,a 3′-cap, or both a 5′-cap and a 3′-cap.

39. The method of claim 38, wherein said 5′-cap is phosphorothioate modification.

40. The method of claim 38, wherein said 3′-cap is an inverted abasic moiety.

41. The method of claim 24, wherein said chemotherapeutic agent is selected from the group consisting of Paclitaxel, Doxorubicin, Cisplatin, and Herceptin.

42. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises at least one sugar modification.

43. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises at least one nucleic acid base modification.

44. The method of claim 24, wherein said enzymatic nucleic acid molecule comprises at least one phosphate backbone modification.

45. The method of claim 42, wherein said sugar modification is a 2′-O-methyl modification.

46. A method for treating conditions associated with the level of HER2 gene using a chemotherapeutic agent in combination with an enzymatic nucleic acid molecule having a formula III:

47. The method of claim 46, wherein the “q” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

48. The method of claim 46, wherein the “n” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 2, 3, 4, 5, 6, and 7.

49. The method of claim 46, wherein the “o” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

50. The method of claim 46, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of the same length.

51. The method of claim 46, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of different length.

52. The method of claim 46, wherein said chemical linkages in the enzymatic nucleic acid molecule are selected from the group consisting of phosphate ester, amide, phosphorothioate, and phosphorodithioate linkages.

53. The method of claim 46, wherein said C in the enzymatic nucleic acid molecule is 2′-deoxy-2′-NH2 or 2′-deoxy-2′-O—NH2.

54. The method of claim 46, wherein said enzymatic nucleic acid molecule is chemically synthesized.

55. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises at least one ribonucleotide.

56. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises no ribonucleotide residues.

57. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises at least one 2′-amino modification.

58. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises at least three phosphorothioate modifications.

59. The method of claim 58, wherein the phosphorothioate modification is at the 5′-end of said enzymatic nucleic acid molecule.

60. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises a 5′-cap, a 3′-cap, or both a 5′-cap and a 3′-cap.

61. The method of claim 60, wherein said 5′-cap is phosphorothioate modification.

62. The method of claim 60, wherein said 3′-cap is an inverted abasic moiety.

63. The method of claim 46, wherein said chemotherapeutic agent is selected from the group consisting of Paclitaxel, Doxorubicin, Cisplatin, and Herceptin.

64. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises at least one sugar modification.

65. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises at least one nucleic acid base modification.

66. The method of claim 46, wherein said enzymatic nucleic acid molecule comprises at least one phosphate backbone modification.

67. The method of claim 64, wherein said sugar modification is a 2′-O-methyl modification.

68. A method for treating cancer using a chemotherapeutic agent in combination with an enzymatic nucleic acid molecule having a formula III:

69. The method of claim 68, wherein the “q” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

70. The method of claim 68, wherein the “n” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 2, 3, 4, 5, 6, and 7.

71. The method of claim 68, wherein the “o” in said enzymatic nucleic acid molecule is an integer selected from the group consisting of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and 15.

72. The method of claim 68, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of the same length.

73. The method of claim 68, wherein said “q” and “o” in said enzymatic nucleic acid molecule are of different length.

74. The method of claim 68, wherein said chemical linkages in the enzymatic nucleic acid molecule is selected from the group consisting of phosphate ester, amide, phosphorothioate, and phosphorodithioate linkages.

75. The method of claim 68, wherein said C in the enzymatic nucleic acid molecule is 2′-deoxy-2′-NH2 or 2′-deoxy-2′-O—NH2.

76. The method of claim 68, wherein said enzymatic nucleic acid molecule is chemically synthesized.

77. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises at least one ribonucleotide.

78. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises no ribonucleotide residues.

79. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises at least one 2′-amino modification.

80. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises at least three phosphorothioate modifications.

81. The method of claim 80, wherein the phosphorothioate modification is at the 5′-end of said enzymatic nucleic acid molecule.

82. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises a 5′-cap,a 3′-cap, or both a 5′-cap and a 3′-cap.

83. The method of claim 82, wherein said 5′-cap is phosphorothioate modification.

84. The method of claim 82, wherein said 3′-cap is an inverted abasic moiety.

85. The method of claim 68, wherein said chemotherapeutic agent is selected from the group consisting of Paclitaxel, Doxorubicin, Cisplatin, and Herceptin.

86. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises at least one sugar modification.

87. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises at least one nucleic acid base modification.

88. The method of claim 68, wherein said enzymatic nucleic acid molecule comprises at least one phosphate backbone modification.

89. The method of claim 86, wherein said sugar modification is a 2′-O-methyl modification.

90. The method of claim 68, wherein said cancer is selected from the group consisting of breast cancer, non-small cell lung cancer, bladder cancer, prostate cancer, and pancreatic cancer.