WO1994022890A1

WO1994022890A1 - Novel 5'-substituted nucleosides and oligomers produced therefrom

Info

Publication number: WO1994022890A1
Application number: PCT/US1994/002993
Authority: WO
Inventors: Ashis Kumar Saha
Original assignee: Sterling Winthop Inc.
Priority date: 1993-03-31
Filing date: 1994-03-21
Publication date: 1994-10-13
Also published as: HU9501994D0; EP0691979A1; JPH08508490A; CA2159632A1; AU6449294A

Abstract

Disclosed are novel 5'-substituted nucleosides and oligonucleotide analog compounds prepared therefrom having from 2 to about 60 bases and having an internucleoside backbone containing one or more 3'-O-PO2H-O-5'-CR1R2- internucleoside linkages instead of the naturally occurring backbone of phosphodiester internucleoside linkages. The present invention also discloses a method of synthesizing oligonucleotide compounds having from 2 to about 60 bases and having an internucleoside backbone containing one or more 3'-O-PO2H-O-5'-CR1R2 internucleoside linkages instead of the naturally occurring backbone of phosphodiester internucleoside linkages, this process comprising preparation of 5'-substituted nucleoside compounds, for example, as illustrated in Figure 1, and utilizing them as synthons in automated DNA synthesizers. Oligonucleotide analogs of the present invention are useful as nuclease resistant, sequence specific antisense compounds.

Description

NOVEL 5' SUBSTITUTED NUCLEOSIDES AND OLIGOMERS PRODUCED THEREFROM

Field of the invention

The present invention relates to novel 5'-substituted nucleosides and to oligonucleotide analogs prepared therefrom having from 2 to about 60 bases and having an intemucleoside backbone containing one or more 3'-0-Pθ2H-0-5'-CRι R2 intemucleoside linkages instead of the naturally occurring backbone of phosphodiester intemucleoside linkages. The present invention also relates to a method of synthesizing oligonucleotide compounds having from 2 to about 60 bases and having an intemucleoside backbone containing one or more 3'-0-P02H-0-5'-CRι R2 intemucleoside linkages instead of the naturally occurring backbone of phosphodiester intemucleoside linkages, this process comprising preparation of 5'-substituted nucleoside compounds, for example, as illustrated in Scheme 1 , and utilizing them as synthons in automated DNA synthesizers. Oligonucleotide analogs of the present invention are useful as nuclease resistant, sequence specific antisense compounds.

Background of the Invention

An antisense compound binds to or hybridizes with a nucleotide sequence in a nucleic acid (RNA or DNA) to inhibit the function (or synthesis) of the nucleic acid. Because they can hybridize with both RNA and DNA, antisense compounds can interfere with gene expression at the level of transcription, RNA processing or translation.

As discussed, e.g., in Klausner, A., Biotechnology. 8:303-304 (1990), the development of practical applications of antisense technology is hampered by a number of technical problems. Thus, natural, phosphodiester- linked antisense oligomer compounds are susceptible to rapid degradation by nucleases that exist in target cells and elsewhere in the body; both exonucleases, which act on either the 3' or the 5' terminus of the nucleic acid, and endonucleases, which cleave the nucleic acid at internal phosphodiester linkages between individual nucleosides. As a result of such nuclease action, the effective half life of many administered antisense compounds is very short, necessitating the use of large, frequently administered, doses. The high cost of producing antisense DNA or RNA on currently available DNA synthesizers is another problem. Armstrong, L, Business Week. March 5, 1990, page 89, estimated the cost of producing one gram of antisense DNA to be about $100,000. There is also a problem regarding delivery of antisense agents to targets within the body (and cell). Thus, antisense agents targeted to genomic DNA must permeate the plasma and the nuclear membrane to gain access to the nucleus. The consequent need for increased hydrophobicity to enhance membrane permeability must be balanced against the need for increased hydrophilicity (water solubility) in body fluids such as the plasma and cell cytosol.

Also, oligonucleotide compounds such as antisense DNA are susceptible to steric reconfiguration around chiral phosphorous centers. This results in stability problems, too, whether the compounds are free within the body or hybridized to target nucleic acids.

To overcome the stability and drug delivery limitations, various oligonucleotide analogs have been investigated. In order to be of practical utility, such analogs should have good cell penetration properties, be resistant to nuclease degradation, have good sequence specific hybridization to target nucleic acids, and be synthesized by chemical methods that are not too difficult or costly.

Recent efforts to overcome the foregoing problems and prepare antisense compounds that are stable, nuclease resistant, relatively inexpensive to manufacture and which can be delivered to and hybridized with nucleic acid targets throughout the body have involved synthesizing oligonucleotide analogs that consist of oligonucleotide analog sequences with intemucleoside linkages that differ from the 'normal' intemucleoside phosphodiester linkage, either by introducing modifications in the phosphodiester structure or by using non-phosphate intemucleoside linkages that approximate the length and orientation of the normal phosphodiester intemucleoside linkage. Uhlman, E. and Peyman, A., Chemical Reviews. 9(4):544-584 (1990).

Among the modified phosphodiester linkages that have been reported are phosphorothioates, alkylphosphotriesters, methylphosphonates and alkylphosphoramidates. Also, a variety of non-ionic oligonucleotide analogs sequences containing non-phosphate intemucleoside linkages, such as carbonate, acetate, carbamate, sulfone, sulfoxide, sulfonamide and dialkyl- or diaryl- silyl derivatives have been synthesized and reported. More recently, chimeric oligonucleotide analogs comprising nucleoside linkages containing two carbon atoms and one nitrogen atom or one oxygen atom, as well as those containing three carbon atoms, have been reported. See, e.g., International Patent Publication WO 9202534. The prior art describes 1 -mononucleosides and mononucleotides substituted at the 5'- position by a variety of substituents, 2- dinucleosides phosphates substituted at the 5'-position of the 3'-terminal nucleoside by methyl, ethyl, propyl and ally I ; it also discloses the corresponding pairs of stereoisomers (Padyukov, A, et al. (1980), Collection of Czechoslovak Chemical Communications, vol 45, 2550-2557). This reference reports that no significant differences were observed between two stereoisomers in pancreatic ribonuclease degradation. The prior art shows that rates of cleavage of δ'-substituted dinucleotide phosphates by nuclease vary unpredictably with the steric configuration at the 5'-position, the nucleoside base and the nuclease used. The prior art is, however, devoid of disclosure of the novel 5'-substituted oligonucleotides of this invention; nor does it contain any suggestion of their excellent nuclease stability or hybridization properties.

The present invention provides novel δ'-substituted nucleosides, as well as oligonucleotide analogs of two bases and longer derived therefrom which are resistant to nucleases and will bind in a sequence specific manner to complementary nucleic acid sequences. Also provided is a method of synthesizing such oligonucleotide analogs using the nucleoside derivatives described in this specification. Another advantageous feature of the present invention is the relative ease with which optically pure isomers of the 5'¹ substituted nucleoside analogs of the invention as compared to phosphorothioate, methylphosphonate and phosphoroamidate nucleosides used in the prior art to synthesize oligonucleotide analogs.

Summary of the Invention

The present invention provides novel δ'-substituted nucleoside analogs and oligonucleotide analogs of 2 to about 60 bases containing 3'-0- Pθ2H-0-δ'-CRι R2-substituted intemucleoside linkages instead of the naturally occurring phosphodiester intemucleoside linkages.

More particularly, in one aspect, the present invention provides novel nucleoside analogs having the structure of Formula I below:

Formula I wherein:

Q is selected from the group consisting of H, OH, NHR, CHO, phosphate, lower-alkyl, lower alkenyl, protected 0-, protected N-, lower alkoxy, lower alkenyloxy, benzyloxy, dimethoxytrityloxy, amino-lower alkyl, amino-lower alkoxy, N3, epoxyethyl, halogen, phosphonium salt and phosphonate;

L is selected from the group consisting of -OP(OCH2CH2CN)(N-iPr₂), H, OH, NHR, phosphate, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt, phosphonate and t-butyldimethylsilyloxy; each R is independently selected from the group consisting of H, OZ, SZ and NHZ; each R₁ and R2 is independently selected from the group consisting of H, OH, lower alkyl, lower alkenyl, lower cycloalkyl, epoxyethyl, amino lower alkyl, amino lower alkoxy, lower alkoxy and lower alkenyloxy; each R3 and R4 is independently selected from the group consisting of H, lower alkyl, lower alkenyl, lower alkoxy and lower alkenyloxy: each Z is independently selected from the group consisting of H, lower alkyl, lower alkenyl, aryl, acetyl and protecting groups for 0-, S-, and N-; each E is independently selected from the group consisting of -OP(OCH₂CH₂CN)(N-iPr₂), H, OH, NHR, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt and phosphonate; each n is independently 0 or an integer from 1 to 4; and each B is independently select from the group consisting of adenine, cytosine, guanine, thymine, uracil or a modification thereof that does not substantially interfere with the affinity of an oligonucleoside or chimeric oligonucleotide analog for its antisense counterpart wherein the bases are selected from the group consisting of adenine, cytosine, guanine, thymine and uracil; or an optical isomer thereof or a pharmaceutically acceptable salt thereof. ln another embodiment, the invention provides oligonucleotide analogs having the structure of Formula II below:

Formula II

5 wherein:

Q is selected from the group consisting of H, OH, NHR, CHO, phosphate, lower-alkyl, lower alkenyl, protected O-, protected N-, lower alkoxy, lower alkenyloxy, benzyloxy, dimethoxytrityloxy, amino-lower alkyl, amino-lower alkoxy, N3, epoxyethyl, halogen, phosphonium salt and 0 phosphonate;

L is selected from the group consisting of -OP(OCH₂CH₂CN)(N-iPr2), H, OH, NHR, phosphate, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt, phosphonate and t-butyldimethylsilyloxy; each R is independently selected from the group consisting of H, OZ,

SZ and NHZ; each R-i and R₂ is independently selected from the group consisting of H, OH, lower alkyl, lower alkenyl, lower cycloalkyl, epoxyethyl, amino lower alkyl, amino lower alkoxy, lower alkoxy and lower alkenyloxy; 0 each R3 and R4 is independently selected from the group consisting of

H, lower alkyl, lower alkenyl, lower alkoxy and lower alkenyloxy: each Z is independently selected from the group consisting of H, lower alkyl, lower alkenyl, aryl, acetyl and protecting groups for 0-, S-, and N-; each E is independently selected from the group consisting of δ -OP(OCH₂CH₂CN)(N-iPr₂), H, OH, NHR, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt and phosphonate; each n is independently 0 or an integer from 1 to 4 each B is independently selected from the group consisting of adenine, cytosine, guanine, thymine, uracil or a modification thereof that does not substantially interfere with the affinity of an oligonucleoside or chimeric oligonucleotide analog for its antisense counterpart wherein the bases are δ selected from the group consisting of adenine, cytosine, guanine, thymine and uracil; each W is selected from 3'-(OP0₂HO)C(Rι R2)-5' and a natural phosphodiester intemucleoside linkage with the proviso that at least one W is 3'-(OP0₂HO)C(Rι R2)-5'; and 0 q is 0 or an integer from 1 to 60.

As used herein, the term 'oligonucleotide' means nucleic acid compounds which contain only 'natural' phosphodiester intemucleoside linkages. On the other hand, the term 'chimeric oligonucleotide analogs' means compounds that comprise sequences containing both 'synthetic' 5 oligonucleoside linkages and oligonucleotide linkages. By the term 'oligonucleotide analogs,' we mean both oligonucleotide analogs that contain only synthetic (as opposed to the naturally occurring phosphodiester) intemucleoside linkages and chimeric oligonucleotide analogs.

The present invention also provides a method of synthesizing 0 oligonucleotide compounds having from 2 to about 60 bases and having an intemucleoside backbone containing one or more 3'-0-PO2H-0-5'-CR-| R2 intemucleoside linkages instead of the naturally occurring backbone of phosphodiester intemucleoside linkages, this process comprising joining a 5'-end nucleoside, a middle unit, and 3'-end nucleoside, by conventional δ synthetic organic procedures known in the art.

Detailed Description pf the Invention

The nucleoside analogs of the present invention have the structure of Formula I below:

Formula I wherein:

L is selected from the group consisting of -OP(OCH2CH₂CN)(N-iPr₂), H, OH, NHR, phosphate, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt, phosphonate and t-butyldimethylsilyloxy; each R is independently selected from the group consisting of H, OZ, SZ and NHZ; each R1 and R2 is independently selected from the group consisting of H, OH, lower alkyl, lower alkenyl, lower cycloalkyl, epoxyethyl, amino lower alkyl, amino lower alkoxy, lower alkoxy and lower alkenyloxy; each R3 and R4 is independently selected from the group consisting of H, lower alkyl, lower alkenyl, lower alkoxy and lower alkenyloxy: each Z is independently selected from the group consisting of H, lower alkyl, lower alkenyl, aryl, acetyl and protecting groups for 0-, S-, and N-; each E is independently selected from the group consisting of -OP(OCH₂CH₂CN)(N-iPr₂), H, OH, NHR, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt and phosphonate; each n is independently 0 or an integer from 1 to 4; and each B is independently select from the group consisting of adenine, cytosine, guanine, thymine, uracil or a modification thereof that does not substantially interfere with the affinity of an oligonucleoside or chimeric oligonucleotide analog for its antisense counterpart wherein the bases are selected from the group consisting of adenine, cytosine, guanine, thymine and uracil or a naturally occurring modification thereof; or an optical isomer thereof or a pharmaceutically acceptable salt thereof.

The oligonucleotide analogs of the invention have the structure of Formula II below:

Formula II wherein:

Q is selected from the group consisting of H, OH, NHR, CHO, phosphate, lower-alkyl, lower alkenyl, protected O-, protected N-, lower alkoxy, lower alkenyloxy, benzyloxy, dimethoxytrityloxy, amino-lower alkyl, amino-lower alkoxy, N3, epoxyethyl, halogen, phosphonium salt and phosphonate;

L is selected from the group consisting of -OP(OCH₂CH₂CN)(N-iPr₂), H, OH, NHR, phosphate, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt, phosphonate and t-butyldimethylsilyloxy; each R is independently selected from the group consisting of H, OZ, SZ and NHZ; each R1 and R₂ is independently selected from the group consisting of H, OH, lower alkyl, lower alkenyl, lower cycloalkyl, epoxyethyl, amino lower alkyl, amino lower alkoxy, lower alkoxy and lower alkenyloxy; each R3 and R4 is independently selected from the group consisting of H, lower alkyl, lower alkenyl, lower alkoxy and lower alkenyloxy: each Z is independently selected from the group consisting of H, lower alkyl, lower alkenyl, aryl, acetyl and protecting groups for 0-, S-, and N-; each E is independently selected from the group consisting of -OP(OCH₂CH₂CN)(N-iPr₂), H, OH, NHR, lower alkyl, lower alkenyl, lower 5 alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt and phosphonate; each n is independently 0 or an integer from 1 to 4 each B is independently selected from the group consisting of adenine, cytosine, guanine, thymine, uracil or a modification thereof that does not 0 substantially interfere with the affinity of an oligonucleoside or chimeric oligonucleotide analog for its antisense counterpart wherein the bases are selected from the group consisting of adenine, cytosine, guanine, thymine and uracil or a naturally occurring modification thereof; each W is selected from 3'-(OP0₂HO)C(Rι R2)-δ' and a natural δ phosphodiester intemucleoside linkage with the proviso that at least one W is 3'-(OPO₂HO)C(Rι R2)-δ'; and q is 0 or an integer from 1 to 60.

As employed above and throughout the disclosure, the following terms, unless otherwise indicated, shall be understood to have the following 0 meanings:

"Alkyl" means a saturated aliphatic hydrocarbon which may be either straight- or branched-chain. Preferred groups have no more than about 12 carbon atoms and may be methyl, ethyl and structural isomers of propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl and dodecyl. δ "Lower alkyl" means an alkyl group as above, having 1 to 7 carbon atoms. Suitable lower alkyl groups are methyl, ethyl, n-propyl, isopropyl, butyl, tert-butyl, n-pentyl, neopentyl, n-hexyl, and n-heptyl.

"Aryl" means phenyl, naphthyl, substituted phenyl and substituted naphthyl. 0 "Substituted phenyl (or naphthyl)" means a phenyl (or naphthyl) group in which one or more of the hydrogens has been replaced by the the same or different substituents selected from halo, lower alkyl, nitro, amino, acylamino, hydroxyl, lower alkoxy, aryl, heteroaryl, lower alkoxy, alkylsulfonyl, and trifluoromethyl. δ "Heteroaryl group" means, pyridyl, furyl, thienyl, or imidazolyl.

"Substituted heteroaryl" means a heteroaryl group in which one or more of the hydrogens has been replaced by the the same or different substituents selected from halo, lower alkyl, nitro, amino, acylamino, hydroxyl, lower alkoxy, aryl, heteroaryl, lower alkoxy, alkylsulfonyl, and trifluoromethyl.

"Lower alkenyl" means an unsaturated aliphatic hydrocarbon having 2 to 8 carbon atoms, such as ethylene, propylene, butylene, isobutylene, δ etc., including all structural and geometrical isomers thereof.

"Halo" means bromo, chloro or fluoro.

An "0-, S-, or N-protecting group" is a radical attached to an oxygen, sulfur, or nitrogen atom, respectively, which radical serves to protect the oxygen, sulfur, or nitrogen functionality against undesired reaction. Such 0 protecting groups are well known in the art; many are described in "The Peptides." E. Gross and J. Meienhofer, Eds. Vol 3 Academic Press, NY (1981 ). The N-protecting groups can be N-acyl, N- alkoxycarbonyl, N-arylmethoxy-carbonyl, trifluoromethylacyl and N- arylsulfonyl protecting groups. Suitable O-protecting groups include benzyl, δ tert-butyl, methyl, tosyl, dimethoxytrityl, tert-butyl-dimethylsilyl, and carbobenzoxy groups. S-Protecting groups include methyl, tert-butyl, benzyl, and carbobenzoxy groups.

The abbreviation "iPr2" as used herein refers to diisopropyl.

The present invention provides a method of synthesizing 0 oligonucleotide compounds having from 2 to about 60 bases and having an intemucleoside backbone containing one or more 3'-0-P02H-0-5'-CR-| R2 intemucleoside linkages instead of the naturally occurring backbone of phosphodiester intemucleoside linkages, this process comprising preparation of δ'-substituted nucleoside compounds, for example, as illustrated in Figure δ 1 , and utilizing them as synthons in automated DNA synthesizers.

Scheme 1 illustrates the preparation of various δ-substituted nucleoside analogs of the invention which, in turn, are useful for the preparation of 3'-0-P02H -0-δ'-C R ι R 2 linked dinucleosides and oligonucleotide analogs of the invention. As shown in Scheme 1 , (when B is 0 thymidine) 3'-t-butyldimethylsilyloxy-2'-deoxy-δ'-formyl-δ'-deoxy-thymidine 2 is a key intermediate for the preparation of various δ'-substituted nucleoside analogs of the invention, including ones containing the δ'-methyl group 5, the 5'-nitromethyl group 8, the δ'-aminomethyl group 9, the δ'-epoxy group 7, and the δ'-azidomethyl group 13. δ Thus, as shown in Scheme 1A, reaction of methylmagnesium bromide with the aldehyde 2 yields the δ'-methyl thymidine 3 which, upon treatment with dimethyltrityl chloride followed by desilylation and reaction with chloro-2-cyanoethyl-N,N-diisopropyl-phosphoramidite, affords the δ'- substituted nucleoside synthon 5. The synthon 5, may be utilized for the synthesis of δ'-modified DNA employing a DNA synthesizer such as ABI 380B Oligomer synthesizer. As shown in Scheme 1 B, the δ'-epoxy compound 7 may be prepared by the reaction of the aldehyde 2 with diazomethane, whereas the δ'-nitromethyl compound 8 may be prepared by the reaction of the aldehyde 2 with nitromethane. The chemical reduction of the nitro group with lithium aluminum hydride affords the desired δ'-aminomethyl compound 9, which may be acylated to yield the trifluoroacetyl amide 10. As illustrated in scheme 1C, azide ring opening of the epoxy compound 7 provides the corresponding azidomethyl analog 12. The amide 11 and azido analog 13 may be prepared, respectively, from compounds 10 and 12 via deprotection of t-butyldimethylsilyloxy group followed by reaction with chloro-2-cyanoethyl- N,N-diisopropyl-phosphoramidite.

Scheme 1 General Synthesis of Target Monomer (B = T) A. 5'-Alkyl Modification

2 3

B. 5'-Aminoalkyl Modification

C. 5'-Azidoalkyl Modification

12

13 This invention also contemplates pharmaceutically acceptable salts of the compounds of Formula I. It is well known in the pharmacological arts that nontoxic addition salts of pharmacologically active amine compounds do not differ in activities from their free base. All stereoisomers as δ well as optical isomers related to the novel antisense agents described in this disclosure are also considered to be within the scope of this invention.

Pharmaceutically acceptable salts include both acid and base addition salts. "Pharmaceutically acceptable salt" refers to those salts which retain the biological effectiveness and properties of the free bases and which 0 are not biologically or otherwise undesirable. Suitable pharmaceutically acceptable acid addition salts can be formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, and p-toluenesulfonic acid, and the like.

Pharmaceutically acceptable base addition salts include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the 0 like. Particularly preferred are the ammonium, potassium, sodium, calcium and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines, including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, δ tripropylami ne , ethanolami ne , 2-diethylami noethano l , 2- dimethylaminoethanol, dicyclohexylamine, lysine, arginine, histidine, caffeine, procain, hydrabamine, choline, betaine, ethylenediamine, glucosamine, methylglucamine, theobromine, purines, peperizines, piperidine, polyamine resins and the like. Particularly preferred organic non- 0 toxic bases are isopropylamine, diethylamine, ethanol-amine and dicyclohexylamine.

In one embodiment, the compounds of the present invention comprise oligomeric antisense agents, as shown in Formula II, of about 6 to about 60 bases, preferably from about 9 to about δO bases, more preferably δ from about 12 to about 2δ bases, most preferably from 1 δ to 18 bases. An important feature of this invention is that the methyl group present at the δ'- position of the sugar interferes with the hydrolysis of the phosophodiester bond by nucleases. The methyl group present at the δ'-position unexpectedly enhanced the nuclease stability. Another important feature of this invention is the discovery that the novel δ'-substituted nucleosides of the invention may be incorporated at multiple sites within an oligonucleotide analog, and have no appreciable effect on the hybridization stability of the resulting (antisense) δ oligonucleotide analog to its natural 'sense' target oligonucleotide when compared to the hybridization stability to the same 'sense' target of the corresponding unmodified antisense oligonucleotide.

These antisense agents can be formulated into compositions together with one or more non-toxic physiologically acceptable carriers, 0 adjuvants or vehicles which are collectively referred to herein as carriers, for parenteral injection or oral administration, in solid or liquid form, for rectal or topical administration, or the like.

The compositions can be administered to humans and animals either orally, rectally, parenterally (intravenous, intramuscularly or δ subcutaneously), intracistemally, intravaginally, intraperitoneally, locally (powders, ointments or drops), or as a buccal or nasal spray.

Compositions suitable for parenteral injection may comprise physiologically acceptable sterile aqueous or nonaqueous solutions, dispersions, suspensions or emulsions and sterile powders for reconstitution 0 into sterile injectable solutions or dispersions. Examples of suitable aqueous and nonaqueous carriers, diluents, solvents or vehicles include water, ethanol, polyols (propyleneglycol, polyethyleneglycol, glycerol, and the like), suitable mixtures thereof, vegetable oils (such as olive oil) and injectable organic esters such as ethyl oleate. Proper fluidity can be maintained, for δ example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersions and by the use of surfactants.

These compositions may also contain adjuvants such as preserving, wetting, emulsifying, and dispensing agents. Prevention of the action of microorganisms can be ensured by various antibacterial and antifungal 0 agents, for example, parabens, chlorobutanol, phenol, sorbic acid, and the like. It may also be desirable to include isotonic agents, for example sugars, sodium chloride and the like. Prolonged absorption of the injectable pharmaceutical form can be brought about by the use of agents that delay absorption, for example, aluminum monostearate and gelatin. δ Solid dosage forms for oral administration include capsules, tablets, pills, powders and granules. In such solid dosage forms, the active compound is admixed with at least one inert customary excipient (or carrier) such as sodium citrate or dicalcium phosphate or (a) fillers or extenders, as for example, starches, lactose, sucrose, glucose, mannitol and silicic acid, (b) binders, as for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidone, sucrose and acacia, (c) humectants, as for example, glycerol, (d) disintegrating agents, as for example, agar-agar, calcium δ carbonate, potato or tapioca starch, alginic acid, certain complex silicates and sodium carbonate, (e) solution retarders, as for example paraffin, (f) absorption accelerators, as, for example, quaternary ammonium compounds, (g) wetting agents, as for example, cetyl alcohol and glycerol monostearate, (h) adsorbents, as, for example, kaolin and bentonite, and (i) lubricants, as, 0 for example, talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate or mixtures thereof. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents.

Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules, using such excipients as lactose δ or milk sugar as well as high molecular weight polyethyleneglycols, and the like.

Solid dosage forms such as tablets, dragees, capsules, pills and granules can be prepared with coatings and shells, such as enteric coatings and others well known in the art. They may contain opacifying agents, and 0 can also be of such composition that they release the active compound or compounds in a certain part of the intestinal tract in a delayed manner. Examples of embedding compositions which can be used are polymeric substances and waxes.

The active compounds can also be in micro-encapsulated form, δ if appropriate, with one or more of the above-mentioned excipients.

Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art, such as water or other 0 solvents, solubilizing agents and emulsifiers, as for example, ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1 ,3-butyleneglycol, dimethylformamide, oils, particularly cottonseed oil, ground-nut oil, corn germ oil, olive oil, castor oil and sesame oil, glycerol, tetrahydrofurfuryl alcohol, polyethyleneglycols and δ fatty acid esters of sorbitan or mixtures of these substances, and the like. Besides such inert diluents, the composition can also include adjuvants, such as wetting agents, emulsifying and suspending agents, sweetening, flavoring and perfuming agents. Suspensions, in addition to the active compounds, may contain suspending agents, as for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, or mixtures of δ these substances, and the like.

Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of the present invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethyleneglycol or a suppository wax, which are solid at ordinary 0 temperatures but liquid at body temperature and, therefore, melt in the rectum or vaginal cavity and release the active component.

Dosage forms for topical administration include ointments, powders, sprays and inhalants. The active component is admixed under sterile conditions with a physiologically acceptable carrier and any δ preservatives, buffers or propellants as may be required. Opthalamic formulations, eye ointments, powders and solutions are also contemplated.

Actual dosage levels of the active ingredient in the compositions may be varied so as to obtain an amount of active ingredient that is effective to obtain a desired therapeutic response for a particular composition and 0 method of administration. The selected dosage level therefore depends upon the desired therapeutic effect, on the route of administration, on the desired duration of treatment and other factors.

The total daily dose of the active ingredients administered to a host in single or divided doses may be in amounts, for example, of from about δ O.δ mg to about 10 mg per kilogram of body weight. Dosage unit compositions may contain such amounts or such submultiples thereof as may be used to make up the daily dose. It will be understood, however, that the specific dose level for any particular patient will depend upon a variety of factors including the body weight, general health, sex, diet, time and route of 0 administration, rates of absorption and excretion, combination with other drugs and the severity of the particular disease being treated.

The present invention is further directed to a method of inhibiting the expression of a gene that comprises administering to a host mammal in need of such inhibition an inhibition-effective amount of a compound of δ Formula II, in which that compound hybridizes to a nucleotide sequence of the gene.whose expression is to be inhibited. In a preferred embodiment, the compound of Formula II is dissolved or dispersed in a physiologically tolerable carrier. As discussed elsewhere herein, inhibition of the expression of a gene can be effected by interfering with transcription, translation, or RNA processing. Hence, the activity of an antisense molecule can be at the level of messenger RNA or genomic DNA. So, for example, when an antisense δ molecule hybridizes to messenger RNA, translation is inhibited. When an antisense molecule hybridizes to genomic DNA, transcription is inhibited. An antisense molecule may also bind to other nucleic acid species in a cell, including heterogeneous nuclear RNA (hnRNA) and pre-messenger RNA.

A host mammal in need of the inhibition of the expression of a 0 gene suffers from a disease state in which the expression of the gene is implicated. Such disease states include a variety of cancers, in which the expression of an oncogene or oncogenes is implicated, cystic fibrosis, Huntington's chorea, and other such disease states in which the aberrant expression of a normal gene or the expression of an abnormal gene is δ responsible, in whole or in part, for the disease condition.

As used herein, an "inhibition-effective amount" is the amount of a compound of the present invention which is sufficient to inhibit the expression of the gene whose expression is to be inhibited. Means for determining an inhibition-effective amount will depend, as is well known in 0 the art, on the nature of the gene to be inhibited, the type of inhibition desired (i.e., inhibition of translation or transcription or both), the mass of the subject being treated, and the like.

It is to be understood that the compound of the Formula II used in the inhibition of the expression of a gene must hybridize to a sequence of δ that gene in such a way as the expression of that gene is inhibited. That is, the nucleotide bases used to make a compound of the Formula II (B in Formula II as defined above) must hybridize to the nucleotide sequence of the gene whose expression is to be inhibited. Such sequence can readily be ascertained from the known sequence of that gene, and the appropriate 0 antisense molecule of Formula II can therefore be prepared. Hybridization of greater than about 90 percent homology (identity), and more preferably about 99 percent homology, is contemplated in the present invention.

The following examples further illustrate the invention and are δ not to be construed as limiting of the specification and claims in any way. EXAMPLES:

Example 1 N£-Benzovl-3'-t-butvldimethvlsilvloxv-2'-deoxv-5YRS^mfithvl- adenosine δ

A solution of DMSO (2 mM, 142 μl) in methylene chloride (O.δ ml) was added to a stirred solution of oxalyl chloride (2.δ ml) at -78°C under nitrogen. After δ minutes, a solution of N6-benzoyl-3'-t-butyldimethylsilyloxy- 2'-deoxy-adenosine (1 mM, 469 mg) in DMSO/CH2CI2 (0.4 ml/1.16 ml) was 0 added over a ten minute period. Stirring was continued for 20 minutes and then triethylamine (δ mM, 700 μl) was added. The reaction mixture was stirred for an additional δ minutes. Methyl- magnesium bromide ( 3 M in ether, 2 mM, 666 μl) was added via syringe, and the reaction mixture was stirred for 1 hour at -78°C, followed by warming to room temperature δ overnight. Water was added and the mixture was extracted into chloroform (2x40 ml), washed with brine and dried over anhydrous sodium sulfate. The crude product was purified by flash chromatography (silica gel; 90% EtOAc/Hexane). Yield 390 mg (81%). Mol. Wt.:483.3 for C24H33N50S FAB- MS: (M+H)+ = 484.2. 0

Example 2 N£-Benzoyl-3'-t-butyldimethylsilyloxy-2'-deoxy-5'- dimethoxvtritvl-δ'mSVmethvl-adenosine

4,4-Dimethoxytrityl chloride (0.992 mM, 336 mg) was added to a δ solution of N⁶-benzoyl-3'-t-butyldimethylsilyloxy-2'-deoxy-δ'(RS)-methyl- adenosine (0.824 mM, 400 mg), triethylamine (1.12 mM, 1 δ6 μl) and 4- dimethylaminopyridine (0.04 mM, 4.88 mg) in pyridine/ethylene chloride (1 :1 ;

32 ml) and stirred under nitrogen at 60°C for 1 hour. Then the reaction mixture was heated to 100°C and progress of the reaction was monitored by 0 thin layer chromatography (TLC). As required, more dimethoxytrityl chloride

(2x200 mg) was added while maintaining the temperature at 100°C. The reaction was stopped after 18 hours by addition of water, extraction into ethyl acetate and drying the pooled organic layers over anhydrous sodium sulfate.

The crude product was purified by flash chromatography (silica gel; 20% δ EtOAc/Hexane). Yield: 307 mg (δ4%). Mol Wt: 78δ.3 for C45H51 N5O6SL

FAB-MS: (M+H)+ = 786.3. Example 3 N£-Benzoyl-2'-deoxy-5'-dimethoxvtritvl-57RS⁾-methyl- adenosine

Tetra-n-butyl ammonium fluoride (1 M in THF; 0.764 mM) was δ added dropwise via syringe to a solution of 3'-t-butyldimethylsilyloxy-2'- deoxy-δ'-dimethoxytrityl-δ'(RS)-methyl-adenosine (0.382 mM, 300 mg) in anhydrous THF (4 ml). The reaction was stirred under nitrogen for 6 hours at room temperature. After a standard aqueous work-up, the crude product was purified by flash chromatography (silica gel; 100% EtOAc). Yield: 260 mg 0 (97%) Mol. Wt. 671.4 for C39H37N5O6. FAB-MS: (M + H)+ = 672.4.

Example 4 N£-Benzovl-2'-deoxv-δ'-dimethoxvtritvl-5YRS -methvl- adenosine-3'-0- SH2-cvanoethvl-N.N-diisopropvl-Dhosphoramidite

5 A solution of ch loro-2-cyanoethyl-N , N-diisopropyl- phosphoramidite (0.345 mM, 66.2 μl) in anhydrous THF (2 ml) was added to a solution of Nδ-benzoyl^'-deoxy-δ'-dimethoxytrityl-δ RSJ-methyl-adenosine (0.23δ mM, 160 mg), diisopropylethylamine ( 0.92 mM, 200 μl) and 4- dimethylaminopyridine (8 mg) in anhydrous THF (2 ml), and stirred under 0 nitrogen for 3 hours. After an aqueous work-up, the crude product was purified by flash chromatography (silica gel; δ0% EtOAc/Hexane. Yield: 140 mg (68.4%) Mol. Wt.: 871.0 for C-4δH 4N7θ7P. FAB-MS: (M + H )+ = 872.3.

Example δ 3'-t-Butyldimethylsilyloxy-2'-deoxy-δ'(RS)-methyl-thvmidine δ

To a solution of 3'-t-butyldimethylsilyloxy-2'-deoxy-thymidine (14 mM, δ g) in 140 ml of methylene chloride was added at room temperature (8.98 g , 21 mmol) of Dess-Martin periodinane reagent. After 30 minutes of reaction time, the mixture was diluted with 1δ0 ml of ether, and a mixture of 0 Na2S2θ3 (19.9 g, 126 mmol) in 1 δ0 ml of saturated sodium bicarbonate was added, and stirring continued for 1 δ minutes. The reaction mixture was poured over 1 δ0 ml of ethyl acetate and the organic layer was separated, washed with saturated sodium bicarbonate solution (2x150 ml), dried over anhydrous sodium sulfate and concentrated in vacuo. The crude aldehyde in 5 600 ml of benzene was azeotroped (Dean Stark) and the solvent was removed in vacuo to afford 4 g of the crude aldehyde.

To a solution of the above aldehyde (4 g) in 1 δ0 ml of THF at -78°C was added dropwise methylmagnesium bromide in ether (3.0 M, 90 ml, 20 eq.); after stirring for 1 hour, the reaction mixture was poured over a mixture of 1000 ml of ice/saturated ammonium chloride and 10 ml of acetic acid. The resulting mixture was extracted with ethyl acetate (δx200 ml) and the organic layer was washed with saturated sodium bicarbonate (2x4δ0 ml) and brine (1 x4δ0 ml), dried over anhydrous sodium sulfate and concentrated in vacuo. The product was purified by flash chromatography (100 g silica gel; δ0% EtOAc/Hexane). Yield: 1.93 g.

Example 6 3'-t-Butyldimethylsilyloxy-2'-deoxy-δ'-dimethoxytrityl-δ7RS^- methvl-thvmidine

To a solution of 3'-t-butyldimethylsilyloxy-2'-deoxy-δ'(RS)- methyl-thymidine (300 mg, 0.8 mmol) in 2.7 ml of pyridine at room temperature was added 98 mg (1 eq.) of dimethylamino-pyridine, 0.6 ml (5 eq.) of triethylamine and 1.37 g (5 eq.) of dimethoxytrityl chloride. The reaction mixture was allowed to react at 7δ°C overnight. The mixture was diluted with ethyl acetate, washed with water, followed by saturated ammonium chloride solution, and the organic layer was dried with anhydrous sodium sulfate and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel; 30% EtOAc/Hexane). Yield: 22δ mg.

Example 7 2'-Deoxy-5'-dimethoxytrityl-5ΪRS -methyl-thvmidine

Tetra-n-butyl ammonium fluoride (1.1 M in THF; 0.68 mM, 0.9 ml) was added dropwise via syringe to a solution of 3'-t-butyldimethylsilyloxy-2'- deoxy-δ'-dimethoxytrityl-δ'(RS)-methyl-thymidine (0.68 mM, 460 mg) in anhydrous THF (3.44 ml). The reaction was stirred under nitrogen for 4 hours at room temperature. After a standard aqueous work-up the crude product was purified by flash chromatography (silica gel; 60 - 7δ% EtOAc/Hexane). Yield: 340 mg (92%). Example 8 2'-Deoxy-5'-dimethoxytrityl-5' S methyl-thvmidine-3'-0-(RSW2- cyanoethyl-N.N-diisopropyl-phosphoramidite)

To a solution of 2'-deoxy-5'-dimethoxytrityl-δ'(RS)-methyl- δ thymidine (0.δ8 mM, 320 mg) in 6 ml of methylene chloride at -40°C was added diisopropylethylamine (1.5 eq., 1 δδ mg), followed by chloro-2- cyanoethyl-N,N-diisopropyl-phosphoramidite (170 mg, 1.3 eq.). The reaction mixture was stirred at -30°C for 2 hours, and at 0°C for two additional hours. Methanol (0.1 ml) was added to the mixture and the resulting reaction mixture 0 was stirred at 0°C for 1/2 hour, diluted with ethyl acetate, and washed with saturated ammonium chloride solution. The organic layer was dried over anhydrous sodium sulfate and concentrated in vacuo. The crude product was purified by flash chromatography (silica gel; 40% EtOAc/Hexane). Yield: 376 mg (65%). 5

Example 9 3'-t-Butyldimethylsilyloxy-2'-deoxy-57RSH1 -carbmethoxy-1 - phenylsulfonyπmethyl-thvmidine

To the crude aldehyde from Example δ (3 mmol) was added 0 dropwise at -78°C a solution of sodium methyl phenylsulfonylacetate in 6 ml of THF. After allowing the mixture to react at -78°C overnight, the reaction mixture was worked-up according to the procedure described in Example δ.

The product was purified by flash chromatography (silica gel; δ0%

EtOAc/Hexane). FAB-MS: (M + H )+ = δ69. δ

Example 10 3'-t-Butyldimethylsilyloxy-2'-deoxy-5'-epoxyethyl-5'-deoxy- thvmidine

The crude aldehyde from Example δ (O.δ mmol) was added 0 dropwise via syringe at -78°C to a solution of diazomethane (approx. 1.δ mmol) in ether. After 2 hours of reaction time, the mixture was allowed to stand at -78°C for overnight. The reaction mixture was worked-up according to the procedure described in Example δ. The product was purified by flash chromatography (silica gel; δ0% EtOAc/Hexane). Yield: 100 mg. FAB-MS δ shows the desired mol ion for the title epoxide. Example 1 1 Oligomer Synthesis Using 2'-Deoxy-5'-dimethσxytrityl-5ΪRS^- methyl-thvmidine-3'-O-(RSH2-cyanoethyl-N.N-diisopropyl-phosphoramidite^

The synthesis of the oligomers listed in Table 1 was conducted 5 using an ABI 380B synthesizer in accordance with the manufacturer's protocols. Synthesis of strands at one micromole scale using monomer (e.g., 2'-deoxy-δ'-dimethoxytrityl-δ'(RS)-methyl-thymidine-3'-0-(RS)-(2-cyanoethyl- N,N-diisopropyl-phosphoramidite) was carried out. Monomer was dried just before DNA synthesis. The purification of DNA product was conducted with 0 DMT + reverse phase HPLC with slicing through major peak.

TABLE 1

Oligomer Sequence number δ 1 δ'-TTT TTT TTT T^*T-3' (SEQ ID NO:1 )

2 δ'-TTT TTT TTT TT-3' (SEQ ID NO:2)

3 δ'-TTT TTT TT ^*T^*T-3' (SEQ ID NO:3)

4 δ'-TTT TTT^* TTT TT-3' (SEQ ID NO:4) δ δ'-TT^*T TTT^* TTT ^*TT^*T-3' (SEQ ID NO:δ) 0 6 δ'-GGG TGT GTG T^*TA GCG GG-3' (SEQ ID NO:6)

7 δ'-GGG TGT GTG TT^*A GCG GG-3' (SEQ ID N0.7)

8 δ'-GGG TGT GTG^* T^*T^*A GCG GG-3' (SEQ ID

NO:8) δ'-CCC GC^*T ^*A^*A CAC ACA CCC-3' (SEQ ID δ NO:9)

In the above Table 1 , the ^* in the sequence signifies the location of a δ'-methyl-phosphodiester bond instead of a natural phosphodiester bond. 0

Example 11 Analysis of Nuclease Stability

For the nuclease stability studies, oligonucleotides were labelled at the δ' terminus with ³²P by using T4 polynucleotide kinase and δ standard end-labelling procedures. Unincorporated ³²P-ATP was removed by passing over a NucTrap column followed by purification over Sephadex G- 2δ. A trace (1-1 OμM) of ³²P-labelled oligonucleotide was combined with unlabelled oligomer at a concentration of 1 μM. These conditions minimize any variation incurred due to differences in oligomer labelling efficiencies and simulate concentrations used in typical antisense experiments. The oligomer was added to Dulbecco's minimal essential medium (DMEM) cell culture media containing 20% fetal calf serum (FCS) which serves as a source of 3' δ exonuclease activity. After incubation at 37°C for 2.δ hours, the mixture was denatured for 2 minutes at 90°C and analyzed by denaturing polyacrylamide gel electrophoresis (PAGE; 20% polyacrylamide/8 M urea; 19:1 acrylamide:bis-acrylamide; 89 mM Tris/89 mM boric acid/2 mM EDTA). As a 0 hour control, the oligonucleotide was added to serum-free DMEM media prior 0 to PAGE analysis. Gels were dried between sheets of cellulose drying film, imaged, and quantitative data obtained using a Phosphorimager. The gel lanes demonstrate the effect observed for the various modified oligonucleotides as compared to the control phosphodiester oligomer. Multiple reactions were run for each oligonucleotide, and the results proved to δ be reproducible. Furthermore, more dramatic results were obtained in experiments in which only a trace of ³²P-labelled oligonucleotide (i.e., 1 -10 μM total oligomer) was added to media containing 10% or 20% FCS.

Oligodeoxynucleotide #1 (δ'-TT TTT TTT TT^*T-3'; SEQ ID NO:1 ; containing a 3'-end cap modification with a methyl group at the δ' carbon of 0 the sugar at the penultimate thymidylate residue) was added to a final concentration of 3 nM to tubes on ice containing RPMI 1640 media with L- glutamine (GIBCO). Also added were: HEPES (GIBCO) to a final concentration of 20 mM, and fetal bovine serum to 10%. Total reaction volume was 400 μl. Tubes which were incubated for 0 time (controls) did not δ receive serum. Tubes were incubated at 37°C for 5, 30, 60, and 120 minutes. Time 0 tubes were kept on ice. An extra 120 min reaction lacking serum was also incubated at 37°C as a control to check for chemical degradation of the oligomer. As a positive control, d(T)ι 1 oligodeoxynucleotide (Oligomer #2

(SEQ ID NO:2), prepared in the same manner as the other, experimental 0 oligomers) was assayed at time 0 and at 120 minutes without serum.

Reactions were stopped by extraction with equal volumes of a 24:1 mixture of chloroform and isoamyl alcohol, five times. The final aqueous layer was filtered through a Spin-X, 0.22 μM cellulose acetate filter unit. Fifty microliters of final sample, kept at 4°C, was loaded onto a Gen Pak Fax 5 anionic exchange column by automatic injection, and eluted in 15 mM sodium phosphate, 1 mM EDTA mobile phase, pH 8.0, with a 0-0.5 M NaCI gradient utilizing a LKB HPLC system. The gradient went from 0 to 0.4 M NaCI in 5δ minutes, was held to 60 minutes, increase to O.δ M NaCI at 6δ minutes, and held to 70 minutes. Elution was monitored at 269 nm.

Parent oligomer and reaction product peaks were integrated for peak areas. Peak retention times were compared to controls and d(T) δ oligomer standards that had been previously analyzed on this HPLC system.

The results of the assay show that the parent oligomer (Oligomer #1 , an 11- mer (retention time of 41.76 min)), was rapidly digested, by 3'->δ' exonucleolytic activity present in the 10% fetal bovine serum. The product was an extremely stable, N-1 reaction product, a 10-mer (retention time of 0 38.64 min), the result of cleavage of the 3'-terminal thymidylate residue by the enzyme. The 10-mer remained undigested for up to 120 minutes in the presence of serum, based on the resulting peak areas.

Thus, the 3'-modification provides protection to the remaining oligomer against further digestion by inhibiting the activity of the 3'->δ' exonuclease present in the serum. It is concluded that the methyl group present at the δ' position of the sugar interferes with the hydrolysis of the phosophodiester bond by the nuclease enzyme.

Example 13 Hybridization fTm) Testing 0

Two nanomoles of each of the 17-mer antisense oligonucleotides of Table 1 (oligomer numbers 6, 7, 8 and 9) were combined with two nanomoles of their respective complementary sense strands in a buffer containing δ0 mM Na2HPθ4/100 mM NaCI/1 mM EDTA, denatured at δ 8δ°C, and annealed by slow cooling to room temperature. The annealed DNA was heated from 3δ°C to 8δ°C and absorbance data at 260 nM collected at 0.2 °C intervals. From this data, melting curves were generated and values for melting temperature (Tm) derived.

The T_m for the sense and antisense control (normal, unmodified 0 phosphodiester [PDE]) strands annealed together is 68 +/- O.δ degrees. The T_m for each of Oligomers 6 (SEQ ID NO:6) and 7 (SEQ ID NO:7) was 68°C. The Tm observed for Oligomer # 8 (SEQ ID NO:8) annealed with sense PDE strand was 67.8 degrees. The T_m for Oligomers 8 (SEQ ID NO:8) and 9 (SEQ ID NO:9) annealed together is 66.8 degrees. The results show that there is δ virtually no loss of duplex stability when the normal PDE bond is replaced with this substituted PDE bond. The results further show that the methyl-PDE bond does not at all interfere in Watson Crick base paring even when both members of the pair that anneal to each other are methyl-PDE modified (i.e., Oligomers 8 and 9). This result indicates that the racemic δ'-methyl analogs of nucleosides can be incorporated at multiple sites within an oligonucleotide, and have essentially no effect on hybridization stability.

δ SEQUENCE LISTING

(1 ) GENERAL INFORMATION:

0 (i) APPLICANT: Saha, Ashis

(ii) TITLE OF INVENTION: NOVEL δ' SUBSTITUTED NUCLEOSIDES AND OLIGOMERS PRODUCED THEREFROM

6 (iii) NUMBER OF SEQUENCES: 9

(iv) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: Sterling Winthrop, Inc.

(B) STREET: 9 Great Valley Parkway 0 (C) CITY: Malvern

(D) STATE: PA

(E) COUNTRY: USA (F) ZIP: 193δδ

δ (v) COMPUTER READABLE FORM:

(A) MEDIUM TYPE: Floppy disk

(B) COMPUTER: IBM PC compatible

(C) OPERATING SYSTEM: PC-DOS/MS-DOS

(D) SOFTWARE: Patentln Release #1.0, Version #1.25 0

(vi) CURRENT APPLICATION DATA:

(A) APPLICATION NUMBER:

(B) FILING DATE:

(C) CLASSIFICATION: 5 (viii) ATTORNEY/AGENT INFORMATION:

(A) NAME: Newman, Irving

(B) REGISTRATION NUMBER: 22,638

(C) REFERENCE/DOCKET NUMBER: PRF 161 δ

(ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: (21 δ) 889-8824

0 (2) INFORMATION FOR SEQ ID NO:1 :

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 11 base pairs

(B) TYPE: nucleic acid δ (C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic)

0 (ix) FEATURE:

(A) NAME/KEY: misc eature

(B) LOCATION: (10^Λ11)

(D) OTHER INFORMATION: /note= "The bases are linked by a δ'-methyl-phosphodiester bond." δ

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:1 :

I I I I I I I I I I T 11 0

(2) INFORMATION FOR SEQ ID NO:2:

(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 11 base pairs δ (B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic)

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:

I I I I I I I I I I T 11

(2) INFORMATION FOR SEQ ID NO:3: 0

(i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 10 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single δ (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic)

0 (ix) FEATURE:

(A) NAME/KEY: misc eature

(B) LOCATION: (8^Λ9)

(ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (9^Λ10)

(D) OTHER INFORMATION: /note= "The bases are linked by a 0 δ'-methyl-phosphodiester bond."

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:

δ U N I I I I I I 10 (2) INFORMATION FOR SEQ ID N0:4: (i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 11 base pairs

(B) TYPE: nucleic acid δ (C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic)

0

(ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (6^Λ7)

(D) OTHER INFORMATION: /note= "The bases are linked by a δ δ'-methyl-phosphodiester bond."

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:

0 I I I I I I I I I I T 11

(2) INFORMATION FOR SEQ ID NO:δ:

(i) SEQUENCE CHARACTERISTICS: δ (A) LENGTH: 12 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

0 (ii) MOLECULE TYPE: DNA (genomic)

(ix) FEATURE:

(A) NAME/KEY: miscjeature δ (B) LOCATION: (2^Λ3)

(D) OTHER INFORMATION: /note= "The bases are linked by a δ'-methyl-phosphodiester bond." (ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (δ^Λ6)

(ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (6^Λ7) 0 (D) OTHER INFORMATION: /note- "The bases are linked by a δ'-methyl-phosphodiester bond."

(ix) FEATURE:

(A) NAME/KEY: miscjeature 5 (B) LOCATION: (9^Λ10)

(D) OTHER INFORMATION: /note- "The bases are linked by a δ'-methyl-phosphodiester bond."

(ix) FEATURE: 0 (A) NAME/KEY: miscjeature

(B) LOCATION: (10^Λ11 )

(D) OTHER INFORMATION: /note= "The bases are linked by a δ'-methyl-phosphodiester link."

δ (ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (11 ^Λ12)

(D) OTHER INFORMATION: /note= "The bases are linked by a δ'-methyl-phosphodiester bond." 0

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:δ:

I I I I I I I I I I TT 12 δ

(2) INFORMATION FOR SEQ ID NO:6: (i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 17 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single δ (D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic)

(ix) FEATURE: 0 (A) NAME/KEY: miscjeature

(B) LOCATION: (10^Λ11)

(D) OTHER INFORMATION: /note= "The bases are linked by a δ'-methyl-phosphodiester bond."

δ (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:

GGGTGTGTGT TAGCGGG 17

(2) INFORMATION FOR SEQ ID NO:7:

0 (i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 17 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear δ

(ii) MOLECULE TYPE: DNA (genomic)

(ix) FEATURE:

(A) NAME/KEY: miscjeature 0 (B) LOCATION: (11 ^Λ12)

δ (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:

GGGTGTGTGT TAGCGGG 17 (2) INFORMATION FOR SEQ ID NO:8: (i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 17 base pairs

(B) TYPE: nucleic acid δ (C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(ii) MOLECULE TYPE: DNA (genomic)

0 (ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (9^Λ10)

(ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (10^Λ11 )

(ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (11 ^Λ12) δ (D) OTHER INFORMATION: /note= "The bases are linked by a δ'-methyl-phosphodiester bond."

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:

0 GGGTGTGTGT TAGCGGG 17

(2) INFORMATION FOR SEQ ID NO:9:

(i) SEQUENCE CHARACTERISTICS: δ (A) LENGTH: 17 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic)

(ix) FEATURE: δ (A) NAME/KEY: miscjeature

(B) LOCATION: (δ^Λ6)

0 (ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (6^Λ7)

(ix) FEATURE:

(A) NAME/KEY: miscjeature

(B) LOCATION: (7^Λ8)

(xi) SEQUENCE DESCRIPTION:SEQ ID NO:9: CCCGCTAACACACACCC 17

Claims

WE CLAIM:

1. A compound having the structural formula:

Formula I δ wherein:

Q is selected from the group consisting of H, OH, NHR, CHO, phosphate, lower-alkyl, lower alkenyl, protected 0-, protected N-, lower alkoxy, lower alkenyloxy, benzyloxy, dimethoxytrityloxy, amino-lower alkyl, amino-lower alkoxy, N3, epoxyethyl, halogen, phosphonium salt and 0 phosphonate;

L is selected from the group consisting of -OP(OCH2CH2CN)(N-iPr2), H, OH, NHR, phosphate, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt, phosphonate and t-butyldimethylsilyloxy; δ each R is independently selected from the group consisting of H, OZ,

SZ and NHZ; each R-i and R2 is independently selected from the group consisting of H, OH, lower alkyl, lower alkenyl, lower cycloalkyl, epoxyethyl, amino lower alkyl, amino lower alkoxy, lower alkoxy and lower alkenyloxy; 0 each R3 and R₄ is independently selected from the group consisting of

H, lower alkyl, lower alkenyl, lower alkoxy and lower alkenyloxy: each Z is independently selected from the group consisting of H, lower alkyl, lower alkenyl, aryl, acetyl and protecting groups for 0-, S-, and N-; each E is independently selected from the group consisting of 6 -OP(OCH₂CH₂CN)(N-iPr2), H, OH, NHR, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt and phosphonate; each n is independently 0 or an integer from 1 to 4; and each B is independently select from the group consisting of adenine, 0 cytosine, guanine, thymine, uracil or a modification thereof that does not substantially interfere with the affinity of an oligonucleoside or chimeric oligonucleotide analog for its antisense counterpart wherein the bases are selected from the group consisting of adenine, cytosine, guanine, thymine and uracil; or an optical isomer thereof or a pharmaceutically acceptable salt thereof.

2. A compound having the structural formula II below:

Formula II

wherein: 0 Q is selected from the group consisting of H, OH, NHR, CHO, phosphate, lower-alkyl, lower alkenyl, protected 0-, protected N-, lower alkoxy, lower alkenyloxy, benzyloxy, dimethoxytrityloxy, amino-lower alkyl, amino-lower alkoxy, N3, epoxyethyl, halogen, phosphonium salt and^' phosphonate; δ L is selected from the group consisting of -OP(OCH2CH2CN)(N-iPr2),

H, OH, NHR, phosphate, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt, phosphonate and t-buty Idi methylsi l loxy ; each R is independently selected from the group consisting of H, OZ, 0 SZ and NHZ; each R-i and R2 is independently selected from the group consisting of H, OH, lower alkyl, lower alkenyl, lower cycloalkyl, epoxyethyl, amino lower alkyl, amino lower alkoxy, lower alkoxy and lower alkenyloxy; each R3 and R4 is independently selected from the group consisting of δ H, lower alkyl, lower alkenyl, lower alkoxy and lower alkenyloxy: each Z is independently selected from the group consisting of H, lower alkyl, lower alkenyl, aryl, acetyl and protecting groups for 0-, S-, and N-; each E is independently selected from the group consisting of -OP(OCH2CH₂CN)(N-iPr₂), H, OH, NHR, lower alkyl, lower alkenyl, lower alkoxy, lower alkenyloxy, amino-lower alkyl, amino-lower alkoxy, N3, halogen, epoxyethyl, phosphonium salt and phosphonate; 5 each n is independently 0 or an integer from 1 to 4 each B is independently selected from the group consisting of adenine, cytosine, guanine, thymine, uracil or a modification thereof that does not substantially interfere with the affinity of an oligonucleoside or chimeric oligonucleotide analog for its antisense counterpart wherein the bases are 0 selected from the group consisting of adenine, cytosine, guanine, thymine and uracil; each W is selected from 3'-(OPθ2HO)C(Rι R2)-δ' and a natural phosphodiester intemucleoside linkage with the proviso that at least one W is 3'-(OP0₂HO)C(Rι R2)-δ'; and δ q is 0 or an integer from 1 to 60.

3. The compound of claim 2, wherein W is 3'-(0-Pθ2H-0)-δ'-

CH(CH₃)-.

4. The compound of claim 2, wherein at least one W is a natural 0 phosphodiester intemucleoside linkage.

δ. The compound of claim 2, wherein q is 2, 3 or 4.

6. The compound of claim 2, wherein q is from 9 to δO. δ

7. The compound of claim 2, wherein q is from 12 to 2δ.

8. The compound of claim 2, wherein q is from 15 to 18.

0 9. A method of synthesizing oligonucleotide compounds having from 2 to about 60 bases and having an intemucleoside backbone containing one or more 3'-0-P02H-0-5'-CR-| R2 intemucleoside linkages instead of the naturally occurring backbone of phosphodiester intemucleoside linkages, this process comprising using a compound of claim 1 as a synthon in a δ conventional synthetic organic process for synthesizing oligonucleotides.

10. The method of claim 9, wherein the synthesis is carried out in an automated DNA synthesizer.

11. A method of inhibiting the expression of a gene that comprises administering to a host mammal in need of such inhibition an inhibition-effective amount of a compound of claim 2, said compound δ hybridizing to a nucleotide sequence of said gene.

12. A pharmaceutical composition comprising a compound of claim 2 dissolved or dispersed in a physiologically tolerable carrier.