WO1999054459A2 - Nucleic acid molecules with novel chemical compositions capable of modulating gene expression - Google Patents

Abstract

The invention features nucleic acid molecules with novel combinations of chemical modifications which are able to modulate gene expression.

Description

DESCRIPTION

Nucleic Acid Molecules With Novel Chemical Compositions Capable Of Modulating Gene Expression

This patent application relates to the patent application entitled, "NUCLEIC ACID MOLECULES WITH NOVEL CHEMICAL COMPOSITIONS CAPABLE OF

MODULATING GENE EXPRESSION", U.S.S.N. 60/082,404, which was filed with the

U.S. patent and trademark office on April 20, 1998. The earlier patent application listed

Thompson et al. as inventors.

Background Of The Invention This invention relates to novel chemically modified nucleic acid molecules that are capable of modulating gene expression through a variety of mechanisms. Specifically, the invention concerns novel combinations of chemical modifications in an oligonucleotide which enhance nuclease resistance, binding affinity, and/ or potency.

The following is a discussion of relevant art, none of which is admitted to be prior art to the present invention.

Since the discovery of the mechanisms underlying gene expression, specifically nucleic acid based transcription and translation, a great deal of effort has been placed on blocking or altering these processes for a variety of purposes, such as understanding biology, gene function, disease processes, and identifying novel therapeutic targets. Approaches involving nucleic acid molecules for modulating gene expression have gained popularity in recent years. For example, nucleic acid molecules have been designed which are capable of binding to specific mRNA sequences by Watson-Crick base pairing interaction and blocking translation (Crooke, 1996, Medicinal Res. Rev. 16, 319-344). Another approach involves complexation of DNA with triplex forming oligonucleotides to prevent transcription of bound DNA sequences thereby inhibiting gene expression (Kim et ah, 1998, Biochemistry. 37, 2299-2304). The interaction of antisense oligonucleotides, 2- 5A antisense chimera, or ribozymes with target RNA have been used to prevent gene expression. All of these nucleic acid molecules are highly specific to their matching target sequences and therefore may offer lower toxicity compared to traditional approaches such as chemotherapy.

The use of oligonucleotides for modulation of gene expression generally requires stabilization of oligonucleotides from degradation by nucleases that are present in biological systems. Cellular efficacy may be effected if the nucleic acid molecule is degraded before it reaches its desired target. Chemical modifications of nucleic acid molecules have been found to be advantageous in making them inaccessible to degradation by cellular nucleases. Uhlmann and Peyman, 1990, Chem. Reviews 90, 543, review the use of nucleoside modifications to stabilize antisense oligonucleotides. Besides improved stability, chemical modifications have also been shown to increase binding affinity, improve cellular penetration, and enhanced target specificity (Monia et al., 1993, J Biol Chem. 268, 14514-14522; Wu-Pong, 1994, BioPharm, 22-33).

One of the most studied and utilized chemical alteration in oligonucleotides has been backbone modifications such as phosphorothioates. Phosphorothioate oligonucleotides are nucleic acid molecules whose phosphodiester linkage has been modified by substituting a sulfur atom in place of an oxygen atom. In addition to increased nuclease resistance, phosphorothioate oligonucleotides are substrates for ribonuclease H (RNase H) (Monia, supra; Crooke et al, 1995, Biochem. J. 3112, 599-608). RNase H is an endonuclease which catalyzes the degradation of RNA in an RNA-DNA heteroduplex (Hostomsky et al., 1993 in Nucleases, Linn et al., eds., Cold Spring Harbor Laboratory Press, NY, 341-376). RNA/DNA heteroduplexes, called Okazaki fragments, are formed naturally during DNA replication. Therefore, the normal function of RNase H is to degrade the RNA portion of the heteroduplex to complete DNA replication. In experiments with E. coli RNase H, the phosphorothioate oligonucleotide activated the enzyme more efficiently (2-5 fold) compared to a standard phosphodiester containing oligonucleotide (Crooke, 1995, supra).

Binding of DNA to RNA is not as thermodynamically favorable as an RNA to RNA interaction (Altmann et al, 1996, Chimia 50, 168-176). Inoe & Ohtsuka, 1987, Nucleic Acids Research 115, 6131, first proposed an oligonucleotide with a central region consisting of oligodeoxynucleotides flanked by 2'-O-methyl modified nucleotide regions. The region of oligodeoxynucleotides in such a chimeric molecule is recognized by RNase H when bound to target RNA; and facilitates cleavage of target RNA by RNase H. (Inoe & Ohtsuka, 1987, EE_3SLett. 215, 327; Shibahara & Morisava, 1987, Nucleic Acids Res. 15, 4403). Such chimeric oligonucleotides were proposed to interact with target RNA more stably than an all DNA oligonucleotide.

Subsequent developments included the introduction of nuclease resistant modifications of the chimeric oligonucleotides, such as methylphosphonates (Tidd & Gibson, 1988, Anticancer Drug Design 3, 117), phosphorothioates (Agrawal & Pederson, 1990, Proc Nat. Acad. Set USA 87, 1407), and phosphoramidates (Potts & Runyun, 1991, Proc Nat. Acad. Sci. USA 88, 1516). Additionally, the flanking sequences have been modified with 2'-O-methyl and 2 '-E-modifications (Cook, 1993, Antisense Research and Applications, CRC Press, 150-181).

Agrawal et al., US Patent No. 5,652,355, describe a phosphorothioate-containing nucleic acid molecule with at least two 2'-O-methyl modifications on the 5' and 3' ends. Agrawal, US Patent No. 5,652,356, describes an oligonucleotide which consists of a region of 2'-O-substituted oligonucleotide located between two oligodeoxyribonucleotide regions. The DNA regions of this nucleic acid molecule consists of phosphorothioate modifications at every position.

Cook et al., US Patent No. 5,623,065, describe the use of a nucleic acid molecule which contains an RNase H cleavable region flanked by certain specifically modified nucleotides, for inhibition of gene expression of a ras gene.

Cook et al., US Patent No. 5,587,362, describe a nucleic acid molecule having "substantially chirally pure inter-sugar linkages", for modulation of gene expression.

Ohtsuka et al., US Patent No. 5,013,830, describe mixed oligomers having a DNA region and a 2'-O-methyl modified region, useful for modulation of gene expression.

Walder et al, US Patent No. 5,491,133, describe a method for modulating gene expression using chimeric oligonucleotides with 3' -phosphodiester linkage modifications.

Cohen et al, US Patent No. 5,276,019, and Cohen et al, US Patent No. 5,264,423 describe the use of oligodeoxynucleotides of no more than 32 nucleotides in length, containing at least one phosphorothioate intemucleoside linkage which are capable of preventing foreign nucleic acid replication.

Cohen et al, US Patent No. 5,286,717, describe an oligodeoxyribonucleotide with at least one phosphorothioate modification capable of inhibiting oncogenes.

Sproat et al., US Patent No. 5,334,711, describe 2'-O-R modified hammerhead and hairpin ribozymes, where R is ALKYL, ALKYNYL OR ALKΕNYL.

Crooke et al, 1996, Exp. Opin. Ther. Patents 6, 855, list and discuss various patents and PCT publications in the field of antisense technology.

Sproat et al., US Patent No. 5,678,731, describe 2'-O-R modified oligonucleotides where R is ALKYL, ALKYNYL OR ALKΕNYL. Usman et al., US Patent No. 5,652,094, describe enzymatic nucleic acid molecules which include nucleic acid analogues or deoxyribonucleotides.

Joyce, International Publication No. WO 96/17086, describes a DNA enzyme capable of cleaving RNA.

Rossi et al, US Patent No. 5,144,019, describe chimeric hammerhead ribozymes with the binding arms and stem II region modified with deoxyribonucleotides. Molecules have also been devised which include non-nucleotides capable of binding to nucleic acid. These peptide nucleic acid (PNA) molecules bind by Watson- Crick base-pairing and may also function through an antisense mechanism. These molecules have been used to augment hammerhead ribozyme activity by altering the structure of target RNAs and increasing accessibility of cleavage sites (Jankowsky et ah, 1997, Nucleic Acids Research 25, 2690-2693).

Summary of the Invention

This invention relates to novel nucleic acid molecules which are useful for modulation of gene expression. The nucleic acid molecule of the instant invention are distinct from other nucleic acid molecules known in the art. Specifically, the nucleic acid molecules of the present invention have novel combinations of chemical modifications and are capable of binding to RNA or DNA to facilitate modulation of gene expression. These novel combinations of chemical modifications may be used to form antisense oligonucleotides, triplex forming oligonucleotides, 2-5A antisense chimera, and enzymatic nucleic acid molecules.

In a preferred embodiment, the invention features a nucleic acid molecule having the following formulae: Formula I:

5' C (X)H-(Y)„— (X)o— C¹ 3' Formula II:

5' C (Y)_n (X)— C" 3'

Formula III:

5' C (X)ϊ (Y)_n C 3'

In a preferred embodiment, the invention features an enzymatic nucleic acid molecule having the formula: Formula IV:

5' C (X)_s (Z)_p (X)₀- (Y)n — (X)_q— C 3' Formula V:

5' C (X — (Y)ri-(X)o-(Z)_p-(X)_q— C- 3'

Formula VI:

5' c — (Y)_n — (Z)_D — (X —cr 3' Formula VII

5' C (X)_q (Z)_p (Y)_n C 3'

In each of the above formula (I- VII), X represents independently a nucleotide which may be same or different; where m and o are integers independently greater than or equal to 4 and preferably less than about 100, more specifically 5, 6, 7, 8, 9, 10, 11, 12, 15, or 20; r is an integer greater than or equal to four, more specifically 5, 6, 7, 10, 15, or 20; the nucleic acid molecule may be symmetric (m = O) or asymmetric (m O); (X)_m, (X)_o, and (X)_q are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid molecule (the target can be an RNA, DNA or RNA/DNA mixed polymers); Y represents independently a deoxyribonucleotide which may be same or different; n is an integer greater than or equal to 4, specifically 5, 6 7, 8, 9, 10, 11, or 12; Z represents an oligonucleotide including nucleotides capable of facilitating the cleavage of a target sequence; p is of length greater than or equal to 4 but less than 100, preferably 5, between 10-20, specifically 25-55, specifically between 30-45, more specifically 35-50; q is an integer greater than or equal to 0, preferably 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 20; represents a chemical linkage (e.g. a phosphate ester linkage, amide linkage or others known in the art); and each (X)_m, (X)₀, (X)_r, (X)_q, and/or (Y)_n independently comprise phosphorothioate linkages, more specifically each (X)_m, (X)_o, (X)_r, (X)_q, and/or (Y)_n independently comprise at least one phosphodiester linkage and one phosphorothioate linkage; each C and C independently represents a cap structure which may independently be present or absent; and (Z)_p may optionally include a phosphorothioate linkage. The nucleotides in the each of the formula I-VII are unmodified or modified at the sugar, base, and/or phosphate as known in the art.

Preferably, each of X represents independently a nucleotide which may be same or different; where m and o are integers independently greater than or equal to 5; (X)_m and (X)_o are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid molecule; each (X)_r comprises independently at least one phosphodiester linkage and one phosphorothioate linkage; Y represents independently a deoxyribonucleotide which may be same or different; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; n is an integer greater than or equal to 4; each (X)_m, and (X)₀ comprise independently at least one phosphodiester linkage and one phosphorothioate linkage; (Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'-S-phosphorothioate, or 5'-S-phosphorodithioate, or a 3'-S-phosphorothioate or a 3'-S-phosphorodithioate linkage or a mixture thereof; and each C and C independently represents a cap structure which may independently be present or absent.

By "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. Nucleotide generally comprise a base, 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, supra; Eckstein et al, International PCT Publication No. WO 92/07065; Usman et al, International PCT Publication No. WO 93/15187; Uhlman & Peyman, supra) all are hereby incorporated by reference herein). There are several examples of modified nucleic acid bases known in the art and has recently been 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 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), propyne, and others (Burgin et al, 1996, Biochemistry, 35, 14090; Uhlman & Peyman, supra). By "modified bases" in this aspect is meant nucleotide bases other than adenine, guanine, cytosine and uracil at 1' position or their equivalents; such bases may be used at any position, for example, within the catalytic core of an enzymatic nucleic acid molecule and/or in the substrate-binding regions of the nucleic acid molecule. By "unmodified nucleotide" is meant a nucleotide with one of the bases adenine, cytosine, guanine, thymine, uracil joined to the 1' carbon of β-D-ribo-furanose.

By "modified nucleotide" is meant a nucleotide which contains a modification in the chemical structure of an unmodified nucleotide base, sugar and/or phosphate.

By "sufficient length" is meant an oligonucleotide of greater than or equal to 4 nucleotides. 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). The interaction is stable either alone or in conjunction with (Y)_n and (Z)_p where applicable. By "chimeric nucleic acid molecule" or "chimeric oligonucleotide" is meant that, the molecule may be comprised of both modified or unmodified DNA or RNA.

By "cap structure" is meant chemical modifications which have been incorporated at the terminus of the oligonucleotide. These terminal modifications protect the nucleic acid molecule from exonuclease degradation, and may help in delivery and/or localization within a cell.

In another preferred embodiment (X)_m, (X)₀, (X)_q, (Y)_n and/or (Z)_p independently include modifications selected from a group comprising 2'-O-alkyl (e.g. 2'-O-allyl; Sproat et al, supra); 2'-O-alkylthioalkyl (e.g. 2'-O-methylthiomethyl; Karpeisky et al, 1998,

Nucleosides & Nucleotides 16, 955-958); L-nucleotides (Tazawa et al, 1970, Biochemistry 3499; Ashley, 1992, J Am. Chem. Soc. 114, 9731; Klubmann et al, 1996,

Nature Biotech 14, 1112); 2'-C-alkyl (Beigelman et al, 1995,J. Biol Chem. 270, 25702);

1-5-Anhydrohexitol; 2,6-diaminopurine (Strobel et al, 1994, Biochem. 33, 13824-13835);

2'-(N-alanyl) amino-2'-deoxynucleotide; 2'-(N-beta-alanyl) amino; 2'-deoxy-2'-(lysyl) amino; 2'-O-amino (Karpeisky et al, 1995, Tetrahedron Lett. 39, 1131); 2'-deoxy-2'-(N- histidyl) amino; 5-methyl (Strobel, supra); 2'-(N-b-carboxamidine-beta-alanyl) amino; 2'- deoxy-2'-(Ν-beta-alanyl) (Matulic-Adamic et al, 1995, Bioorg. & Med. Chem. Lett.

5,2721-2724); xylofuranosyl (Rosemeyer et al, 1991, Helvetica Chem. Ada, 74, 748;

Seela et al, 1994, Helvetica Chem. Acta, 11, 883; Seela et al, 1996, Helvetica Chem.

Ada, 79, 1451). In a preferred embodiment, the invention features a nucleic acid molecule of any of formula I-NII, where each X and/or Z, independently include a nucleotide modification having formula IX:

Where, each B is independently a modified or an unmodified nucleic acid base; Rl is independently a fluoroalkyl or an alkylthiofluoroalkyl; E is independently a phosphorus- containing group; and D is independently an O, blocking group or a phosphorus- containing group.

In another preferred embodiment, the invention features a nucleic acid molecule of any of formula I-NII, where each X and/or Z, independently include a nucleotide modification having formula X:

Wherein, each B is independently a modified or an unmodified nucleic acid base;

Rl is independently an aklyl, an alkylthioalkyl, a fluoroalkyl or an alkylthiofluoroalkyl; E is independently a phosphorus-containing group; and D is independently an O, blocking group or a phosphorus-containing group.

An "alkyl" group refers to a saturated aliphatic hydrocarbon, including straight- chain, branched-chain, and cyclic alkyl groups. Preferably, the alkyl group has 1 to 12 carbons. More preferably it is a lower alkyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, =O, =S, ΝO2 or N(CH3)2, amino, or SH. The term also includes alkenyl groups which are unsaturated hydrocarbon groups containing at least one carbon-carbon double bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkenyl group has 1 to 12 carbons. More preferably it is a lower alkenyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkenyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, =O, =S, NO2, halogen, N(CH3)2, amino, or SH. The term "alkyl" also includes alkynyl groups which have an unsaturated hydrocarbon group containing at least one carbon-carbon triple bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkynyl group has 1 to 12 carbons. More preferably it is a lower alkynyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkynyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, =O, =S, NO2 or N(CH3)2, amino or SH.

Such alkyl groups may also include aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester groups. An "aryl" group refers to an aromatic group which has at least one ring having a conjugated p electron system and includes carbocyclic aryl, heterocyclic aryl and biaryl groups, all of which may be optionally substituted. The preferred substituent(s) of aryl groups are halogen, trihalomethyl, hydroxyl, SH, OH, cyano, alkoxy, alkyl, alkenyl, alkynyl, and amino groups. An "alkylaryl" group refers to an alkyl group (as described above) covalently joined to an aryl group (as described above. Carbocyclic aryl groups are groups wherein the ring atoms on the aromatic ring are all carbon atoms. The carbon atoms are optionally substituted. Heterocyclic aryl groups are groups having from 1 to 3 heteroatoms as ring atoms in the aromatic ring and the remainder of the ring atoms are carbon atoms. Suitable heteroatoms include oxygen, sulfur, and nitrogen, and include furanyl, thienyl, pyridyl, pyrrolyl, N-lower alkyl pyrrolo, pyrimidyl, pyrazinyl, imidazolyl and the like, all optionally substituted. An "amide" refers to an -C(O)-NH-R, where R is either alkyl, aryl, alkylaryl or hydrogen. An "ester" refers to an -C(O)-OR', where R is either alkyl, aryl, alkylaryl or hydrogen.

A "blocking group" is a group which is able to be removed after polynucleotide synthesis and/or which is compatible with solid phase polynucleotide synthesis. A "phosphorus containing group" can include phosphorus in forms such as dithioates, phosphoramidites and/or as part of an oligonucleotide.

In yet another preferred embodiment C is selected from a group comprising inverted abasic residue,. 4',5'-methylene nucleotide; l-(beta-D-erythrofuranosyl) nucleotide, 4'-thio nucleotide, carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L- nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; t/zreø-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 abasic moiety; 3'-2'-inverted nucleotide moiety; 3'-2'-inverted abasic 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).

In yet another preferred embodiment C is selected from a group comprising, 4',5'- methylene nucleotide; l-(beta-D-erythrofuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 5'-amino-alkyl phosphate; l,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; t/Veo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5'- 5'-inverted nucleotide moeity; 5'-5'-inverted abasic moeity; 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 moeities (for more details see Beaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by reference herein).

In another preferred embodiment (Z)_p includes a non-nucleotide linker. Thus, in a preferred embodiment, the invention features an enzymatic nucleic acid molecule having one or more non-nucleotide moieties, and having enzymatic activity to cleave an RNA or DNA molecule. 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 abasic 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. By the phrase "enzymatic nucleic acid" 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 may have complementarity in a substrate binding region (e.g. (X)_m, (X)₀, (X)q and (Y)_n in formulae IV-VII) 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% may also be useful in this invention. The nucleic acids may 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, nucleozyme, DNAzyme, RNA enzyme, endoribonuclease, endonuclease, minizyme, leadzyme, oligozyme, chimeric ribozyme, chimeric enzymatic nucleic acid, or DNA enzyme. All of these terminologies describe nucleic acid molecules with enzymatic activity.

By "complementarity" is meant a nucleic acid that can form hydrogen bond(s) with other RNA sequence by either traditional Watson-Crick or other non-traditional types (for example, Hoogsteen type) of base-paired interactions.

By "oligonucleotide" as used herein, is meant a molecule comprising two or more nucleotides.

By "enzymatic portion" is meant that part of the enzymatic nucleic acid molecule essential for cleavage of a nucleic acid substrate By "substrate binding region" or "substrate binding domain" is meant that portion/region of a nucleic acid molecule (e.g. ribozyme) 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 may be base- paired. Such arms are shown generally in Figures 1 and 3. That is, in a ribozyme example, these arms contain sequences within a ribozyme which are intended to bring ribozyme and target RNA together through complementary base-pairing interactions. The ribozyme of the invention may have binding arms that are contiguous or non-contiguous and may be of 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).

By "DNAzyme" or "catalytic DNA" or "DNA enzyme" is meant, an enzymatic nucleic acid molecule lacking a 2' -OH group.

By "nucleic acid molecule" as used herein is meant a molecule comprising nucleotides. The nucleic acid can be composed of modified or unmodified nucleotides or non-nucleotides or various mixtures and combinations thereof.

In another preferred embodiment, the nucleic acid molecule of the present invention is conjugated with another moiety including but not limited to abasic nucleotides, polyether, polyamine, polyamides, peptides, carbohydrates, lipid, or polyhydrocarbon compounds. Those skilled in the art will recognize that these molecules may be linked to one or more of any nucleotides comprising the nucleic acid molecule at several positions on the sugar, base or phosphate group. In yet another preferred embodiment, the nucleic acid molecule of the present invention can form structures including but not limited to antisense, triplexes, 2-5A chimera antisense, or enzymatic nucleic acid (ribozymes).

By "antisense" is meant a non-enzymatic nucleic acid molecule that binds to target RNA, for example, 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).

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).

By "triplex DNA" it is meant an oligonucleotide that can bind to a double-stranded DNA in a sequence-specific manner to form a triple-strand helix. Triple-helix formation has been shown to inhibit transcription of the targeted gene (Duval- Valentin et al, 1992 Proc. Natl Acad. Sci. USA 89, 504).

In another preferred embodiment, the invention features an antisense oligonucleotide which is capable of interacting with the target RNA and sterically blocking translation, where the oligonucleotide has a 5' and a 3' Cap structure and the oligonucleotide may include modifications at the base, sugar or the phosphate groups. Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

Description of the Preferred Embodiments

The drawings will first briefly be described.

Drawings: Figure 1 is a diagrammatic representation of a nucleic acid molecule with 7-9 phosphorothioate oligodeoxyribonucleotide sequence flanked by 9 non- deoxyribonucleotide containing oligonucleotides, binding to a target molecule.

Figure 2 displays schematic representations of certain chemical structures which may be incorporated into the nucleic acid molecule of the invention. Figure 3 shows the secondary structure model for seven different classes of enzymatic nucleic acid molecules. Arrow indicates the site of cleavage. indicate the target sequence. Lines interspersed with dots are meant to indicate tertiary interactions. - is meant to indicate base-paired interaction. Group I Intron: P1-P9.0 represent various stem-loop structures (Cech et al, 1994, Nature Struc. Bio., 1, 273). RNase P (M1RNA): EGS represents external guide sequence (Forster et al, 1990, Science, 249, 783; Pace et al, 1990, J Biol Chem., 265, 3587). Group II Intron: 5'SS means 5' splice site; 3' SS means 3 '-splice site; IBS means intron binding site; EBS means exon binding site (Pyle et al, 1994, Biochemistry, 33, 2716). VS RNA: I-VI are meant to indicate six stem-loop structures; shaded regions are meant to indicate tertiary interaction (Collins, International PCT Publication No. WO 96/19577). HDV Ribozyme: : I-IV are meant to indicate four stem-loop structures (Been et al, US Patent No. 5,625,047). Hammerhead Ribozyme: : I-III are meant to indicate three stem-loop structures; stems I-III can be of any length and may be symmetrical or asymmetrical (Usman et al, 1996, Curr. Op. Struct. Bio., 1, 527). Hairpin Ribozyme: Helix 1, 4 and 5 can be of any length; Helix 2 is between 3 and 8 base-pairs long; Y is a pyrimidine; Helix 2 (H2) is provided with a least 4 base pairs (i.e., n is 1, 2, 3 or 4) and helix 5 can be optionally provided of length 2 or more bases (preferably 3 - 20 bases, i.e., m is from 1 - 20 or more). Helix 2 and helix 5 may be covalently linked by one or more bases (i.e., r is 1 base). Helix 1, 4 or 5 may also be extended by 2 or more base pairs (e.g., 4 - 20 base pairs) to stabilize the ribozyme structure, and preferably is a protein binding site. In each instance, each N and N' independently is any normal or modified base and each dash represents a potential base- pairing interaction. These nucleotides may be modified at the sugar, base or phosphate. Complete base-pairing is not required in the helices, but is preferred. Helix 1 and 4 can be of any size (i.e., o and p is each independently from 0 to any number, e.g., 20) as long as some base-pairing is maintained. Essential bases are shown as specific bases in the structure, but those in the art will recognize that one or more may be modified chemically (abasic, base, sugar and/or phosphate modifications) or replaced with another base without significant effect. Helix 4 can be formed from two separate molecules, i.e., without a connecting loop. The connecting loop when present may be a ribonucleotide with or without modifications to its base, sugar or phosphate, "q" is 2 bases. The connecting loop can also be replaced with a non-nucleotide linker molecule. H refers to bases A, U, or C. Y refers to pyrimidine bases. " " refers to a covalent bond. (Burke et al, 1996,

Nucleic Acids & Mol Biol, 10, 129; Chowrira et al, US Patent No. 5,631,359). Figure 4 is a graph comparing cell proliferation rates of MCF-7 cells treatment with active and inactive ribozyme with mismatch arms targeted to estrogen receptor delivered with GSV transfection reagent. The sequence for the active ribozyme is given as Seq. ID. No.2725 and the inactive is 2726.

Figure 5 is a graph comparing RNA levels of c-raf RNA in PC-3 cells following treatment with antisense (Seq. ID. No 2717) and scrambled antisense (mismatch) controls. Figure 6a and 6b displays several possible ribozymes comprising oligodeoxyribonucleotides. The symbols used in the diagram include: N' represents a nucleotide complementary to a nucleotide on the target molecule; N7 represents position 7 in the ribozyme molecule (Hertel, K. J., et al, 1992, Nucleic Acids Res.. 20, 3252); N' represents a deoxyribonucleotide complementary to a nucleotide on the target molecule; s represents a phosphorothioate modification; C represents a chemical modification at the 5' end of the ribozyme; and C represents a chemical modification at the 3' end.

Figure 7 shows examples of nucleotide modifications for incorporation into oligonucleotides. Figure 8 is a graph demonstrating the level of c-raf mRNA in PC-3 cells following treatment with c-raf sequence targeting antisense nucleic acid molecules. The antisense molecules target regions within the intron/exon junction (Seq. I.D. Nos.2731-2735), intron (Seq. I.D. 2736) and exon (Seq. I.D. 2737). The results demonstrate the molecules' ability to inhibit c-raf mRNA compared to the untreated or mismatch control at two concentrations.

Figure 9 is a graph which demonstrates the ability of an antisense molecule represented by Seq. I.D. No. 2738 (phosphorothioate modifications at every deoxynucleotide position) to inhibit c-raf message in PC-3 cells over a period of five days compared to the untreated and mismatch controls at three different concentrations. Figure 10 is a graph which demonstrates the ability of an antisense molecule represented by Seq. I.D. No. 2737 (three phosphorothoate modified nucleotides at both the 5' and 3' ends of the oligonucleotide) to inhibit c-raf message in PC-3 cells over a period of five days compared to the untreated control at three different concentrations.

Figure 11 is a graph which demonstrates the ability of an antisense molecule represented by Seq. I.D. No. 2744 (9 phosphorothioate modified DNA flanked by 7 2'-O- methylthiomethyl RNA nucleotides at the 5' and 3' end) to inhibit c-raf message in PC-3 cells over a period of five days compared to the untreated and mismatch control at three different concentrations.

Figure 12 is a graph showing the level of cellular proliferation inhibition exhibited by antisense oligonucleotides represented by Seq. I.D. Nos. 2738 and 2741. Also shown within the graph is the cellular proliferation after treatment of cells with a mismatch control (Seq. I.D. 2739).

Figure 13 is a graph showing the ability of oligonucleotides with different chemical modifications to inhibit c-raf mRNA. Each antisense molecule is compared to an untreated and mismatch control. Figure 14 is a graph demonstrating a dose dependent inhibition of C-raf in PC-3 cells following treatment with antisense oligonucleotides (Seq. I.D. Nos. 2741 and 2738).

Figure 15 is a graph showing inhibition of bcl-2 mRNA by antisense oligonucleotides compared to untreated and mismatch controls. Figure 16 is a graph showing the ability of several k-ras targeting antisense molecules to inhibit k-ras message

Figure 17 is a graph showing the ability of oligonucleotides with different chemical modifications to inhibit estrogen receptor mRNA. Each antisense molecule is compared to an untreated and mismatch control. Figure 18 shows a scheme for the synthesis of 3'-deoxy-3'-thio guanosine nucleoside (scheme 1).

Figure 19 shows a scheme for the synthesis of S-(pyridyl-2-disulfanyl) derivative (scheme 2).

Figure 20 shows a scheme for the synthesis of 3'-deoxy-3'-thio guanosine phosphoramidite.

Figure 21 shows a scheme for the preparation of 5'-thio-nucleoside phosphoramidite and succinates.

Figure 22 shows a scheme for the synthesis of 3'-thio-2'-O-methyl uridine.

Synthesis of Nucleic acid Molecules Synthesis of nucleic acids greater than 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 (e.g., antisense oligonucleotides, hammerhead or the hairpin ribozymes) are used for exogenous delivery. The simple structure of these molecules increases the ability of the nucleic acid to invade targeted regions of RNA structure. The molecules of the instant invention were chemically synthesized.

Oligodeoxyribonucleotides were synthesized using standard protocols as described in

Caruthers et al, 1992, Methods in Enzymology 211,3-19, and is incorporated by reference.

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 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 synthesis were conducted on a 394 Applied Biosystems, Inc. synthesizer using a modified 2.5 μmol scale protocol with a 5 min coupling step for alkylsilyl protected nucleotides and 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. A 6.5-fold excess (163 μL of 0.1 M = 16.3 μmol) of phosphoramidite and a 24-fold excess of S-ethyl tetrazole (238 μL of 0.25 M = 59.5 μmol) relative to polymer-bound 5'-hydroxyl was used in each coupling cycle. 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 2% 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 (Millipore). B & J Synthesis Grade acetonitrile was used directly from the reagent bottle. S-Ethyl tetrazole solution (0.25 M in acetonitrile) was made up from the solid obtained from American International Chemical, Inc.

Deprotection of the RΝA was performed as follows. The polymer-bound oligoribonucleotide, trityl-off, was transferred from the synthesis column to a 4mL glass screw top vial and suspended in a solution of methylamine (MA) 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:MeCΝ:H2θ/3:l :l, 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 (250 μL of a solution of 1.5mL N-methylpyrrolidinone, 750 μL TEA and 1.0 mL TEA^»3HF to provide a 1.4M HF concentration) and heated to 65°C for 1.5 h. The resulting, fully deprotected, oligomer was quenched with 50 mM TEAB (9 mL) prior to anion exchange desalting.

For anion exchange desalting of the deprotected oligomer, the TEAB solution was loaded onto a Qiagen 500® anion exchange cartridge (Qiagen Inc.) that was prewashed with 50 mM TEAB (10 mL). After washing the loaded cartridge with 50 mM TEAB (10 mL), the RΝA was eluted with 2 M TEAB (10 mL) and dried down to a white powder. Inactive hammerhead ribozymes 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).

The average stepwise coupling yields were >98% (Wincott et al, 1995 Nucleic Acids Res. 23, 2677-2684).

Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and joined together 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)

Administration of Nucleic Acid Molecules

Methods for the delivery of nucleic acid molecules is 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 may be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules may 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 may be directly delivered ex vivo to cells or tissues with or without the aforementioned vehicles. Alternatively, the nucleic acid/vehicle combination is 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 and Draper et al, PCT WO93/23569 which have been incorporated by reference herein.

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. The negatively charged polynucleotides of the invention can be administered (e.g.,

RNA, DNA or protein) and introduced into a patient by any standard means, 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 may 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.

The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the above compounds, e.g., acid addition salts, for example, salts of hydrochloric, hydrobromic, acetic acid, and benzene sulfonic acid.

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 to reach a target cell (i.e., a cell to which the negatively charged polymer is desired to be delivered to). For example, pharmacological compositions injected into the blood stream should be soluble. Other factors are known in the art, and include considerations such as toxicity and forms which prevent the composition or formulation from exerting its effect.

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., nucleic acids, 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 can facilitate the association of drug with the surface of cells, such as, lymphocytes and macrophages is also useful. This approach may 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 the cancer cells.

The invention also features the use of the a composition comprising surface- modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long- circulating liposomes or stealth liposomes). These formulations offer an 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 α/., 1995, Biochim. Biophys. Acta, 1238, 86-90). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, 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.

The present invention also includes 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. For example, preservatives, stabilizers, dyes and flavoring agents may be provided. Id. at 1449. These include sodium benzoate, sorbic acid and esters of τ hydroxybenzoic acid. In addition, antioxidants and suspending agents may be used. Jd 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.

Mechanism of action of Nucleic Acid Molecules of the Invention

Antisense: Antisense molecules may be RNA or DNA oligonucleotides and primarily function by specifically binding to matching sequences resulting in inhibition of peptide synthesis (Wu-Pong, Nov 1994, BioPharm, 20-33). The oligonucleotide binds to target RNA by Watson Crick base-pairing and blocks gene expression by preventing ribosomal translation of the bound sequences. Antisense molecules may also alter protein synthesis by interfering with RNA processing or transport from the nucleus into the cytoplasm (Mukhopadhyay & Roth, 1996, Crit. Rev. in Oncogenesis 1, 151-190). In addition, binding of single stranded DNA to RNA may result in nuclease degradation of the heteroduplex (Wu-Pong, supra; Crooke, supra). To date, the only backbone modified DNA chemistry which will act as substrates for RNase H are phosphorothioates and phosphorodithioates. In experiments with E. coli, the oligodeoxyribonucleotides phosphorothioate modification activated RNase H more efficiently (2-5 fold) compared to the natural phosphodiester containing oligodeoxynucleotide (Crooke, 1995, supra). Applicant describes here for the first time that oligonucleotides with 5'-thiophosphate modification can activate RNase H cleavage of RNA. Triplex Forming Oligonucleotides (TFOV. Single stranded DNA may 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 may result in gene expression or cell death since binding may be irreversible (Mukhopadhyay & Roth, supra).

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, 2-5 A 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. (2'-5')oligoadenylate structures may be covalently linked to antisense molecules to form chimeric oligonucleotides capable of RNA cleavage (Torrence, supra). These molecules putatively bind and active 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. Enzymatic Nucleic acid: Seven basic varieties of naturally-occurring enzymatic

RNAs are known presently. In addition, several in vitro selection (evolution) strategies (Orgel, 1979, Proc. R. Soc. London, B 205, 435) have been used to evolve new nucleic acid catalysts capable of catalyzing cleavage and ligation of phosphodiester linkages (Joyce, 1989, Gene, 82, 83-87; Beaudry et al, 1992, Science 257, 635-641; Joyce, 1992, Scientific American 261, 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., 1, 442; Santoro et al, 1997, Proc. Natl. Acad. Set, 94, 4262; Tang et al, 1997, RNA 3, 914; Nakamaye & Eckstein, 1994, supra; Long & Uhlenbeck, 1994, supra; Ishizaka et al., 1995, supra; Vaish et al, 1997, Biochemistry 36, 6495; all of these are incorporated by reference herein). Each can catalyze a series of reactions including the hydrolysis of phosphodiester bonds in trans (and thus can cleave other RNA molecules) under physiological conditions. Table I summarizes some of the characteristics of some of these ribozymes. 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 will destroy 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.

The enzymatic nature of a ribozyme is advantageous over other technologies, since the concentration of ribozyme necessary to affect a therapeutic treatment is lower. This advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribozyme molecule is able to cleave many molecules of target RNA. In addition, the ribozyme 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 a ribozyme.

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 supra).

Because of their sequence-specificity, tr< s-cleaving ribozymes 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). Ribozymes 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.

Optimizing Ribozyme Activity

Catalytic activity of the ribozymes described in the instant invention can be optimized as described by Draper et al., supra. The details will not be repeated here, but include altering the length of the ribozyme binding arms, or chemically synthesizing ribozymes 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; and Rossi et al, International Publication No. WO 91/03162; Sproat, US Patent 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 RNA molecules). Modifications which enhance their efficacy in cells, and removal of bases from stem loop structures to shorten RNA synthesis times and reduce chemical requirements are desired. (All these publications are hereby incorporated by reference herein).

There are several examples in the art describing sugar, base and phosphate modifications that can be introduced into enzymatic nucleic acid molecules without significantly effecting catalysis and with significant enhancement in their nuclease stability and efficacy. Ribozymes are modified to enhance stability and/or enhance catalytic 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 enzymatic nucleic acid molecules have been extensively described in the art (see Eckstein et al, International Publication PCT No. WΟ 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, US Patent No. 5,334,711 and Beigelman et al, 1995 J. Biol. Chem. 270, 25702; all of the references are hereby incorporated in their totality by reference herein). 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 catalysts of the instant invention.

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 ribozymes 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 ribozymes herein are said to "maintain" the enzymatic activity on all RNA ribozyme. Therapeutic ribozymes 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, ribozymes must be resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of RNA (Wincott et al, 1995 Nucleic Acids Res. 23, 2677; incorporated by reference herein) have expanded the ability to modify ribozymes by introducing nucleotide modifications to enhance their nuclease stability as described above.

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 ribozyme stability. In this invention, the product of these properties is increased or not significantly (less that 10 fold) decreased in vivo compared to an all RNA ribozyme.

In yet another preferred embodiment, nucleic acid catalysts having chemical modifications which maintain or enhance enzymatic activity is 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 ribozymes 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 ribozymes herein are said to "maintain" the enzymatic activity on all RNA ribozyme.

Inhibition Of Estrogen Receptor Gene Expression Breast Cancer is one of the leading causes of death in women (Jiang and Jordan,

1992, J. Natl. Cancer Inst. 84, 580-591). There has been an intense effort to understand the molecular mechanisms for hormonal regulation of cell proliferation in breast cancer over the last several decades. It has been shown that many breast and endometrial cancers are dependent on estrogen for their growth and progression (Borras et al, 1994, J. Steroid Biochem. Molec. Biol. 48, 325-336). Estrogen receptor plays a pivotal role in these cancers and thus controlling the expression of this gene is of paramount interest to researchers and clinicians. The estrogen receptor is a member of the steroid hormone receptor gene family that displays it's biological function as a ligand binding-dependent transcription factor. Tamoxifen is a nonsteroidal antiestrogen which treats all stages of breast cancer and may be used as a preventative compound in those predisposed to breast cancer (Jordan and Murphy, 1990, Endocr. Rev. 11; 578-610).

Most breast tumors are initially dependent upon estrogen for growth, and the estrogen receptor has been a key indicator for endocrine response, prognosis and survival from breast cancer. The MCF-7 human breast cancer cell line expresses high levels of estrogen receptor and is responsive to the effects of added estrogen (Borras et al., 1996, J. Steroid Biochem. Molec. Biol 57, 203-213; Pink and Jordan, 1996, Cancer Res. 56, 2321- 2330). They are an excellent model system to study the effects of regulation of estrogen receptor in breast cancer. Ribozymes and antisense oligonucleotides represent a direct means of affecting the levels of estrogen receptor message. In estrogen dependent cell lines, decreased amounts of estrogen receptor transcript should lower overall amounts of estrogen receptor protein and prevent proliferation of those cells. The effects of estrogen receptor on sexual differentiation of brain has been examined using antisense oligonucleotides (McCarthy et al, 1993 Endocrinology 133, 433-439). This application documents the effects of ribozymes and antisense oligonucleotides to estrogen receptor RNA levels and proliferation in MCF-7 cells.

Estrogen receptor may be inhibited using nucleic acid molecules, including the nucleic acid molecules of the present invention. Other references describe the use of antisense molecules to down regulate estrogen receptor RNA (Defazio et al, 1997, Cell Growth Differ. 8, 903-911; Santagati et al, 1997, Mol Endocrinol. 11, 938-949; Williard et al., 1994, Gene 149, 21 -24; Jiang & Jordan, supra).

The nucleic acid molecules may be chemically synthesized and delivered using methods described above, or may be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, 1985 Science 229, 345; McGarry and Lindquist, 1986 Proc. Natl. Acad. Sci. USA 83, 399; Scanlon et al, 1991, Proc. Natl. Acad. Sci. USA, 88, 10591- 5; Kashani-Sabet et al, 1992 Antisense Res. Dev., 2, 3-15; Dropulic et al, 1992 J Virol, 66, 1432-41; Weerasinghe et al, 1991 J Virol, 65, 5531-4; Ojwang et al, 1992 Proc. Natl. Acad. Sci. USA 89, 10802-6; Chen et al, 1992 Nucleic Acids Res., 20, 4581-9; Sarver et al, 1990 Science 247, 1222-1225; Thompson et al, 1995 Nucleic Acids Res. 23, 2259; Good et al, 1997, Gene Therapy, 4, 45; all of the references are hereby incorporated in their totality by reference herein). Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by a ribozyme (Draper et al, PCT WO 93/23569, and Sullivan et al, PCT WO 94/02595; Ohkawa et al, 1992 Nucleic Acids Symp. Ser., 27, 15-6; Taira et al, 1991, Nucleic Acids Res., 19, 5125-30; Ventura et al, 1993 Nucleic Acids Res., 21, 3249-55; Chowrira et al, 1994 J. Biol. Chem. 269, 25856; all of the references are hereby incorporated in their totality by reference herein).

One type of nucleic acid molecules known as ribozymes, which can cleave target molecules, are expressed from transcription units (see for example Couture et al, 1996, TIG., 12, 510) inserted into DNA or RNA vectors. The recombinant vectors are preferably DNA plasmids or viral vectors. Ribozyme expressing viral vectors could be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. Preferably, the recombinant vectors capable of expressing the ribozymes are delivered as described above, and persist in target cells. Alternatively, viral vectors may be used that provide for transient expression of ribozymes. Such vectors might be repeatedly administered as necessary. Once expressed, the ribozymes cleave the target mRNA. The active ribozyme contains an enzymatic center or core equivalent to those in the examples, and binding arms able to bind target nucleic acid molecules such that cleavage at the target site occurs. Other sequences may be present which do not interfere with such cleavage. Delivery of ribozyme expressing vectors could be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al, 1996, TIG., 12, 510).

In one aspect the invention features, an expression vector comprising nucleic acid sequence encoding at least one of the nucleic acid molecules of the instant invention is disclosed. The nucleic acid sequence encoding the nucleic acid catalyst of the instant invention is operable linked in a manner which allows expression of that nucleic acid molecule.

In another aspect the invention features, the expression vector comprises: a transcription initiation region (e.g., eukaryotic pol I, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); c) a gene encoding at least one of the nucleic acid catalyst of the instant invention; and wherein said gene is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. The vector may optionally include an open reading frame (ORF) for a protein operably linked on the 5' side or the 3 '-side of the gene encoding the nucleic acid catalyst of the invention; and/or an intron (intervening sequences).

Transcription of the ribozyme sequences are driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters will be expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type will depend on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990 Proc. Natl. Acad. Sci. U S A, 87, 6743-7; Gao and Huang 1993 Nucleic Acids Res., 21, 2867-72; Lieber et al, 1993 Methods Enzymol, 217, 47-66; Zhou et al., 1990 Mol Cell Biol, 10, 4529-37). Several investigators have demonstrated that ribozymes expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992 Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992 Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al, 1992 Nucleic Acids Res., 20, 4581-9; Yu et al., 1993 Proc. Natl Acad. Sci. USA, 90, 6340-4; L'Huillier et al, 1992 EMBO J. 11, 4411-8; Lisziewicz et al, 1993 Proc. Natl Acad. Sci. U S. A., 90, 8000-4; Thompson et al, 1995 Nucleic Acids Res. 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus NA RΝA are useful in generating high concentrations of desired RΝA molecules such as ribozymes in cells (Thompson et al, supra; Couture and Stinchcomb, 1996, supra; Νoonberg et al, 1994, Nucleic Acid Res., 22, 2830; Νoonberg et al, US Patent No. 5,624,803; Good et al, 1997, Gene Ther. 4, 45; Beigelman et al, International PCT Publication No. WO 96/18736; all of these publications are incorporated by reference herein. The above ribozyme transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra). In yet another aspect the invention features an expression vector comprising nucleic acid sequence encoding at least one of the catalytic nucleic acid molecule of the invention, in a manner which allows expression of that nucleic acid molecule. The expression vector comprises in one embodiment; a) a transcription initiation region; b) a transcription termination region; c) a gene encoding at least one said nucleic acid molecule; and wherein said gene is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. In another preferred embodiment the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an open reading frame; d) a gene encoding at least one said nucleic acid molecule, wherein said gene is operably linked to the 3'-end of said open reading frame; and wherein said gene is operably linked to said initiation region, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. In yet another embodiment the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) a gene encoding at least one said nucleic acid molecule; and wherein said gene is operably linked to said initiation region, said intron and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule. In another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame; e) a gene encoding at least one said nucleic acid molecule, wherein said gene is operably linked to the 3'-end of said open reading frame; and wherein said gene is operably linked to said initiation region, said intron, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

Target Nalidation

One of the most challenging tasks in drug discovery is the choice of a therapeutic target. Historically, traditional biochemical and other studies have offered limited information in this regard. However, recent advances in genomics offer the potential to revolutionize both the speed and certainty of therapeutic target identification. Progress in characterizing the genes in the human genome has been very rapid, and it is now estimated that the entire complement of genes in the human genome may be sequenced before the end of this century. However, this mass of information is coming to the scientific world without a road map. Converting pure gene sequence information into a functional understanding of their role in human disease is proving to be a much more difficult problem. Even after a group of genes is associated with a particular disease, the process of validating which genes are appropriate for use as therapeutic targets is often slow and costly. Most companies with genomics activities now have access to myriad partial or full sequences, but do not possess adequate technologies to determine which of those sequences is an appropriate therapeutic target. As a result, only a few genes have been unequivocally identified as the causative agent for a specific disease.

The nucleic acid molecules of the present invention can inhibit gene expression in a highly specific manner by binding to and causing the cleavage of the mRΝA corresponding to the gene of interest, and thereby prevent production of the gene product (Christoffersen, Nature Biotech, 1997, 2, 483-484). Appropriate delivery vehicles can be combined with these nucleic acid molecules (including polymers, cationic lipids, liposomes and the like) and delivered to appropriate cell culture or in vivo animal disease models as described above. By monitoring inhibition of gene expression and correlation with phenotypic results, the relative importance of the particular gene sequence to disease pathology can be established. The process may be both fast and highly selective, and allow for the process to be used at any point in the development of the organism. The novel chemical composition of these nucleic acid molecules may allowed for added stability and therefore increased efficacy.

Examples

The following are non-limiting examples demonstrating the utility of the nucleic acid molecules of the instant invention. Those in the art will recognize that certain experimental conditions such as temperatures, reaction times, media conditions, transfection reagents and RNA assays are not meant to be limiting and can be readily modified without significantly altering the protocols.

Example 1: Identification of Potential Nucleic Acid Molecule Binding Sites

The sequences of target RNAs were screened for accessible sites using a computer folding algorithm. Regions of the mRNA that did not form secondary folding structures were identified. For ribozyme sites, regions of mRNA that did not form secondary structure and contained potential hammerhead and/or haripin cleavage sites were identified.

Example 2: Selection of Ribozyme Cleavage Sites in Estrogen Receptor RNA

To test whether the sites predicted by the computer-based RNA folding algorithm corresponded to accessible sites in estrogen receptor. Ribozyme target sites were chosen by analyzing genomic sequences of Genbank Sequence HSERR1 (Green et al, 1986, Nature 320, 134-139) and prioritizing the sites on the basis of folding. Ribozymes were designed that could bind each target (see Figure 3) and were individually analyzed by computer folding (Christoffersen et al, 1994 J. Mol. Struc. Theochem, 311, 273; Jaeger et al, 1989, Proc. Natl. Acad. Sci. USA, 86, 7706) to assess whether the ribozyme sequences fold into the appropriate secondary structure. Those ribozymes with unfavorable intramolecular interactions between the binding arms and the catalytic core were eliminated from consideration. As noted below, varying binding arm lengths can be chosen to optimize activity. Generally, at least 5 bases on each arm are able to bind to, or otherwise interact with, the target RNA. Hammerhead (Seq. ID. Nos.1-1245) and hairpin ribozymes (2491-2603) are listed in tables IV and V respectively.

Example 3: Inhibition of c-raf RNA Targets using Nucleic Acid Molecules Prostate cancer cells (PC-3) were grown in a growth media consisting of Kaighn's

F-12K media, 10% FBS, 1% glutamine, 20 mM HEPES, and 1% pen strep to sub- confluent densities. A 4X concentration (10 μg/mL) of GSV (Glen Research) was prepared from a 2 mg/mL stock solution as well as a lOμM solution of antisense and its scrambled (mismatch) control. Complexes of antisense and GSV were formed in a 96 well plate by channel pipetting in antisense and GSV to form complex solutions which are twice the final concentrations. 50 μL of the complex solution and 50 μL of growth medium (without antibiotics) were added to PC-3 cells and incubated for 24 hours. The final concentrations of antisense used were 400, 200, and 100 nM, while the GSV concentration was held constant at 2.5 μg/mL. PC-3 cells were then harvested with 150 μL of RLT lysis buffer (Qiagen). RNA was purified using Qiagen' s instructions and RNA was quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. The c-raf RNA concentration was normalized to the c-raf RNA concentrations of the scrambled controls. The antisense sequence (Seq. I.D. No. 2717) and the data is shown in table III A and figure 5. The antisense molecules were capable of reducing c-raf RNA levels up to 80% compared to the mismatch control in PC-3 cells at several concentrations of antisense molecules.

Example 4: Ribozyme in vitro Cleavage Assay

Ribozymes and complementary substrates were synthesized as described above. These ribozymes can be tested for cleavage activity in vitro, for example using the following procedure. The ribozyme sequences are shown in figure 7.

Cleavage Reactions: Full-length or partially full-length, internally-labeled target RNA for ribozyme cleavage assay was prepared by in vitro transcription in the presence of [_a-32p] CTP, passed over a G 50 Sephadex column by spin chromatography and used as substrate RNA without further purification. Alternately, substrates may by 5'-32p-end labeled using T4 polynucleotide kinase enzyme. Assays were performed by pre-warming a 2X concentration of purified ribozyme in ribozyme cleavage buffer (50 mM Tris-HCl, pH 7.5 at 37°C, 10 mM MgCl₂) and the cleavage reaction was initiated by adding the 2X ribozyme mix to an equal volume of substrate RNA (maximum of 1-5 nM) that was also pre-warmed in cleavage buffer. The assays were carried out for 1 hour at 37 C using a final concentration of either 1 μM ribozyme, i.e., ribozyme excess. The reaction was quenched by the addition of an equal volume of 95% formamide, 20 mM EDTA, 0.05% bromophenol blue and 0.05% xylene cyanol after which the sample was heated to 95 C for 2 minutes, quick chilled and loaded onto a denaturing polyacrylamide gel. Substrate RNA and the specific RNA cleavage products generated by ribozyme cleavage were visualized on an autoradiograph of the gel. The percentage of cleavage was determined by Phosphor Imager® quantitation of bands representing the intact substrate and the cleavage products. The ribozymes were able to cleave between 1-80.8% of their complementary substrates after 2 hours (table VI).

Example 5: Inhibition of Cell Proliferation Using Estrogen Receptor Targeted Ribozyme MCF-7 cells were were grown in a T-75 flask to 80% confluency in growth media, which was prepared by mixing 500 mL Alpha-MEM, 10 mL 1M Hepes, 5mL sodium Pyruvate, 5 mL NEAA, 5 mL L-glutamine, 250 μL 2.0 mg/ml insulin, 500 μl Gentamycin, and 10% FBS following by sterile filtration. Ribozyme and cationic lipid was mixed as described in example 4 with final concentrations of 20, 40, and 80 nM ribozyme and 1 μg/mL GSV. The MCF-7 cells were treated with serum free alpha-MEM 24 hours prior to exposure to ribozyme/transfection reagent complexes. The complexes were added to the cells and allowed to continously transfect for 1,2 , 3, 4, and 5 days. At the end of each time point, the media was removed off the cells and proliferation was measured using a CyQuant kit (Molecular Probes). Fluorescence was measured at after 10 minutes of incubation at 485 nm (excitation) and 538 (emission). Inhibition of cellular proliferation by active ribozyme was compared to inactive scrambled ribozyme controls. The sequence for the active ribozyme is given as sequence ID. No. 2725 and the inactive scrambled control is given as Seq. ID. No. 2726. The chimeric enzymatic nucleic acid was able to inhibit MCF-7 cellular proliferation at all of the tested concentrations (figure 4).

Example 6: Inhibition of Estrogen Receptor RNA Targets using antisense nucleic acid molecules

A 5X concentrated solution of oligonucleotide ( lμM) and a 10X solution of GSV (25 μg/mL) (Glen Research) was made prior to complexing. The 5X oligonucleotide solution (8 μL), 10X GSV solution (40 μL), and Optimem media (32 μL) were mixed together and incubated at 37°C for 15 minutes. Media was aspirated off the cells followed by the addition of 80 μL of fresh growth media (Optimem media with 10% FBS, 1% non- essential amino acids, 1% sodium pyruvate, 20mM HEPES, 1 μg/mL insulin) and 20 μL of 5X complex solution. The complex was left on the cells for 20 hours and then harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. This cellular delivery assay was used for several RPI targets in varying cell lines and the data is shown in table IIIA. The levels of target RNA were either normalized to mismatch control RNA or to an internal housekeeping gene such as actin. Antisense nucleic acid molecules, which are given as Seq. ID. Nos. 2718-2723, were able to knock down estrogen receptor RNA by varying degrees. The levels of RNA inhibition ranged from 48-64% depending on the antisense sequence.

Example 7: Inhibition of Estrogen Receptor RNA using Ribozymes

Ribozymes and GSV transfection reagents were mixed together using a protocol similar to the one found in example 6. Target RNA was purified using a Qiagen kit. RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. The ribozyme specific to estrogen receptor is given as sequence ID. No. 2724 and was able to inhibit the gene by 50%.

Example 8: Inhibition of c-Raf mRNA and Cellular Proliferation Using Antisense Nucleic Acid Molecules

24 Hour RNA endpoint assay: The effect of targeting intron, exon, and intron-exon junction sites with antisense molecules was tested on c-raf RNA using in vitro cell culture assays. Seven chimeric antisense oligonucleotides with various chemical modifications were tested and the results were compared to an untreated control and an oligonucleotide modified at every nucleotide position with a phosphorothioate modification. Prostate cancer cells (PC-3) were grown in growth media consisting of Kaighn's F-12K media, 10% FBS, 1% glutamine, 20 mM HEPES, and 1% pen/strep in 96 well plates (15,000 cells per well). For the 24 hour delivery experiments, 2.5 mg/mL of GSV transfection reagent (Glen Research) was complexed to either 200 or 400 nM concentration of antisense molecules. The complex was left on the cells for 24 hours and the cells were then harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. C-raf RNA levels were normalized to actin controls and the data is shown in Figure 8. All compounds demonstrated an ability to inhibit c-raf message. Of the compounds tested, sequence I.D. 2732, 2736 and 2737 seemed particularly effective.

Sustained delivery RNA endpoint assay: Prostate cancer cells (PC-3) were grown in growth media consisting of Kaighn's F-12K media, 10% FBS, 1% glutamine, 20 mM HEPES, and 1% pen/strep in 96 well plates (15,000 cells per well). The cells were plated to 2500 cells per well in a 96 well plate and incubated at 37°C. Antisense nucleic acid molecules (Seq. I.D. Nos. 2738, 2737, 2744; Table IV) and GSV transfection reagent were complexed as in described under example 4 to a final concentration of antisense molecules of 100, 200 or 400 nM with 1.0 μg/mL of GSV transfection reagent. For seq. I.D. No. 2744, a mismatch control with similar base composition was also tested as a control. The complex was left on the cells and allowed to continuously transfect for 1, 3, or 5 days. At the end of each time period, the cells were harvested with 150 μL of RLT lysis buffer (Qiagen); and RNA levels quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. The inhibition of c-raf expression by molecules represented by Seq. I.D. Nos. 2738, 2737, and 2744 (table IV) are shown in Figures 9, 10, and 11 respectively. All three of these molecules demonstrated the ability to reduce c-raf RNA between 60-90% compared to the untreated control.

Proliferation Assay: Chimeric oligonucleotides and delivery reagents were mixed as described in example 6 where the final concentration of antisense oligonucleotide is 200 nM (Seq. I.D. No.2738 and 2741) and GSV is 1 μg/mL. A mismatch antisense control was also tested (Seq. I.D. No. 2739) in this experiment. The MCF-7 cells were treated with serum free alpha-MEM 24 hours prior to exposure to antisense/transfection reagent complexes. The complexes were added to the cells and allowed to continuously transfect for 1, 3, or 5 days. At the end of each time point, the media was removed off the cells and proliferation was measured using a CyQuant kit (Molecular Probes). Fluorescence was measured after 10 minutes of incubation at 485 nm (excitation) and 538 (emission). Inhibition of cellular proliferation by active oligonucleotide was compared to scrambled mismatch controls. The antisense molecules targeting c-raf mRNA were able to inhibit cellular proliferation by up to 55%.

Varying Chemical Modifications: Referring to Figure 13 and Table IV, alterations of the chemical composition of antisense molecules were made while keeping the oligonucleotide sequence constant. All of the sequences were the same except for the mismatch controls and Seq. I.D. Nos. 2738 and 2739 (table IV) which were two nucleotides shorter than the others. Antisense molecules and GSV transfection reagent were mixed using the protocol described under example 6. The complexes were added to the cells and allowed to continuously transfect for 24 hours. The cells were then harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. All c-raf levels were normalized using actin RNA as a control. Referring to Figure 13, antisense molecules which utilized phosphorothioate modifications, inverted abasic caps, 2'-O-methyl or 2'-O-methylthiomethyl modifications inhibit c-raf mRNA.

Dose dependent Inhibition: 0, 50, 100 150, and 200 nM of antisense molecules (seq. I.D. No. 2738 or 2737) were mixed with mismatch control antisense molecules to give a final antisense/mismatch antisense concentration of 200nM for each sample. The antisense nucleic acid and GSV were complexed as in example 6 with a final GSV transfection reagent concentration at 2.5 μg/mL. The complexes were added to the cells and allowed to continuously transfect for 24 hours. At the end of each time period, the cells were harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. All c-raf levels were normalized using actin RNA as a control. The results (Figure 14) show that c-raf is inhibited in a dose dependent manner and that the IC50 is approximately 35 nM for each of the antisense molecules.

Example 9: Ribonuclease Protection Assay of MCF-7 Cells treated with Antisense Nucleic Acid Molecules Targeting BCL-2

MCF-7 cells were plated in RPMI 1640 (10% FBS, 1% 1-glutamine, 20 mM HEPES) at 100,000 cells per well for 24 hours. On the following day, the cells were treated with 150 nM of antisense nucleic acid molecules (Seq. I.D. Nos. 2749-2753; Table VIII) complexed with 5.4 μM of LipofectAMINE (LFA) for 4 hours. The antisense/LFA complex was then aspirated off and fresh RPMI 1640 media was added to the cells. 24 hours later the cells were harvested using RLT lysis buffer (Qiagen). A ribonuclease protection assay (Ambion) was then performed using the manufacturers protocol to quantitate RNA levels and then harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. Bcl-2 RNA levels were normalized to GAPDH controls and is shown in Figure 15. The antisense oligonucleotides specifically inhibited Bcl-2 expression in MCF-7 cells.

Example 10: Inhibition of k-ras in DLD-1 Cells

96-well plates with DLD-1 cells at 10,000 cells per well were plated in complete RPMI 1640 media ((10% FBS, 1% 1-glutamine, 20 mM HEPES, 1% pen/strep). Antisense molecules (Seq. I.D. Nos. 2754-2757; Table VIII) were complexed with GSV transfection reagent (Glen Research) using the method described in example 6. The final concentrations delivered to the cells were 200 nM antisense oligonucleotide and 1.25 μg/mL of GSV. The complex was added to the cells for 26 hours and at the end of the time period, the cells were harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. All k-ras levels were normalized using actin RNA as a control. The data (Figure 16) demonstrates that the antisense molecules can inhibit approximately 50-90% k-ras expression compared to the untreated or mismatch controls.

Example 11 : Inhibition of Estrogen Receptor mRNA Using Antisense Molecules of varying Chemical Composition

Alteration of the chemical composition of antisense molecules were made while keeping the oligonucleotide sequence constant. All of the sequences (Table VII: Seq. I.D. Nos. 2758, 2760, 2762, 2764, 2766, 2768) were the same except for the mismatch controls (Table VII: Seq. I.D. Nos. 2759, 2761, 2763, 2765, 2767, 2769). Antisense molecules and GSV transfection reagent was mixed using the protocol described in example 6. The complexes were added to MCF-7 cells and allowed to continuously transfect for 24 hours. The cells were harvested with 150 μL of RLT lysis buffer (Qiagen). RNA levels were then quantified using Taqman reagents and the 7700 Prism (Perkin Elmer) using the manufacturer's protocol. All estrogen receptor mRNA levels were normalized using actin RNA as a control. The antisense molecules which included phosphorothioate modifications, inverted abasic caps, 2'-O-methyl or 2'-O-methylthiomethyl modifications appeared to decrease estrogen receptor RNA (Figure 17).

Example 12: Synthesis of 3'-deoxy-3'-thio Guanosine and it's 3'-Thiophosphoramidite

Referring to Figures 18, Applicant has developed an efficient method for the synthesis of 3'-deoxy-3'-thio guanosine (13) and its 3'-thiophosphoramidite 23 from guanosine. Reaction of suitably protected guanosine with a-acetoxyisobutyryl bromide (a-AIBBr) afforded stereoselectively 3'-deoxy-3'-bromo-2'-O-acetyl-b-D-xylofuranosyl derivative 3 which was converted into the 7:3 mixture of S-acyl ribofuranosyl derivatives 5 (or 6) and 3 ',4 '-unsaturated derivative 4. S-acylated derivatives 5 and 6 were then converted in three steps into 3'-deoxy-3'-S-pyridylsulfanyl-5^,-O-(4,4'- dimethoxytrityl)guanosine (11) which served as a common intermediate for the preparation of free nucleoside 13 and 3'-thiophosphoramidite 23. Oligonucleotides containing 3'-S-phosphorothiolate linkage have attracted increasing interest as probes for studying the interaction of nucleic acids and their processing enzymes. In particular these analogs have been used in revealing the involvement of metal ions in phosphoester transfer reactions catalyzed by RNA (Piccirilli et al, J. Am. Chem. Soc. 1996, 118, 10341) and ribonucleoprotein enzymes (Sontheimer et al, Nature 1997, 308, 801). The synthesis of 3'-S-phosphorothiolate linked deoxyribodinucleotides have been reported using solution chemistry and solid phase chemistry (Cosstick et al, Nucleic Acids. Res. 1990, 18, 829; Li et al, Tetrahedron 1992, 48, 2729; Li et al, J. Chem. Soc. Perkin Trans. 1 1994, 2123; Vyle et al, Biochemistry 1992, 31, 3012).

The synthesis of ribonucleotide 3'-S-phosporothiolate analogs has been limited to the preparation of UspU (Liu et al, Tetrahedron Lett. 1996, 37, 925) and IspU (Weinstein et al, J. Am. Chem. Soc. 1996, 118, 10341) dimers using solution chemistry. Recently, Sun et al. (RNA 1997, 3, 1352) described direct incorporation of 3'-S- phosphorothioamidites into RNA using standard phosphoramidite solid phase synthesis.

One general approach to the synthesis of 3'-thio ribonucleosides involves preparation of 3-thio ribose derivative, followed by the attachment of the desired nucleoside base (Ryan et al, J. Org. Chem. 1968, 33, 1783; Cao, et al, Bioorg. Med. Chem. Lett. 1994, 4, 807). While glycosylation reactions using pyrimidines proceed in high yields, purine bases generally give more complex mixtures because both N-7 and N- 9 of the purine base are reactive towards glycosylation. Sun et al, supra, reported the first synthesis of 3'-thio guanosine derivatives using the above described approach. Coupling of per-acylated 3'-thioribose with persilylated Λ^-acetylguanine proceeded in ca 40% yield and subsequent synthetic steps proceeded in a low overall yield. Synthesis of 3'-thio adenosine (Mengel, et al, Tetrahedron Lett. 1977,1177), 3'- thio uridine (Liu et al, 1996 supra) and 3'-thio inosine (Higson et al, Tetrahedron 1996, 52, 1027) all starting from preformed nucleosides are also reported.

Applicant describes a novel and improved process for the synthesis of 3'-deoxy-3'- thio guanosine (13) and its phosphoramidite 23 from guanosine as a starting material. It was recently reported (He et al, Tetrahedron Lett. 1995, 39, 6991) that the reaction of N²-(dimethylaminomethylene)-guanosine 1 with a-AIBBr (the Mattocks-Moffatt reagent; Russell et al, J. Am. Chem. Soc. 1973,95, 4025) proceeded stereoselectively yielding exclusively 3'-bromo-3'-deoxy-b-D-xylofuranosyl derivative. In general, reactions of base-unprotected purine nucleosides with this reagent result in the mixtures of trans bromo acetates of xylo- and arabino- configuration. Applicant used this reaction on the suitably 5'-protected N²-(dimethylaminomethylene)guanosine derivative 2 (Scheme 1; Figure 18). 5'- protection in 2 helps to reduce the complexity of reaction products by eliminating possible formation of the mixture of 5' -OH, 5'-(2,5,5-trimethyl-l,3-dioxolan-4-on-yl) and/or 5'-O-acylated derivatives in reaction with a-AIBBr. This way, identification of the reaction products becomes straightforward. Applicant has chosen the t-butyldiphenylsilyl (TBDPS) protection because of its relatively high stability towards acidic conditions required during the reaction with a-AIBBr in moist acetonitrile. This group is also expected to undergo selective cleavage in the presence of S-acyl groups. Reaction of 1 with TBDPS-C1 proceeded quantitatively to afford the 5'-O-silyl derivative 2 which reacted smoothly with a-AIBBr yielding the desired 3'-bromo-3'-deoxy-b-D-xylofuranosyl derivative 3 in a high yield. Reaction of 3 with potassium thioacetate or potassium thiobenzoate yielded the 3'-S-Ac or 3'-S-Bz derivatives 5 and 6, respectively, along with 3 ',4 '-unsaturated derivative 4. The latter is formed by competing elimination reaction. The ratio was 7:3 in favor of the substitution products 5 and 6 which could not be separated from the elimination product 4 at this stage. The mixture of 4 and 5 (or 4 and 6) was treated with tetrabutylammonium fluoride (TBAF) buffered with an excess of acetic acid; following chromatographic separation the desired 5' de-protected derivative 7 was obtained in a good yield. The unsaturated derivative 4 was unstable under the acidic reaction conditions and could not be isolated in a pure state by silica gel column chromatography. When triethylamine trihydrofluoride (TEA*3HF) reagent was used for deprotection, desilylation did not proceed to completion.

It is desirable to keep guanosine derivatives protected with lipophylic groups during synthetic transformations because of the solubility problems encountered with unprotected derivatives. For that reason 7 and 8 were re-protected in high yields with 4,4'-dimethoxytrityl (DMT) group to give the fully protected derivatives 9 and 10, respectively. DMT group provided a hydrophobic tag which simplified work-up and purification of subsequent synthetic intermediates. Next, 9 and 10 were converted into S- (pyridyl-2-disulfanyl) derivative 11 using aqueous methylamine followed by the disulfide exchange reaction with 2,2'-dipyridyl disulfide. It is reported that the removal of 2'-O- acyl protection in ribofuranosyl derivatives similar to 9 and 10 proceeds with difficulty. Applicant found that 40% aqueous methylamine easily removed all acyl protecting groups from 9 and 10 and was the base of choice because, contrary to aqueous ammonia, it completely solubilised the fully protected substrates. In situ protection of SH as S-pyridyl- 2-disulfanyl derivative was achieved using 2,2'-dipyridyl disulfide in DMF to afford 11 in 85% yield for these two steps. In order to synthesize the free nucleoside, 13, 11 was treated with dithiothreitol

(DTT) in chloroform. When triethylamine was added to the reaction mixture the reaction was faster than in it's absence but at the same time 12 was converted into its S-TEA salt. Final deprotection of the DMT group of 12 was achieved with IN HC1 in methanol in the presence of DTT which quenched the released DMT-cation. In the absence of DTT, quantitative S-alkylation took place. Applicant is the first to report on the synthesis of the guanosine 3'-thio analog 13. When unbuffered TBAF in THF was used to desilylate the mixture of 4 and 5, S-Ac protecting group was also removed leading to formation of the disulfide 14 (Scheme 2; Figure 19). Under these conditions the 3 ',4 '-unsaturated derivative 15 remained intact and was separated from 14 by silica gel column chromatography. Products were invariably contaminated with TBAF. Attempted rechromatography of 15 led to its decomposition, though. Disulfide 14 was 5'-DMT protected to afford 16.

The selective removal of the 3'-acetyl group of 16 (Scheme 2; Figure 19), followed by the introduction of 2'-O-t-butyldimethylsilyl (TBDMS) protection, then reduction of 3 '-disulfide and 3'-phosphitylation would be the shortest way to prepare the desired 3'-thiophosphoramidite building block. Reactions of 16 with mild deacylating agents like basic ion exchangers in OH- or CN^_ form selectively removed 2'-O-acetyl protection, but at the same time nucleoside was strongly absorbed on the resin, resulting in low recoveries. Applicant used basic treatment followed by S-protection with S-pyridyl group, as used for the preparation of the S-pyridyl-2-disulfanyl derivative 11 from S- acylated 9 and 10. In this manner 11 was obtained from the disulfide 16 in 67% yield.

The phosphoramidite synthesis is shown in Scheme 3 (Figure 20). Reaction of 11 with N,N-dimethylformamide dimethyl acetal yielded the desired N-protected derivative 18 in 23% yield. Unfortunately, this reagent also effected the cleavage of the S-pyridyl protection leading to formation of disulfide 17 in 33% yield. 18 was smoothly 2' protected with TBDMS group using t-butyldimethylsilyl trifluoromethanesulfonate (TBDMS-Tf). Alternatively, 11 was silylated with TBDMS-C1 to afford 20 and then N- protected using isobutyric anhydride (t-Bu₂O) in the presence of 4-dimethylaminopyridine (DMAP) yielding the fully protected 21. In the absence of DMAP only starting material was recovered. On the other hand, reaction of 20 with isobutyryl chloride led to N-bis- acylation. Reduction of 21 with DTT afforded 3'-SH derivative 22, which appeared as a mixture of two rotamers in ^]H ΝMR. Resonances of the major rotamer were in accordance with the ones reported by Sun et al. Phosphitylation of 22 under standard conditions afforded 3'-thiophosphoramidite 23. Applicant has described an efficient synthesis of 3'-deoxy-3'-thio guanosine. Keeping all synthetic intermediates protected with lipophylic groups enabled their chromatographic purification and, consequently, a good recovery of the products.

Experimental Section

General. All reactions were carried out under a positive pressure of argon in anhydrous solvents. Commercially available reagents and anhydrous solvents were used without further purification. ^!H (400.075 MHz) and ³¹P (161.947 MHz) ΝMR spectra were recorded in CDCI3, unless stated otherwise, and chemical shifts in ppm refer to TMS and H3PO4, respectively. Analytical thin-layer chromatography (TLC) was performed with Merck Art.5554 Kieselgel 60 F254 plates and flash column chromatography using Merck 0.040-0.063 mm silica gel 60. Mass spectra were obtained by fast atom bombardment method.

5'-0-^-ButyldiphenyIsiIyl-N²-(dimethylaminomethylene)guanosine (2). To a stirred solution of N²-(dimethylaminomethylene)guanosine (1) (5.5 g, 16.3 mmol) in pyridine (100 mL) t-butyldiphenylsilyl chloride (6.2 ml, 23.8 mmol) was added under argon. The reaction mixture was stirred at rt for 16 h, then quenched with methanol ( 20 ml) and evaporated to a syrup in vacuo. The residue was crystallized from ethanol-ether ( 9 g, 96%), mp, "H ΝMR (DMSO-d₆ + D₂O) d 8.46 (s, IH, CH=Ν), 7.89 (s, IH, H-8), 7.58-7.31 (m, 10H, Ph), 5.81 (d, Jι>_;2>=4.8, IH, H-1'), 4.46 (app t, J_2',r=4.8, IH, H-2'), 4.23 (app t, J₃>₎₂'⁼⁵ IH, H-3'), 3.97 (m, IH, H-4'), 3.84 (dd, J₅>₎₄>=2.8, J₅>_j5»=12.0, IH, H-5'), 3.74 (dd, J₅»₎₄>=4.4, J₅» ₅-=12.0, IH, H-5"), 3.05 (s, 3H, Me), 2.97 (s, 3H, Me), 0.94 (s, 9H, t-Bu), HRMS (FAB⁺) calcd for C₂₉H₃₆N₆O₅Si (MH⁺): calc 577.2595, found 577.26095. l-(2-0-Acetyl-5-0-ι'-Butyldiphenylsilyl-3-deoxy-3-bromo-b-D-xylofuranosyI)- N²-(dimethylaminomethylene)guanosine (3). To a cooled (0 °C) solution of 2 (5.8 g, 10 mmol) and water (0.12 ml) in acetonitrile (130 ml) a-acetoxyisobutyryl bromide (5.56 ml, 38 mmol) was added and the mixture was stirred at rt for 3 h. The solution was poured into saturated aq. NaHCO₃ (100 mL) and extracted with CH₂C1₂ (3 x 200 mL). The combined organic layers were dried (Na SO₄) and concentrated to give chromatographically pure white foam (6 g, 87%), 'H NMR d 8.97 (br s, IH, NH), 8.62 (s, IH, CH=N), 7.82 (s, IH, H-8), 7.73-7.31 (m, 10H, Ph), 6.09 (s, IH, H-2'), 5.92 (d, Jι>_)2'=1.6, IH, H-1'), 4.42 (m, IH, H-4'), 4.36 (m, IH, H-3'), 4.06 (dd, J₅>_j4'=5.6, J₅>_;5»=10.4, IH, H-5'), 3.97 (dd, J₅»_)4'=6.4, J₅»_;5<=10.4, IH, H-5"), 3.17 (s, 3H, N-Me), 3.07 (s, 3H, N-Me), 2.19 (s, 3H, O-Ac), 1.07 (s, 9H, t-Bu), HRMS (FAB+) calcd for C₃₁H₃₇BrΝ₆Ο₅Si (MH⁺): calc 681.1856, found 681.1850. l-(2-0-Acetyl-5-0-^*-butyldiphenylsilyl-3-deoxy- b -O-glycero-pent-3- enofuranosyl-N²-(dimethylaminomethylene)guanosine (4) and 2'-0-ace yl-5'-(?-/- butyldiphenyl-silyI-3'-deoxy-3'-S-thioacetyl--V²(dimethylaminomethylene)- guanosine (5). 3 (5.4 g, 7.9 mmol) was dissolved in dry DMF (50 ml) and potassium thioacetate (2.7 g, 23.6 mmol) was added to the solution. The reaction mixture was stirred at 60 °C for 16 h and then evaporated to a syrup under reduced pressure. The residue was partitioned between aq. NaHCO₃-brine 1 :1 solution and dichloromethane, the organic layer was dried (Na₂SO₄), evaporated to dryness and chromatographed on the column of silicagel using 2- 10% gradient of methanol in dichloromethane 4 and 5 co-eluted yielding, after evaporation, a yellowish foam (4.8 g). ¹H NMR indicated a 3:7 ratio of 4 to 5.

When potassium thiobenzoate was used instead of potassium thioacetate an inseparable mixture of 4 and 2'-0-acetyl-5'-0-ι'-butyldiphenylsilyl-3'-deoxy-3'-S- thiobenzoyl-N²(dimethylaminomethy!ene)guanosine (6) was obtained in a similar yield and ratio to the unsaturated derivative 4 as above.

2'-0-Acetyl-3'-deoxy-3'-S-thioacetyl--V²(dimethylaminomethylene) guanosine (7). The above mixture of 4 an 5 (0.9 g) was dissolved in THF (15 ml) and acetic acid (0.37 ml, 6.5 mmol) was added followed by TBAF^»3H₂O (0.82 g, 2.6 mmol). The reaction mixture was stirred at rt for 5 h, then diluted with dichloromethane, washed with water and 10% aq. NaHCO₃- Aqueous layers were back- washed with dichloromethane, organic layers were combined, dried (Na₂SO₄) and evaporated to dryness. Silica gel column chromatography using 2-10% gradient of methanol in dichloromethane afforded 7 as a yellowish foam (300 mg, ca 74%), Η NMR d 8.87 (br s, IH, NH), 8.78 (s, IH, CH=N), 7.73 (s, IH, H-8), 5.80 (d, J_r,_2'=2.0, IH, H-1'), 5.76 (dd, J_2'.ι»=2.0, J_2',_3'=6.4, IH, H-2'), 4.94 (dd, J₃._>2.=6.4, J₃>₄>=9.6, IH, H-3'), 4.22 (d, J₄>_;3>=9.6, IH, H-4'), 4.04 (br s, IH, 5'-OH), 3.99 (d, J₅> ₅»=12.0, IH, H-5'), 3.71 (d, J₅» ₅=12.0, IH, H-5"), 3.19 (s, 3H, N-Me), 3.04 (s, 3H, N-Me), 2.34 (s, 3H, S-Ac), 2.13 (s, 3H, O-Ac), HRMS (FAB⁺) calcd for C,₇H₂₂Ν₆Ο₆S (MH⁺): 439.1355, found 439.1405. 2'-0-Acetyl-3'-deoxy-3'-5'-thiobenzoyl-iV (dimethylaminomethylene) guanosine (8). Using the same procedure as above, 8 was synthesized from the mixture of 4 and 6 in ca 70% yield, Η NMR d 8.90 (br s, IH, NH), 8.57 (brs, IH, NH), 7.69 (s, IH, H-8), 5.88 (m, 2H, H-l',H-2'), 5.30 (m, IH, H-3'), 4.34 (d, J_4'j3'=9.2, IH, H-4'), 4.04 (d, J₅>_<5'.=12.8, IH, H5'), 3.80 (dd, J₅^_OH=9.6, J₅<>_<5 ^«=12.8, IH, H-5"), 3.69 (br s, IH, 5'- OH), 3.25 (s, 3H, N-Me), 3.10 (s, 3H, N-Me), 2.16 (s, 3H, O-Ac), HRMS (FAB⁺) calcd for C₁₇H₂₂Ν₆Ο₆S (MH⁺): 501.1556, found 501.1561.

2' -O- Acetyl^-deoxy^-S-thioacetyl-S'-O^, 4 '-dimethoxytrityl)- N²(dimethyIamino-methylene)guanosine (9). 7 (720 mg, 1.64 mmol) was dissolved in dry pyridine (15 ml) and DMT-C1 (1.1 g, 3.3 mmol) was added. The reaction mixture was stirred at rt for 4 h, qenched with methanol and evaporated to a syrup which was partitioned between 5% aq. NaHCO^ and CH₂C1 . Organic layer was washed with brine, dried (Na₂SO₄) and evaporated to dryness in vacuo. The residue was purified by silica gel column chromatography using 1-5% gradient of methanol in dichloromethane to yield the product as a colorless foam (0.85 g, 70%), 'H NMR d 8.69 (s, IH, CH=N), 8.58 (br s, IH, NH), 7.69 (s, IH, H-8), 7.38-6.74 (m, 13H, H-8, aromatic), 6.06 (dd, J₂.₎₃>=6.4, J₂',i'=1.2, IH, H-2'), 5.82 (d, Jr,_2'=l-2, IH, H-1'), 4.73 (dd, J₃. ₄.=10.6, J_3'.₂-6.4, IH, H-3'), 4.21 (dq, J₄. ₃.=10.6, J =3.0, J₄._,5-=4.4, IH, H-4'), 3.78 (s, 6H, 2xOMe 3.36 (m, 2H, H-5', H- 5"), 3.07 (s, 3H, N-Me), 3.05 (s, 3H, N-Me), 2.26 (s, 3H, S-Ac), 2.15 (s, 3H, O-Ac), HRMS (FAB⁺) calcd for C₃₈H₄₀Ν₆O₈S (MH⁺): 741.2707, found 741.2692. 2'-0-Acetyl-3'-deoxy-3'-S-thiobenzoyl-5'-0-(4,4'-dimethoxytrityl)- 7V (dimethyl-aminomethylene)guanosine (10). Using similar procedure as described above, 8 was converted into 10 in 69% yield, Η NMR d 8.80 (s, IH, CH=N), 8.65 (br s, IH, NH), 7.70 (s, IH, H-8), 7.88-6.66 (m, 19H, aromatic), 6.17 (d, J₂-_;3>=5.8, IH, H-2'), 5.86 (d, Jr,2'=l-2, IH, H-1'), 5.08 (dd, J₃._,4>=10.4, J₃._,2-=5.8, IH, H-3'), 4.31 (m, IH, H- 4'), 3.67 (s, 6H, 2xOMe_}, 3.45 (m, 2H, H-5', H-5"), 3.06 (s, 6H, 2XN-Me) 2.15 (s, 3H, O- Ac), HRMS (FAB⁺) calcd for C₄₃H₄₂Ν₆O₈S (MH⁺): 803.2863, found 803.2855.

3'-Deoxy-3'-S-pyridyIsulfanyl-5'-0-(4,4'-dimethoxytrityl)-guanosine (11). A. 9 (530 mg, 0.38 mmol) was dissolved in 40% aqueous methylamine (50 ml) and the mixture is kept at rt for 16 h. The solvent is removed in vacuo and the residual syrup dissolved in argon purged DMF (30 ml) containing 2,2'-dipyridyl disulfide (340 mg, 1.54 mmol). The reaction mixture is heated at 60 °C for 10 h and then evaporated to a syrup in vacuo. Column chromatography on silica gel using 1-12% gradient of methanol in dichloromethane afforded 11 as a colorless solid (460 mg, 85%), Η NMR d 10.64 (br s, IH, NH), 8.39 (m, IH, Pyr), 7.83 (s, IH, H-8), 7.73-6.72 (m, 16H, aromatic), 6.50 (d, ^TOH_,2'=4-80, IH, OH-2'), 6.45 (br s, 2H, NH₂), 5.81 (d, J_r,_2'=2.4, IH, H-1'), 4.83 (m, IH, H-2'), 4.34 (m, IH, H-4'), 4.09 (dd, J₃.₂.=6.00, J_3'.4'=7.8, IH, H-3*), 3.70 (s, 6H, 2XOMe), 3.11 (dd, J₅. ₅-=11.2_ J₅-.._4'=4.8, IH, H-5"), HRMS (FAB⁺) calcd for C_3όH₃₄N₆O₆S₂ (MH⁺): 711.2060, found 711.2076.

B. Using the same procedure as above, but starting from S-benzoyl derivative 10, 11 was prepared in 80% yield. C. Starting from 16 (830 mg, 1.12 mmol) and using the above conditions

11 (570 mg, 67%) was obtained .

3'-Deoxy-3'-thio-5'-0-(4,4'-dimethoxytrityl)-guanosine (12). To the solution of 11 (240 mg, 0.34 mmol) in chloroform (14 ml) dithiothreitol (DTT) (125 mg, 0.81 mmol) was added and the reaction mixture was stirred at rt for 3 h. It was then evaporated to a syrup in vacuo, and the product was precipitated by addition of peroxide-free ether, precipitate was filtered off, washed with ether and dried (230 mg of the crude material), "H NMR (DMSO-d₆) d 10.63 (br s, IH, NH), 7.86 (s, IH, H-8), 7.32-6.80 (m, 13H, aromatic), 6.49 (br s, 2H, NH₂), 5.81 (s, IH, H-1'), 4.43 (d, J_2'._3'=4.8, IH, H-2'), 3.93 (m, IH, H-4'), 3.79 (dd, J₃.₂.=4.8, J₃..₄.=9.6, IH, H-3*), 3.71 (s, 6H, 2XOMe), 3.16 (dd, J₅ - ₅ ^,=10.4, J₅- ₄-=4.8, IH, H-5"). 3'-Deoxy-3'-thio-guanosine (13). The mixture of the crude 12 (230 mg, 0.33 mmol) and DTT (150 mg) was dissolved in 1 N methanolic HC1 (12 ml) and the reaction mixture was kept at rt for 3 h. It was then concentrated in vacuo and the residue coevaporated with toluene two times. Addition of ethyl acetate afforded precipitate which was filtered off, washed well with ethyl acetate and dried to afford 13 (90 mg, 79%). The product was reprecipitated from water, ^!H NMR (CD₃OD) d 8.10 (s, IH, H-8), 5.91 (s, IH, H-1'), 4.37 (d, _J2>_.3-=5.2, IH, H-2'), 3.97 (m, 2H, H-4', H-5'), 3.82 (dd, J₅ • =13.0, J₅»_,4-=3.4, IH, H-5"), 3.64 (dd, J₃-_.2-=5.2, J_{3 4} =9.6, IH, H-3'), HRMS (FAB⁺) calcd for C₁₀H₁₃N₅O₄S (MH⁺): 300.0767, found 300.0767. Bis (2-0-ace yl-iV²-(dimethylaminomethylene)guanosin-3-yl)disulfide (14 ) and l-(2-0-acetyl-3-deoxy- b -D- /vcero-pent-3-enofuranosyI)- V²-(dimethyI- aminomethylene) guanosine (15 ). The mixture of 4 and 5 (4.8 g) was dissolved in THF (100 mL) and 1M TBAF in THF (10 mL) was added. The reaction mixture was stirred for 3 h at rt and then evaporated to a syrup in vacuo. Silica gel column chromatography using 2-10% gradient of methanol in dichloromethane yielded the faster eluting 15 (1 g, 35% for two steps from 3, colorless foam), 'H NMR d 8.96 (br s, IH, NH), 8.57 (s, IH, CH=N), 7.65 (s, IH, H-8), 6.41 (s, IH, H-2'), 6.04 (s, IH, H-1'), 5.42 (m, IH, H-3'), 4.32 (m, 2H, H-5',H-5"), 3.19 (s, 3H, N-Me), 3.06 (s, 3H, N-Me), 2.11 (s, 3H, Ac). The slower eluting 14 was obtained as a yellowish solid (0.9 g, 29% for two steps), Η ΝMR (DMSO-d₆) d 11.34 (br s, IH, ΝH), 8.53 (s, IH, CH=Ν), 8.00 (s, IH, H-8), 5.97 (d, Jι>_>2'=2.4, IH, H-1'), 5.89 (dd, J_2',r=2.4, J_2',₃'=6.0, IH, H-2'), 5.23 (t, J_OH)5>=5.6, IH, 5'-OH), 4.11 (m, IH, H- 4'), 4.02 (dd, J_3',2'=6.0, J₃>₄>=8.4, IH, H-3'), 3.78 (dm, J₅>₎₅»=12.0, IH, H-5'), 3.60 (dm, J₅»^=12.0, IH, H-5"), 3.10 (s, 3H, N-Me), 3.00 (s, 3H, N-Me), 2.06 (s, 3H, O-Ac), HRMS (FAB⁺) calcd for C₃oH3₈Ν₁₂Ο₁₀S₂ (MH⁺): 791.2354, found 791.2355. Bis (2-0-acetyl-5-0-(4,4'dimethoxytrityl)-iV²-(dimethylaminomethylene) gua- nosin-3-yl) disulfide (16). To the solution of 14 (400 mg, 0.5 mmol) in dry pyridine (10 ml) DMT-C1 (508 mg, 1.5 mmol) was added and the mixture was stirred 4 h at rt. Methanol (10 ml) was added and the solution evaporated to dryness. The residue is partitioned between saturated NaHCO₃ and dichloromethane, organic layer washed with brine, dried (Na₂SO₄) and evaporated to a syrup. Silica gel column chromatography using 2-10% gradient of methanol in dichloromethane yielded product as a yellowish foam (620 mg, 71% yield), Η NMR d 8.72 (br s, IH, NH), 8.01 (s, IH, CH=N), 7.48-7.21 (m, 14H, H-8, aromatic), 6.25 (d, J_2',_3'=4.8, IH, H-2'), 5.78 (s, IH, H-1'), 4.00 (m, 2H, H-3', H-4'), 3.78 (s, 6H, 2xOMe_}, 3.50 (br s, 2H, H-5',H-5"), 3.14 (s, 3H, N-Me), 3.13 (s, 3H, N-Me), 1.82 (s, 3H, O-Ac), HRMS (FAB⁺) calcd for C72H74Ν12Ο14S2 (MH+): 1395.4967, found 1395.4943. Bis (5-0-(4,4'dimethoxytrityl)-N²-(dimethylaminomethyIene) guanosin-3-yl)- disulfide (17). A. 16 (60 mg, 0.04 mmol) is dissolved in dry methanol and ion exchange resin AG 1X8 (OH-) (1 g) is added. The mixture was stirred at 55 °C for 16 h, the resin was filtered off and washed well with hot methanol. The filtrate was evaporated to dryness in vacuo yielding pure 17 as a colorless solid (16 mg, 28%), 'H NMR (DMSO-d₆) d 11.34 (br s, IH, NH), 8.48 (s, IH, CH=N), 7.92 (s, IH, H-8), 7.31-6.73 (m, 13H, aromatic), 6.27 (d, J_O =5.2, IH, 2'-OH), 5.88 (d, J_{r 2}-=1.2, IH, H-1'), 4.60 (m,lH, H- 2*), 4.16 (m, IH, H-4'), 4.08 (m, IH, H-3'), 3.65 (s, 6H, 2XOMe), 3.65 (m, 2H, H-5', H- 5"), 3.02 (s, 3H, N-Me), 2.97 (s, 3H, N-Me), HRMS (FAB⁺) calcd for C₆₈H₇₀Ν₁₂O₁₂S₂ (MH⁺): 1311.4756, found 1311.4746.

B. Using Amberlyst A-26 (CN") under the the above reaction conditions, 17 was obtained from 16 in 21% yield.

3'-Deoxy-3'-S-pyridylsulfanyl-5'-0-(4,4'-dimethoxytrityl)-N²-(dimethylamino- methyIene)guanosine (18) and 17. To the solution of 11 (400 mg, 0.56 mmol) in dry pyridine (5 ml), NN-dimethylformamide dimethyl acetal (1.2 ml, 9 mmol) was added and the reaction mixture was stirred at rt for 16 h. Solvents were removed in vacuo and the residue chromatographed on the column of silica gel using 1-50% gradient of methanol in dichloromethane. Fractions containing the faster running material were combined and concentrated in vacuo to give 18 (110 mg, 23%), ^!H ΝMR d 8.73 (br s, IH, ΝH), 8.53 (s, IH, CH=Ν), 8.49 (m, IH, pyridine), 7.71 (s, IH, H-8), 7.62 (m, IH, pyridine), 7.44-6.79 (m, 15H, aromatic), 6.09 (s, IH, H-1'), 4.55 (d, J₂..₃.=4.8, IH, H-2'), 4.23 (dq, J_4',3-=10.5, J₄. ₅.=2.8, J₄- ₅..=3.4, IH, H-4'), 4.14 (dd, J₃.₂.=4.8, J₃. ₄-=10.5, IH, H-3'), 3.78 (s, 6H, 2XOMe), 3.57 (dd, J₅.₅-=10.6. J_5',4.=2.8. IH, H-5*), 3.41 (dd, J_{v 5}„=10.6, J₅-._4'=3.4, IH, H-5"), 3.08 (s, 3H, N-CH₃), 3.05 (s, 3H, N-CH₃). Fractions containing the slower running compound were collected and evaporated to dryness in vacuo to give 17 as a colorless foam (120 mg, 33%), ^H ΝMR identical to that of 17 obtained obtained using the above procedures.

2'-0-/-ButyldimethylsilyI-3'-deoxy-3'-S-pyridylsulfanyl-5'-0-(4,4'- dimethoxytrity —Λ^^dimethylamino-methylene) guanosine (19). 18 (110 mg, 0.14 mmol) was dissolved in dry pyridine (1 ml) and TBDMS-Tf (0.103 ml, 0.45 mmol) was added to the solution. The reaction mixture was stirred at rt for 5 h, then qunched with methanol and evaporated to a syrup in vacuo. The residue was dissoved in dichloromethane, washed with 5% aqueous ΝaHCO₃, then brine and the organic layer was dried (Na₂SO₄) and concentrated to the syrup. Column chromatography on silica gel using 1-10% gradient of methanol in ethyl acetate afforded 19 as a colorless solid (90 mg, 71%), 'H NMR d 8.69 (br s, IH, NH), 8.50 (s, IH, CH=N), 8.37 (m, IH, pyridine), 7.81 (s, IH, H-8), 7.50-6.74 (m, 16H, aromatic), 5.98 (d, J _,2-=2.4, IH, H-1'), 4.75 (dd, J₂. ₃.=5.0, J_2U<=2.4, IH, H-2'), 4.50 (m,lH, H-4'), 3.99 (dd, J₃.₂.=5.0, J_3'.4'=8.4, IH, H-3'), 3.76 (s, 6H, 2XOCH₃), 3.62 (dd, J_5I;5»=10.9. J₅._.4.=2.2. IH, H-5'), 3.38 (dd, J₅._j5»=10.9, J₅.._j4^4.4, IH, H-5"), 3.06 (s, 3H, NCH₃), 3.04 (s, 3H, NCH₃), 0.93 (s, 9H, t-Bu), 0.17 (s, 3H, Me), 0.10 (s, 3H, Me), HRMS (FAB⁺) calcd for C₄₅H₅₃Ν₇O₆S₂Si (MH⁺) 880.3346, found 880.3357.

2^,-0- -BuryldimethylsiIyI-3'-deoxy-3'-S-pyridylsuIfanyI-5^,-0-(4,4'- dimethoxytrityl) guanosine (20). 3'-Deoxy-3'-S-pyridylsulfanyl-5'-O-(4,4'- dimethoxytrityl)guanosine 11 (410 mg, 0.58 mmol) was dissolved in dry pyridine (36 ml) and imidazole (2.36 g, 35 mmol) and TBDMS-Cl (4.29 g, 28 mmol) were added. The reaction was stirred at rt 16 h, then evaporated to a syrup in vacuo. The residue was partitioned between dichloromethane and saturated aq. NaHCO₃, organic layer washed with water, dried (Na SO₄) and concentrated to a syrup. Column cgromatography on silica gel using 1-10% gradient of methanol in dichloromethane afforded the product as a white foam (430 mg, 85%), Η NMR (DMSO-d₆) d 11.99 (br s, IH, NH), 8.39 (m, IH, Pyr), 7.84 (s, IH, H-8), 7.71 (m, IH, Pyr), 7.62-6.72 (m, 15H, aromatic) 6.41 (br s, 2H, NH₂), 5.80 (d, J_r,_2'=4-4, IH, H-1'), 5.04 (app t, Jr ₃-=4.4, IH, H-2'), 4.39 (m, IH, H-4'), 4.01 (app t, J₃._,4'=6.4, IH, H-3'), 3.69 (s, 6H, 2XOMe), 3.13 (dd, J_{5 5}>=11.0, J₅-_>4-=4.6, IH, H-5"), 0.82 (s, 9H, t-Bu), 0.08 (s, 3H, Me), 0.06 (s, 3H, Me), HRMS (FAB⁺) calcd for C₄₂H₄₈N₆O₆S₂Si (MH⁺) 825.2924, found 825.2977.

2'-0^-Butyldimethylsilyl-3'-deoxy-3'-S-pyridyIsuIfanyl-5^,-0-(4,4'- dimethoxytritylJ-Λ^-isobutyrylguanosine (21). To the solution of 20 (310 mg, 0.38 mmol) in dry pyridine (5 ml) isobutyric anhydride (0.19 ml, 1.14 mmol) and DMAP (46 mg, 0.38 mm) were added and the mixture was stirred at rt 16 h. It was then stirred at 50 °C for 5 h, quenched with methanol (2 ml) and evaporated to a syrup in vacuo. The residue was partitioned between dichloromethane and 5% aqueous NaHCO₃, the organic layer was washed with brine, dried (Na₂SO₄) and evaporated to a syrup. Column chromatography on silica gel using 1-5% gradient of methanol in CH₂C1₂ afforded product as a colorless foam (320 mg, 95%), Η NMR d 11.94 (br s, IH, NH), 8.36 (m, IH, Pyr), 7.85 (m, IH, Pyr), 7.80 (s, IH, H-8), 7.58-6.71 (m, 16H, NH, aromatic), 5.83 (d, J_r.₂>=5.2, IH, H-1'), 5.22 (app t, J_r r=5.2, IH, H-2'), 4.50 (m, IH, H-4'), 4.27 (app t, J_{3 r}=6.4, IH, H-3'), 3.76 (s, 3H, OMe), 3.75 (s, 3H, OMe), 3.56 (dd, J₅>_ι5«=11.0, J_{r 4}-1.8, IH, H5'), 2.98 (dd, J_{5 5} =11.0, J_{5 r}=3.0, IH, H-5"), 1.69 (m, IH, CHMe₂), 0.94 (d, J=7.2, 3Η, CH₃), 0.76 (d, J=7.2, 3H, CH₃), 0.88 (s, 9H, t-Bu), 0.11 (s, 3H, Me), 0.06 (s, 3H, Me), HRMS (FAB⁺) calcd for C₄₆H₅₄N₆O₇S₂Si (MH⁺) 895.3343, found 895.3380. 2^,-0-/-Buryldimethylsilyl-3'-deoxy-3'-thio-5^,-0-(4,4^,-dimethoxytrityl)-N²- isobutyrylguanosine (22). To the solution of 21 (340 mg, 0.38 mmol) in chloroform (20 ml) TEA (0.4 ml) and dithiotreitol DTT (140 mg, 0.91 mmol) were added and the reaction mixture was stirred for 1 h at rt. The reaction miture was washed with saturated aqueous NaHCO₃, water, dried (Na₂SO₄) and concentrated to a syrup. Silica gel column chromatography using 0.5-2% gradient of methanol in CH C1₂ afforded 22 (270 mg, 90%), Η NMR for the major rotamer: d 11.92 (br s, IH, NH), 7.93 (s, IH, H-8), 7.63-6.80 (m, 16H, NH, aromatic), 5.83 (d, J_{V 2} =2.8, IH, H-1'), 4.74 (dd, Jr _r=2.8, J₂-._3'=5.4, IH, H-2'), 4.13 (dd, J₄-_,3<=7.6, J₄-_,5 =1.2, IH, H-4'), 3.78 (s, 3H, OMe), 3.73 (s, 3H, OMe), 3.63 (dd, J₅^=11.0, J_5',4'=1.2, IH, H5'), 3.27 (dd, J₅^=11.0, J₅<-_>4'=3.0, IH, H-5"), 1.63 (d, J_{SH 3} =8.4, IH, SH), 2.08 (m, IH, CHMe₂), 1.09 (d, J=6.8, 3Η, CH₃), 0.98 (d, J=6.8, 3H, CH₃), 0.91 (s, 9H, t-Bu), 0.14 (s, 3H, Me), 0.08 (s, 3H, Me), HRMS (FAB⁺) calcd for C₄₁H₅ ,N₅O₇SSi (MH⁺) 786.3357, found 786.3354.

2'-0- -ButyldimethylsilyI-3'-deoxy-3'-thio-5'-0-(4,4'-dimethoxytrityl)-7V²- isobutyrylguanosine 3'-S-(2-cyanoethyl N,N-diisopropylphoramidite (23). Phosphitylation of 22 as described by Sun et al. afforded product which was purified by flash chromatography using 0.5% ethanol in CH₂C1₂ containing 1% TEA. Final product was obtained as a white powder by precipitation from toluene-pentane at 0 °C (76% yield), 31p NMR d 163.5 (s), 159.6 (s), HRMS (FAB⁺) calcd for C₅₀H₆₈N₇O₈PSSi (MH⁺) 986.4435, found 986.4406.

Example 13: Synthesis of 5'- thiophosphate nucleoside phosphoramidite and preparation of solid support

Referring to Figure 21, Applicant shows a scheme for synthesis of 5'-deoxy-5'- thionucleoside phosphoramidites and succinates. For example Lehmann et al, (NAR 1989, 17, 2379; incorporated by reference herein) describes the preparation of the more base-stable sarcosyl modified solid support.

Matulic-Adamic. et al in Nucleosides & Nucleosides 1997, 16, 1933, describes the incorporation of 5'-thio modification into oligonucleotides. Applicant additionally describes the a method where, the cleavage of the 5'-protecting group on the solid support in order to elongate the chain is accomplished by using, instead of AgNO3 in CH3CN, 0.1M l,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in CH3CN or 20% piperidine in CH3CN.

Note that 5'S-DMT protection is cleaved with iodine (Henningfeld et al. JACS 1996, 118, 11701) thus complicating the oligo synthesis, while S-Fm is reported to be resistant to 0.1 M iodine in DMF. Oligonucleotides were synthesized with 5'-thiophosphate linkage and tested in vitro in a standard RNase H cleavage assay described in McSwiggen, US Patent No. 5,525,468; incorporated by reference herein.

Example 14: Synthesis of 5'-O-dimethoxytrityl-3'-deoxy-3'-thio-3'-S-r2-Cvanoethyl-N.N- Diisopropylphosphoramidite-2'-O-methyl uridine (6) (Figure 22)

5 '-O-tert-butyldiphenylsilyl-2 '-O-methyl uridine (1): To a solution of 2'-O- methyl uridine stirring at 0 C under positive pressure argon in anhydrous pyridine was added tert-butyldiphenylsilyl chloride (1.2 eq.) The reaction mixture was allowed to warm to rt and was maintained at rt for 18 hours at which time ethanol was added, pyridine removed in vacuo, and the reaction residue partitioned between dichloromethane and sat. aq. sodium bicarbonate. The organic layer was then dried over sodium sulfate. Flash chromatography using an ethyl acetate/hexanes gradient gave (1) as a white foam.

5 '-O-tert-butyldiphenylsilyl-2 '-O-methyl-2, 3 '-anhydro uridine (2): To a solution of (1) and DEAD (3.5 eq.) stirring at 0 C under argon in anhydrous THF was added triphenylphosphine (3.5 eq.). The reaction mixture was warmed to rt and stirred at rt under argon for 18 hours, after which THF was removed in vacuo. The crude reaction residue was partitioned between dichloromethane and sat. aq. sodium bicarbonate, the organics dried over sodium sulfate preceding flash chromatography. An ethyl acetate/hexanes gradient afforded (2) as an off white foam. 5 '-O-tert-butyldiphenylsilyl-3 '-S-acetyl-2 '-O-methyl uridine (3): Compound (2) was treated with thiolacetic acid in dioxane at 100 C for 18 hours while stirring in a stainless steel bomb. The reaction mixture was evaporated in vacuo then purified by flash silica gel chromatography to give (3) as a light yellow foam.

5 '-O-dimethoxytrityl-3 ' -S-acetyl-2 '-O-methyl uridine (4): To a solution of (3) stirring at rt under positive pressure argon was added IM TBAF in THF buffered with acetic acid. The resulting clear, light yellow solution was stirred at rt for one hour, then THF removed in vacuo. Crude (4) was flash silica purified using an ethanol/dichloromethane gradient. The purified product was then co-evaporated with anhydrous pyridine, then dissolved in anhydrous pyridine. Dimethoxytrityl chloride was added to the reaction at rt and the resulting clear, reddish solution stirred at rt for 18 hours. Pyridine was removed in vacuo after quenching with ethanol, and the resulting crude foam partitioned between dichloromethane and sat. aq. sodium bicarbonate and the organics dried over sodium sulfate. Flash chromatography using an ethyl acetate/hexanes gradient furnished pure (4). 5 '-O-dimethoxytrityl-3 '-deoxy-3 '-thio-2 '-O-methyl uridine (5): Compound (4) was dissolved in 40% aq. methylamine in the presence of DTT. The reaction mixture was stirred at rt for one hour then evaporated in vacuo. Flash chromatography using an ethyl acetate/hexanes gradient gave (5) as an off white foam. 5 '-O-dimethoxytrityl-3 '-deoxy-3 '-thio-3 '-S-(2-Cyanoethyl-N,N-Diisopropylphos- phoramidite-2 ' -O-methyl uridine (6): To a cooled (0 °C) solution of (5) and NN-diiso- propylethylamine in dry CH2CI2 was added 2-cyanoethyl NN-diisopropylchlorophos- phoramidite dropwise via syringe. The mixture was stirred at room temperature until all starting material was consumed (5 hr.) The reaction mixture was quenched with anhydrous ethanol and diluted with hexanes. Flash chromatography using an ethyl acetate/hexanes gradient provided pure (6).

Diagnostic uses

Nucleic acid molecules of this invention may be used as diagnostic tools to examine genetic drift and mutations within diseased cells or to detect the presence of specific RNAs in a cell. The close relationship between for example ribozyme 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 ribozymes described in this invention, one may map nucleotide changes which are important to RNA structure and function in vitro, as well as in cells and tissues. Cleavage of target RNAs with ribozymes may 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 may be defined as important mediators of the disease. These experiments will lead to better treatment of the disease progression by affording the possibility of combinational therapies (e.g., multiple nucleic acid molecules targeted to different genes, nucleic acid molecules coupled with known small molecule inhibitors, or intermittent treatment with combinations of nucleic acid molecules and/or other chemical or biological molecules). Other in vitro uses of nucleic acid molecules of this invention are well known in the art, and include detection of the presence of RNAs related to various conditions. Such RNA is detected by determining the presence of a cleavage product after treatment with for example, an enzymatic nucleic acid molecule using standard methodology.

In a specific example, ribozymes which can cleave only wild-type or mutant forms of the target RNA are used for the assay. The first ribozyme is used to identify wild-type RNA present in the sample and the second ribozyme will be used to identify mutant RNA in the sample. As reaction controls, synthetic substrates of both wild-type and mutant RNA will be cleaved by both ribozymes to demonstrate the relative ribozyme efficiencies in the reactions and the absence of cleavage of the "non-targeted" RNA species. The cleavage products from the synthetic substrates will also serve to generate size markers for the analysis of wild-type and mutant RNAs in the sample population. Thus each analysis will require two ribozymes, two substrates and one unknown sample which will be combined into six reactions. The presence of cleavage products will be 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. The expression of mRNA whose protein product is implicated in the development of a phenotype is adequate to establish risk. If probes of comparable specific activity are used for both transcripts, then a qualitative comparison of RNA levels will be adequate and will decrease the cost of the initial diagnosis. Higher mutant form to wild-type ratios will be correlated with higher risk whether RNA levels are compared qualitatively or quantitatively.

Additional Uses

Potential usefulness of sequence-specific enzymatic nucleic acid molecules of the instant invention might have 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 could 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 ribozyme is ideal for cleavage of RNAs of unknown sequence. Other embodiments are within the following claims.

TABLE I

Characteristics of naturally occurring ribozymes

Group I Introns

Size: -150 to >1000 nucleotides. ^• Requires a U in the target sequence immediately 5' of the cleavage site.

• Binds 4-6 nucleotides at the 5*-side of the cleavage site.

• Reaction mechanism: attack by the 3'-OH of guanosine to generate cleavage products with 3'-OH and 5 '-guanosine.

• Additional protein cofactors required in some cases to help folding and maintainance of the active structure.

• Over 300 known members of this class. Found as an intervening sequence in Tetrahymena thermophila rRNA, fungal mitochondria, chloroplasts, phage T4, blue-green algae, and others.

• Major structural features largely established through phylogenetic comparisons,

1 mutagenesis, and biochemical studies [ , ].

• Complete kinetic framework established for one ribozyme [ , , , ].

7 8 9

• Studies of ribozyme folding and substrate docking underway [ , , ].

1 Michel, Francois; Westhof, Eric. Slippery substrates. Nat. Struct. Biol. (1994), 1(1), 5-7.

2 Lisacek, Frederique; Diaz, Yolande; Michel, Francois. Automatic identification of group I intron cores in genomic DNA sequences. J. Mol. Biol. (1994), 235(4), 1206-17.

³ Herschlag, Daniel; Cech, Thomas R.. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry (1990), 29(44), 10159-71.

⁴ Herschlag, Daniel; Cech, Thomas R.. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme.2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry (1990), 29(44), 10172-80.

⁵ Knitt, Deborah S.; Herschlag, Daniel. pH Dependencies of the Tetrahymena Ribozyme Reveal an Unconventional Origin of an Apparent pKa. Biochemistry (1996), 35(5), 1560-70.

⁶ Bevilacqua, Philip C; Sugimoto, Naoki; Turner, Douglas H.. A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme. Biochemistry (1996), 35(2), 648-58.

⁷ Li, Yi; Bevilacqua, Philip C; Mathews, David; Turner, Douglas H.. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion- controlled and is driven by a favorable entropy change. Biochemistry (1995), 34(44), 14394-9.

⁸ Banerjee, Aloke Raj; Turner, Douglas H.. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme. Biochemistry (1995), 34(19), 6504-12. • Chemical modification investigation of important residues well established f¹⁰,¹ '].

• The small (4-6 nt) binding site may make this ribozyme too non-specific for targeted RNA cleavage, however, the Tetrahymena group I intron has been used to repair a "defective" β-galactosidase message by the ligation of new β-galactosidase sequences onto the defective message [ ].

RNAse P RNA (Ml RNA

Size: -290 to 400 nucleotides.

• RNA portion of a ubiquitous ribonucleoprotein enzyme.

• Cleaves tRNA precursors to form mature tRNA [ ].

2+ • Reaction mechanism: possible attack by M -OH to generate cleavage products with 3'-

OH and 5 '-phosphate.

• RNAse P is found throughout the prokaryotes and eukaryotes. The RNA subunit has been sequenced from bacteria, yeast, rodents, and primates.

• Recruitment of endogenous RNAse P for therapeutic applications is possible through hybridization of an External Guide Sequence (EGS) to the target RNA [ ,¹⁵]

• Important phosphate and 2' OH contacts recently identified [ , ]

⁹ Zarrinkar, Patrick P.; Williamson, James R.. The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme. Nucleic Acids Res. (1996), 24(5), 854-8.

¹⁰ Strobel, Scott A.; Cech, Thomas R.. Minor groove recognition of the conserved G.cntdot.U pair at the Tetrahymena ribozyme reaction site. Science (Washington, D. C.) (1995), 267(5198), 675-9.

¹¹ Strobel, Scott A.; Cech, Thomas R.. Exocyclic Amine of the Conserved G.cntdot.U Pair at the Cleavage Site of the Tetrahymena Ribozyme Contributes to 5'-Splice Site Selection and Transition State Stabilization. Biochemistry (1996), 35(4), 1201-11.

¹² Sullenger, Bruce A.; Cech, Thomas R.. Ribozyme-mediated repair of defective mRNA by targeted trans-splicing. Nature (London) (1994), 371(6498), 619-22.

¹ Robertson, H.D.; Airman, S.; Smith, J.D. J. Biol. Chem., 247, 5243-5251 (1972).

¹⁴ Forster, Anthony C; Airman, Sidney. External guide sequences for an RNA enzyme. Science (Washington, D. C, 1883-) (1990), 249(4970), 783-6.

¹⁵ Yuan, Y.; Hwang, E. S.; Airman, S. Targeted cleavage of mRNA by human RNase P. Proc. Natl. Acad. Sci. USA (1992) 89, 8006-10.

¹⁶ Harris, Michael E.; Pace, Norman R.. Identification of phosphates involved in catalysis by the ribozyme RNase P RNA. RNA (1995), 1(2), 210-18.

¹⁷ Pan, Tao; Loria, Andrew; Zhong, Kun. Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA. Proc. Natl. Acad. Sci. U. S. A. (1995), 92(26), 12510- 14. Group II Introns

• Size: >1000 nucleotides.

• Trans cleavage of target RNAs recently demonstrated [ , ].

• Sequence requirements not fully determined. • Reaction mechanism: 2'-OH of an internal adenosine generates cleavage products with 3'-

OH and a "lariat" RNA containing a 3 '-5' and a 2'-5' branch point.

• Only natural ribozyme with demonstrated participation in DNA cleavage [²⁰,²¹] in addition to RNA cleavage and ligation.

Major structural features largely established through phylogenetic comparisons [²²]. • Important 2' OH contacts beginning to be identified [ ]

• Kinetic framework under development [ ]

Neurospora NS RΝA

• Size: -144 nucleotides.

• TRANS CLEAVAGE OF HAIRPIN TARGET RNAS RECENTLY DEMONSTRATED [²⁵]. • Sequence requirements not fully determined.

• Reaction mechanism: attack by 2'-OH 5' to the scissile bond to generate cleavage products with 2',3'-cyclic phosphate and 5'-OH ends.

¹⁸ Pyle, Anna Marie; Green, Justin B.. Building a Kinetic Framework for Group II Intron Ribozyme Activity: Quantitation of Interdomain Binding and Reaction Rate. Biochemistry (1994), 33(9), 2716-25.

¹⁹ Michels, William J. Jr.; Pyle, Anna Marie. Conversion of a Group II Intron into a New Multiple- Turnover Ribozyme that Selectively Cleaves Oligonucleotides: Elucidation of Reaction Mechanism and Structure/Function Relationships. Biochemistry (1995), 34(9), 2965-77.

²⁰ Zimmerly, Steven; Guo, Huatao; Eskes, Robert; Yang, Jian; Perlman, Philip S.; Lambowitz, Alan M.. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell (Cambridge, Mass.) (1995), 83(4), 529-38.

²¹ Griffin, Edmund A., Jr.; Qin, Zhifeng; Michels, Williams J., Jr.; Pyle, Anna Marie. Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'- hydroxyl groups. Chem. Biol. (1995), 2(11), 761-70.

²² Michel, Francois; Ferat, Jean Luc. Structure and activities of group II introns. Annu. Rev. Biochem. (1995), 64, 435-61.

² Abramovitz, Dana L.; Friedman, Richard A.; Pyle, Anna Marie. Catalytic role of 2'-hydroxyl groups within a group II intron active site. Science (Washington, D. C.) (1996), 271(5254), 1410-13.

²⁴ Daniels, Danette L.; Michels, William J., Jr.; Pyle, Anna Marie. Two competing pathways for self- splicing by group II introns: a quantitative analysis of in vitro reaction rates and products. J. Mol. Biol. (1996), 256(1), 31-49.

²⁵ Guo, Hans C. T.; Collins, Richard A.. Efficient trans-cleavage of a stem- loop RNA substrate by a ribozyme derived from Neurospora VS RNA. EMBO J. (1995), 14(2), 368-76. • Binding sites and structural requirements not fully determined.

• Only 1 known member of this class. Found in Neurospora VS RNA.

Hammerhead Ribozyme (see text for references) • Size: -13 to 40 nucleotides.

• Requires the target sequence UH immediately 5' of the cleavage site.

• Binds a variable number nucleotides on both sides of the cleavage site.

• Reaction mechanism: attack by 2'-OH 5' to the scissile bond to generate cleavage products with 2 ',3 '-cyclic phosphate and 5' -OH ends. • 14 known members of this class. Found in a number of plant pathogens (virusoids) that use RNA as the infectious agent.

• Essential structural features largely defined, including 2 crystal structures [ , ]

• Minimal ligation activity demonstrated (for engineering through in vitro selection) [ ]

• Complete kinetic framework established for two or more ribozymes [ ]. • Chemical modification investigation of important residues well established [ ].

Hairpin Ribozyme

• Size: -50 nucleotides.

• Requires the target sequence GUC immediately 3' of the cleavage site.

• Binds 4-6 nucleotides at the 5'-side of the cleavage site and a variable number to the 3'- side of the cleavage site.

• Reaction mechanism: attack by 2'-OH 5' to the scissile bond to generate cleavage products with 2',3'-cyclic phosphate and 5'-OH ends.

²⁶ Scott, W.G., Finch, J.T., Aaron,K. The crystal structure of an all RNA hammerhead ribozyme: Aproposed mechanism for RNA catalytic cleavage. Cell, (1995), 81, 991-1002.

²⁷ McKay, Structure and function of the hammerhead ribozyme: an unfinished story. RNA, (1996), 2, 395-403.

²⁸ Long, D., Uhlenbeck, O., Hertel, K. Ligation with hammerhead ribozymes. US Patent No. 5,633,133.

²⁹ Hertel, K.J., Herschlag, D., Uhlenbeck, O. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry, (1994) 33, 3374-3385.Beigelman, L., et al., Chemical modifications of hammerhead ribozymes. J. Biol. Chem., (1995) 270, 25702-25708.

³⁰ Beigelman, L., et al., Chemical modifications of hammerhead ribozymes. J. Biol. Chem., (1995) 270, 25702-25708. 3 known members of this class. Found in three plant pathogen (satellite RNAs of the tobacco ringspot virus, arabis mosaic virus and chicory yellow mottle virus) which uses RNA as the infectious agent. Essential structural features largely defined [³¹,³²,³³,³⁴] • Ligation activity (in addition to cleavage activity) makes ribozyme amenable to engineering through in vitro selection [ ]

• Complete kinetic framework established for one ribozyme [ ].

• Chemical modification investigation of important residues begun [³⁷,³⁸].

Hepatitis Delta Virus (HDN Ribozyme • Size: -60 nucleotides.

• Trans cleavage of target R As demonstrated [ ].

Binding sites and structural requirements not fully determined, although no sequences 5' of cleavage site are required. Folded ribozyme contains a pseudoknot structure f⁴⁰].

Hampel, Arnold; Tritz, Richard; Hicks, Margaret; Cruz, Phillip. 'Hairpin' catalytic RΝA model: evidence for helixes and sequence requirement for substrate RΝA. Nucleic Acids Res. (1990), 18(2), 299- 304.

³² Chowrira, Bharat M.; Berzal-Herranz, Alfredo; Burke, John M.. Novel guanosine requirement for catalysis by the hairpin ribozyme. Nature (London) (1991), 354(6351), 320-2.

³³ Berzal-Herranz, Alfredo; Joseph, Simpson; Chowrira, Bharat M.; Butcher, Samuel E.; Burke, John M.. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. EMBO J. (1993), 12(6), 2567-73.

³⁴ Joseph, Simpson; Berzal-Herranz, Alfredo; Chowrira, Bharat M.; Butcher, Samuel E.. Substrate selection rules for the hairpin ribozyme determined by in vitro selection, mutation, and analysis of mismatched substrates. Genes Dev. (1993), 7(1), 130-8.

³⁵ Berzal-Herranz, Alfredo; Joseph, Simpson; Burke, John M.. In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions. Genes Dev. (1992), 6(1), 129-34.

³⁶ Hegg, Lisa A.; Fedor, Martha J.. Kinetics and Thermodynamics of Intermolecular Catalysis by Hairpin Ribozymes. Biochemistry (1995), 34(48), 15813-28.

³⁷ Grasby, Jane A.; Mersmann, Karin; Singh, Mohinder; Gait, Michael J.. Purine Functional Groups in Essential Residues of the Hairpin Ribozyme Required for Catalytic Cleavage of RNA. Biochemistry (1995), 34(12), 4068-76.

³⁸ Schmidt, Sabine; Beigelman, Leonid; Karpeisky, Alexander; Usman, Nassim; Sorensen, Ulrik S.; Gait, Michael J.. Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure. Nucleic Acids Res. (1996), 24(4), 573- 81.

³⁹ Perrotta, Anne T.; Been, Michael D.. Cleavage of oligoribonucleotides by a ribozyme derived from the hepatitis .delta, virus RNA sequence. Biochemistry (1992), 31(1), 16-21.

⁴⁰ Perrotta, Anne T.; Been, Michael D.. A pseudoknot-like structure required for efficient self- cleavage of hepatitis delta virus RNA. Nature (London) ( 1991 ), 350(6317), 434-6. Reaction mechanism: attack by 2'-OH 5' to the scissile bond to generate cleavage products with 2',3 '-cyclic phosphate and 5'-OH ends.

Only 2 known members of this class. Found in human HDV.

Circular form of HDV is active and shows increased nuclease stability f⁴¹]

⁴¹ Puttaraju, M.; Perrotta, Anne T.; Been, Michael D.. A circular trans-acting hepatitis delta virus ribozyme. Nucleic Acids Res. (1993), 21(18), 4253-8. Table II: 2.5 μmol RNA Synthesis Cycle

Reagent Equivalents Amount Wait

Time*

Phosphoramidites 6.5 163 μL 2.5

S-Ethyl Tetrazole 23.8 238 μL 2.5

Acetic Anhydride 100 233 μL 5 sec

N-Methyl Imidazole 186 233 μL 5 sec

TCA 83.2 1.73 mL 21 sec

Iodine 8.0 1.18 mL 45 sec

Acetonitrile ΝA 6.67 mL ΝA

Table IIIA. Antisense Sequences and Correspondmg in vitro Data

Table TV. Hammerhead Ribozyme and Target SequencesFor Estrogen Receptor

Table V. Hairpin Ribozyme and Target sequences

Table VI. Ribozymes for in vitro Cleavage

Table VII. Antisense Nucleic Acid Molecules Targeting c-raf

lower case = 2'-0-methyl nucleotides; UPPER Case = DNA; s = phosphorothioate linkage; m= 5 methyl C;iB=inverted abasic;bo!d lower case=2'-0-methylthiomethyl modified Table VIH. Antisense Nucleic Acid Molecules Targeting Bcl-2 and K-ras

lower case = 2'-0-methyl nucleotides; UPPER Case = DNA; s = phosphorothioate linkage; m= 5 methyl C; iB=inverted abasic; bold lower case=2'-0-methylthiomethyl modified

Claims

Claims

1. A nucleic acid molecule having the formula I: wherein each of X represents independently a nucleotide which may be same or different;

5' C (X)„T-(Y)n— (X)o— C 3'

where m and o are integers independently greater than or equal to 5; (X)_m and (X)₀ are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid molecule; Y represents independently a deoxyribonucleotide which may be same or different; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; n is an integer greater than or equal to 4; represents a chemical linkage; each (X)_m, and (X)₀ comprise independently at least one phosphodiester linkage and one phosphorothioate linkage; (Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'-thiophosphate linkage or a mixture thereof; and each C and C independently represents a cap structure which may independently be present or absent.

2. A nucleic acid molecule having the formula II:

5' C (Y)_ή (X)— C¹ 3'

wherein X represents a nucleotide which may be same or different; where r is an integer greater than or equal to 4; (X)_r is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; Y represents independently a deoxyribonucleotide which may be same or different; n is an integer greater than or equal to 4; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule represents a chemical linkage;

(Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'- thiophosphate linkage or a mixture thereof; each (X)_r comprises independently at least one phosphodiester linkage and one phosphorothioate linkage; and each C and C independently represents a cap structure which may independently be present or absent.

3. A nucleic acid molecule having the formula III:

wherein X represents a nucleotide which may be same or different; where r is an integer greater than or equal to 4; (X)_r is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; Y represents independently a deoxyribonucleotide which may be same or different ; n is an integer greater than or equal to 4; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule represents a chemical linkage;

(Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a mixture of phosphorothioate and phosphorodithioate linkages; each (X)_r comprises independently at least one phosphodiester linkage and one phosphorothioate linkage; and each C and C independently represents a cap structure which may independently be present or absent.

4. An enzymatic nucleic acid molecule having endonuclease activity of the formula IV:

5' C (X)^; — (Z)p — (X)o- (Y)n— (X)_q— C 3'

wherein each of X represents independently a nucleotide which may be same or different; where m, o and q are integers independently greater than or equal to 5; (X)_m and (X)₀ are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid molecule; (X)_q is optionally able to interact with a target nucleic acid molecule; Y represents independently a deoxyribonucleotide which may be same or different; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; n is an integer greater than or equal to 4; represents a chemical linkage; each (X)_m, (X)o and (X)_q comprise independently at least one phosphodiester linkage; (Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'-thiophosphate linkage or a mixture thereof; Z represents an oligonucleotide able to facilitate the cleavage of the target nucleic acid molecule; p is of length greater than or equal to 4; and each C and C independently represents a cap structure which may independently be present or absent.

5. An enzymatic nucleic acid molecule having endonuclease activity of the formula V:

5' C (XfcH— (Y)ri-(X)o-(Z)p-(X)_q— C 3'

wherein each of X represents independently a nucleotide which may be same or different; where m, o and q are integers independently greater than or equal to 5; (X)_m and (X)₀ are oligonucleotides which are of sufficient length to stably interact independently with a target nucleic acid molecule; (X)_q is optionally able to interact with the target nucleic acid molecule; (Y)_n represents independently a deoxyribonucleotide which may be same or different; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; n is an integer greater than or equal to

4; represents a chemical linkage; each (X)_m, (X)₀ and (X)_q comprise independently at least one phosphodiester linkage; (Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'-thiophosphate linkage or a mixture thereof; Z represents an oligonucleotide able to facilitate the cleavage of the target nucleic acid molecule; p is of length greater than or equal to 4; and each C and C independently represents a cap structure which may independently be present or absent.

6. An enzymatic nucleic acid molecule having endonuclease activity of the formula VI:

wherein X represents independently a nucleotide which may be same or different; where q is an integer independently greater than or equal to 1 ; (X)_q is optionally able to interact with a target nucleic acid molecule; Y represents independently a deoxyribonucleotide which may be same or different; (Y)„ is an oligonucleotide which is of sufficient length to stably interact independently with a target nucleic acid molecule; n is an integer greater than or equal to 4; represents a chemical linkage; (Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'-thiophosphate linkage or a mixture thereof; Z represents an oligonucleotide able to facilitate the cleavage of the target nucleic acid molecule; p is of length greater than or equal to 4; and each C and C independently represents a cap structure which may independently be present or absent.

7. An enzymatic nucleic acid molecule having endonuclease activity of the formula VII:

5' C (X)_q (Z)_p (Y)_n C" 3'

wherein X represents independently a nucleotide which may be same or different; where q is an integer independently greater than or equal to 1 ; (X)_q is optionally able to interact with a target nucleic acid molecule; Y represents independently a deoxyribonucleotide which may be same or different; (Y)_n is an oligonucleotide which is of sufficient length to stably interact independently with the target nucleic acid molecule; n is an integer greater than or equal to 4; represents a chemical linkage; (Y)_n comprises a phosphorothioate linkage or a phosphorodithioate linkage or a 5'-S-phosphorothioate linkage or a 5'-S- phosphorodithioate linkage or a 3'-S-phosphorothioate linkage or a 3'-S- phosphorodithioate linkage or a mixture thereof; Z represents an oligonucleotide able to facilitate the cleavage of the target nucleic acid molecule; p is of length greater than or equal to 4; and each C and C independently represents a cap structure which may independently be present or absent.

8. The nucleic acid molecule of any of claims 1-3, wherein each X, independently comprises a nucleotide modification selected from the group consisting of: 2'-O-methyl, 2'-O-allyl, 2'-O-methylthiomethyl, L-nucleotides; 2'-C-allyl; 1-5- Anhydrohexytol; 2,6-diaminopurine; 2'-fluoro; 2'-deoxy-2'-amino; 2'-(N-alanyl) amino; 2'-(N-phenylalanyl)amino; 2'-deoxy-2'-(N-β-alanyl) amino; 2'-deoxy-2'-(lysyl) amino; 2'- O-amino; 2'-Deoxy-2'-(N-histidyl) amino; 6-methyl uridine; 5-methyl cytidine; 2'-(N-β- carboxamidine-β-alanyl)amino-2'-deoxy-nucleotide; 2'-O-methylthioallyl; 2'-O- methylthioethyl; 2'-O-methylthiomethyl; 2'-O-methyl-3'-thiophosphate and xylofiiranosyl.

9. The enzymatic nucleic acid molecule of any of claims 4-7, wherein each X, Z or both X and Z, independently comprises a nucleotide modification selected from the group consisting of: 2'-O-methyl, 2'-O-allyl, 2'-O-methylthiomethyl, L-nucleotides; 2'-C- allyl; 1-5-Anhydrohexytol; 2,6-diaminopurine; 2'-fluoro; 2'-deoxy-2'-amino; 2'-H; 2'-(N- alanyl) amino; 2'-(N-phenylalanyl)amino; 2'-deoxy-2'-(N-β-alanyl) amino; 2'-deoxy-2'- (lysyl) amino; 2'-O-amino; 2'-Deoxy-2'-(N-histidyl) amino; 6-methyl uridine; 5-methyl cytidine; 2'-(N-β-carboxamidine-β-alanyl)amino-2'-deoxy-nucleotide; 2'-O- methylthioallyl; 2'-O-methylthioethyl; 2'-O-methylthiomethyl; 2'-O-methyl-3'- thiophosphate and xylo uranosyl.

10. The enzymatic nucleic acid molecule of any of claims 4-7, wherein, the Z in said nucleic acid molecule is the catalytic core.

11. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said enzymatic nucleic acid is in a hammerhead ribozyme configuration.

12. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said enzymatic nucleic acid is in a hairpin ribozyme configuration.

13. The enzymatic nucleic acid of any of claims 4-7, wherein said enzymatic nucleic acid is in a hepatitis delta virus, group I intron, VS RΝA, group II intron, or RΝase P RΝA configuration.

14. A method of cleaving an RΝA molecule comprising the step of, contacting the enzymatic nucleic acid molecule of any of claims 4-7, with the RΝA molecule under conditions suitable for the cleavage of said RΝA molecule by said enzymatic nucleic acid molecule.

15. The method of claim 14, wherein said cleavage is carried out in the presence of a divalent cation.

16. The method of claim 15, wherein said divalent cation is Mg2+.

17. The nucleic acid molecules of any of claims 1-3, wherein said C, when present, is a cap selected from the group consisting of: inverted abasic residue; 4',5'- methylene nucleotide; l-(beta-D-erythrofuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; t/Veø-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 abasic moiety; 3'-2'-inverted nucleotide moiety; 3'-2'-inverted abasic moiety; 1 ,4-butanediol phosphate; 3'-phosphoramidate; hexylphosphate; aminohexyl phosphate; 3'-phosphate; 3'- phosphorothioate; phosphorodithioate; and methylphosphonate moiety.

18. The nucleic acid molecule of any of claim 1-3, wherein said nucleic acid molecule comprises a 3 '-3' linked inverted ribose moiety at said 3' end.

19. The nucleic acid molecule of any of claims 1-3, wherein said nucleic acid molecule is an antisense nucleic acid molecule.

20. The nucleic acid molecule of claims 1-3 wherein said nucleic acid molecule is a 2-5 A antisense chimera.

21. The nucleic acid molecule of any of claims 1-3 wherein said nucleic acid molecule is a triplex forming oligonucleotide.

22. A nucleic acid molecule comprising any of sequence defined as Seq. ID Nos. 1-30.

23. A mammalian cell including an enzymatic nucleic acid molecule of any of claims 4-7.

24. The mammalian cell of claim 23, wherein said mammalian cell is a human cell.

25. A method of modulating the expression of a gene in a cell comprising the step of administering to said cell a nucleic acid molecule of any of claims 1-3 under conditions suitable for the down regulation of said gene.

26. A method of modulating the expression of a gene in a cell comprising the step of administering to said cell an enzymatic nucleic acid molecule of any of claims 4-7 under conditions suitable for the down regulation of said gene.

27. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said C, when present, is a cap selected from the group consisting of: inverted abasic residue; 4',5'- methylene nucleotide; l-(beta-D-erythroiuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; tΛreo-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 abasic moiety; 3'-2'-inverted nucleotide moiety; 3'-2'-inverted abasic moiety; 1 ,4-butanediol phosphate; 3'-phosphoramidate; hexylphosphate; aminohexyl phosphate; 3'-phosphate; 3'- phosphorothioate; phosphorodithioate; and methylphosphonate moiety.

28. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said C, when present, is a cap selected from the group consisting of: 4',5'-methylene nucleotide; 1- (beta-D-erythrofuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 5'-amino- alkyl phosphate; l,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; t/ eo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; 3,4- dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5'-5'-inverted nucleotide moeity; 5'-5'-inverted abasic moeity; 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 moeities.

29. The nucleic acid molecules of any of claims 1-3, wherein said C, when present, is a cap selected from the group consisting of: 4',5'-methylene nucleotide; ^(beta- D-erythrofuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 5'-amino-alkyl phosphate; l,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; t/zreo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5'-5'-inverted nucleotide moeity; 5'-5'-inverted abasic moeity; 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.

30. A mammalian cell including a nucleic acid molecule of any of claims 1 -3.

31. The mammalian cell of claim 30, wherein said mammalian cell is a human cell.

32. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said enzymatic nucleic acid molecule comprises a 3'-3' linked inverted ribose moiety at said 3' end.

33. The nucleic acid molecule of any of claims 1-3, wherein said (X)_m and (X)₀ are symmetric in length.

34. The nucleic acid molecule of any of claims 1-3, wherein said (X)_m and (X)₀ are asymmetric in length.

35. The enzymatic nucleic acid molecule of any of claims 4-5, wherein said

(X)_m and (X)_o are symmetric in length.

36. The enzymatic nucleic acid molecule of any of claims 4-5, wherein said (X)_m and (X)_o are asymmetric in length.

37. The enzymatic nucleic acid molecule of claim 4, wherein the sum of said o, n and q is equal to said m.

38. The enzymatic nucleic acid molecule of claim 5, wherein the sum of said o, n and m is equal to said q.

39. The enzymatic nucleic acid molecule of claim 4, wherein the sum of said o, n and q is greater than said m.

40. The enzymatic nucleic acid molecule of claim 5, wherein the sum of said o, n and m is greater than said q.

41. The enzymatic nucleic acid molecule of claim 4, wherein the sum of said o, n and q is less than said m.

42. The enzymatic nucleic acid molecule of claim 5, wherein the sum of said o, n and m is less than said q.

43. An enzymatic nucleic acid molecule with RNA cleaving activity, wherein said enzymatic nucleic acid molecule modulates the expression of an estrogen receptor gene.

44. The enzymatic nucleic acid molecule of claim 43, wherein said enzymatic nucleic acid molecule is in a hammerhead configuration.

45. The enzymatic nucleic acid molecule of claim 44, wherein said enzymatic nucleic acid molecule comprises a stem II region of length greater than or equal to 2 base pairs.

46. The enzymatic nucleic acid molecule of claim 43, wherein said enzymatic nucleic acid molecule is in a hairpin configuration.

47. The enzymatic nucleic acid molecule of claim 43, wherein said enzymatic nucleic acid is in a hepatitis d virus, group I intron, group II intron, VS nucleic acid or RNase P nucleic acid configuration.

48. The enzymatic nucleic acid of claim 46, wherein said enzymatic nucleic acid molecule comprises a stem II region of length between three and seven base-pairs.

49. The enzymatic nucleic acid molecule of claim 43, wherein said nucleic acid comprises between 12 and 100 bases complementary to said RNA.

50. The enzymatic nucleic acid molecule of claim 43, wherein said nucleic acid comprises between 14 and 24 bases complementary to said mRNA.

51. The enzymatic nucleic acid molecule of claim 44, wherein said enzymatic nucleic acid molecule consists essentially of any sequence defined as Seq ID Nos 1-1245.

52. A mammalian cell including an enzymatic nucleic acid molecule of any of claim 43.

53. The mammalian cell of claim 52, wherein said mammalian cell is a human cell.

54. An expression vector comprising nucleic acid sequence encoding at least one enzymatic nucleic acid molecule of claim 43, in a manner which allows expression of that enzymatic nucleic acid molecule.

55. A mammalian cell including an expression vector of claim 54.

56. The mammalian cell of claim 13, wherein said mammalian cell is a human cell.

57. A method for treatment of cancer comprising the step of administering to a patient the enzymatic nucleic acid molecule of claim 43.

58. A method for treatment of cancer comprising the step of administering to a patient the expression vector of claim 54.

59. A method for treatment of cancer comprising the steps of: a) isolating cells from a patient; b) administering to said cells the enzymatic nucleic acid molecule of claim 43; and c) introducing said cells back into said patient.

60. A pharmaceutical composition comprising the enzymatic nucleic acid molecule of claim 43.

61. A method of treatment of a patient having a condition associated with the level of estrogen receptor, wherein said patient is administered the enzymatic nucleic acid molecule of claim 43.

62. A method of treatment of a patient having a condition associated with the level of estrogen receptor, comprising contacting cells of said patient with the nucleic acid molecule of claim 43, and further comprising the use of one or more drug therapies.

63. The enzymatic nucleic acid molecule of claim 44, wherein said nucleic acid molecule comprises at least five ribose residues, and wherein said nucleic acid comprises phosphorothioate linkages at at least three of the 5' terminal nucleotides, and wherein said nucleic acid comprises a 2'-C-allyl modification at position No. 4 of said nucleic acid, and wherein said nucleic acid comprises at least ten 2'-O-methyl modifications, and wherein said nucleic acid comprises a 3'- end modification.

64. The enzymatic nucleic acid of claim 63, wherein said nucleic acid comprises a 3'-3' linked inverted ribose moiety at said 3' end.

65. The enzymatic nucleic acid molecule of claim 44, wherein said nucleic acid molecule comprises at least five ribose residues, and wherein said nucleic acid molecule comprises phosphorothioate linkages at at least three of the 5' terminal nucleotides, and wherein said nucleic acid comprises a 2'-amino modification at position No. 4 and/or at position No. 7 of said nucleic acid molecule, wherein said nucleic acid molecule comprises at least ten 2'-O-methyl modifications, and wherein said nucleic acid comprises a 3'- end modification.

66. The enzymatic nucleic acid molecule of claim 44, wherein said nucleic acid molecule comprises at least five ribose residues, and wherein said nucleic acid molecule comprises phosphorothioate linkages at at least three of the 5' terminal nucleotides, and wherein said nucleic acid molecule comprises an abasic substitution at position No. 4 and/or at position No. 7 of said nucleic acid molecule, wherein said nucleic acid comprises at least ten 2'-O-methyl modifications, and wherein said nucleic acid molecule comprises a 3 '-end modification.

67. The enzymatic nucleic acid molecule of claim 44, wherein said nucleic acid molecule comprises of at least five ribose residues, and wherein said nucleic acid comprises phosphorothioate linkages at at least three of the 5' terminal nucleotides, and wherein said nucleic acid molecule comprises a 6-methyl uridine substitution at position No. 4 and/or at position No. 7 of said nucleic acid molecule, wherein said nucleic acid molecule comprises at least ten 2'-O-methyl modifications, and wherein said nucleic acid molecule comprises a 3' end modification.

68. A method for modulating expression of estrogen receptor gene in a mammalian cell by administering to said cell the enzymatic nucleic acid molecule of claim

43.

69. A method of cleaving a separate RNA molecule comprising, contacting the enzymatic nucleic acid molecule of claim 43 with said separate RNA molecule under conditions suitable for the cleavage of said separate RNA molecule.

70. The method of claim 69, wherein said cleavage is carried out in the presence of a divalent cation.

71. The method of claim 70, wherein said divalent cation is Mg2+

72. The nucleic acid molecule of claim 43, wherein said nucleic acid is chemically synthesized.

73. The expression vector of claim 54, wherein said vector comprises: a) a transcription initiation region; b) a transcription termination region; c) a gene encoding at least one said nucleic acid molecule; and wherein said gene is operably linked to said initiation region and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

74. The expression vector of claim 54, wherein said vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an open reading frame; d) a gene encoding at least one said nucleic acid molecule, wherein said gene is operably linked to the 3 '-end of said open reading frame; and wherein said gene is operably linked to said initiation region, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

75. The expression vector of claim 54, wherein said vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) a gene encoding at least one said nucleic acid molecule; and wherein said gene is operably linked to said initiation region, said intron and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

76. The expression vector of claim 54, wherein said vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame; . e) a gene encoding at least one said nucleic acid molecule, wherein said gene is operably linked to the 3'-end of said open reading frame; and wherein said gene is operably linked to said initiation region, said intron, said open reading frame and said termination region, in a manner which allows expression and/or delivery of said nucleic acid molecule.

77. The enzymatic nucleic acid molecule of claim 44, wherein said enzymatic nucleic acid comprises sequences that are complementary to any of sequences defined as Seq ID Nos 1246-2490.

78. The enzymatic nucleic acid molecule of claim 46, wherein said enzymatic nucleic acid molecule consists essentially of any sequence defined as Seq ID Nos 2491- 2603.

79. The enzymatic nucleic acid molecule of claim 46, wherein said enzymatic nucleic acid comprises sequences that are complementary to any of sequences defined as Seq ID Nos 2604-2716..

80. The enzymatic nucleic acid molecule of claim 43, wherein said enzymatic nucleic acid is a DNA enzyme.

81. The enzymatic nucleic acid molecule of claim 43, wherein said enzymatic nucleic acid comprises at least one 2 '-sugar modification.

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

83. The enzymatic nucleic acid molecule of claim 43, wherein said enzymatic nucleic acid comprises at least one phosphorothioate modification.

84. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said enzymatic nucleic acid molecule comprises a 3 '-3' linked inverted deoxyribose moiety at said 3' end.

85. The nucleic acid molecule of any of claims 1-3, wherein said enzymatic nucleic acid molecule comprises a 3'-3' linked inverted deoxyribose moiety at said 3' end.

86. The nucleic acid molecule of any of claims 1-3, wherein said enzymatic nucleic acid molecule comprises a 5'-5' linked inverted deoxyribose moiety at said 5' end.

87. The enzymatic nucleic acid molecule of any of claims 4-7, wherein said enzymatic nucleic acid molecule comprises a 5'-5' linked inverted deoxyribose moiety at said 5' end.

88. The nucleic acid molecule of any of claims 1-3, wherein each X, independently comprises a nucleotide modification having formula IX:

Wherein, each B is independently a modified or an unmodified nucleic acid base; Rl is independently an aklyl, an alkylthioalkyl, a fluoroalkyl or an alkylthiofluoroalkyl; E is independently a phosphorus-containing group; and D is independently an O, blocking group or a phosphorus-containing group.

89. The nucleic acid molecule of any of claims 1-3, wherein each X, independently comprises a nucleotide modification having formula X:

Wherein, each B is independently a modified or an unmodified nucleic acid base; Rl is independently an aklyl, an alkylthioalkyl, a fluoroalkyl or an alkylthiofluoroalkyl; E is independently a phosphorus-containing group; and D is independently an O, blocking group or a phosphorus-containing group.

90. The nucleic acid molecule of any of claims 4-7, wherein each X, Z or both X and Z, independently comprise a nucleotide modification having formula X:

Wherein, each B is independently a modified or an unmodified nucleic acid base; Rl is independently an aklyl, an alkylthioalkyl, a fluoroalkyl or an alkylthiofluoroalkyl; E is independently a phosphorus-containing group; and D is independently an O, blocking group or a phosphorus-containing group.

91. The nucleic acid molecule of any of claims 4-7, wherein each X, Z or both

X and Z, independently comprises a nucleotide modification having formula IX:

Wherein, each B is independently a modified or an unmodified nucleic acid base; Rl is independently an aklyl, an alkylthioalkyl, a fluoroalkyl or an alkylthiofluoroalkyl; E is independently a phosphorus-containing group; and D is independently an O, blocking group or a phosphorus-containing group.

92. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a phosphorothioate linkage.

93. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a phosphorodithioate linkage.

94. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a 5'-S-phosphorothioate linkage.

95. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n consists of phosphorothioate linkage at every position.

96. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n consists of phosphorodithioate linkage at every position.

97. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n consists of 5'-S-phosphorothioate linkage at every position.

98. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorothioate and phosphorodithioate linkages.

99. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorothioate and 5'-S-phosphorothioate linkages.

100. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorodithioate and 5'-S-phosphorothioate linkages.

101. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorothioate, phosphorodithioate and 5'-S- phosphorothioate linkages.

102. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)„ comprises a combination of phosphorothioate and 5'-S-phosphorodithioate linkages.

103. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorodithioate and 5'-S-phosphorodithioate linkages.

104. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorothioate and 3'-S-phosphorothioate linkages.

105. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorodithioate and 3'-S-phosphorothioate linkages.

106. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorothioate and 3'-S-phosphorodithioate linkages.

107. The nucleic acid molecule of any of claims 1-3 and 4-7, wherein (Y)_n comprises a combination of phosphorodithioate and 3'-S-phosphorodithioate linkages.