Oligoribonucleotides and ribonucleases for cleaving RNA

• US 7,432,249 B2
• Filed: 10/25/2002
• Issued: 10/07/2008
• Est. Priority Date: 06/06/1996
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Crooke, Stanley T.
• Primary Examiner(s): MCGARRY, SEAN
• Application Number:
  US10/281,297
• Publication Number:
  US 20030119777A1
• Time in Patent Office: 2,174 Days
• Field of Search: None
• US Class Current: 514/44.00A
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: A61P 9/10 for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 2310/311 Phosphotriesters
• CPC Class Codes: C12N 2310/312 Phosphonates
• CPC Class Codes: C12N 2310/314 Phosphoramidates
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/316 Phosphonothioates
• CPC Class Codes: C12N 2310/318 where the PO2 is completely replaced, e.g. MMI or formacetal
• CPC Class Codes: C12N 2310/3181 Peptide nucleic acid, PNA
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/335 Modified T or U
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/346 : having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3521 : Methyl
• CPC Class Codes: C12N 2310/3525 : MOE, methoxyethoxy
• CPC Class Codes: C12N 2310/3527 : Other alkyl chain
• CPC Class Codes: C12N 9/22 : Ribonucleases RNAses, DNAses catalytic nucleic acids C12N15/113
• CPC Class Codes: Y02A 50/30 : Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
• CPC Class Codes: Y02P 20/582 : Recycling of unreacted starting or intermediate materials

Abstract

Oligomeric compounds including oligoribonucleotides and oligoribonucleosides are provided that have subsequences of 2′-pentoribofuranosyl nucleosides that activate dsRNase. The oligoribonucleotides and oligoribonucleosides can include substituent groups for increasing binding affinity to complementary nucleic acid strand as well as substituent groups for increasing nuclease resistance. The oligomeric compounds are useful for diagnostics and other research purposes, for modulating the expression of a protein in organisms, and for the diagnosis, detection and treatment of other conditions susceptible to oligonucleotide therapeutics. Also included in the invention are mammalian ribonucleases, i.e., enzymes that degrade RNA, and substrates for such ribonucleases. Such a ribonuclease is referred to herein as a dsRNase, wherein “ds” indicates the RNase'"'"'s specificity for certain double-stranded RNA substrates. The artificial substrates for the dsRNases described herein are useful in preparing affinity matrices for purifying mammalian ribonuclease as well as non-degradative RNA-binding proteins.

Claims

1. A composition comprising a pharmaceutically acceptable diluent or carrier and a single-stranded oligomeric compound, wherein said compound:

is 15 to 25 nucleoside subunits in length;

specifically hybridizes with a preselected target RNA;

comprises at least four consecutive nucleosides with 2′

-hydroxyl-pentofuranosyl sugar moieties; and

further comprises at least one sugar modified nucleoside subunit, wherein the modification improves affinity or specificity of said compound to said target RNA or increases resistance of said compound to single-stranded nucleases.

2. The composition of claim 1 wherein said compound further comprises at least one modified internucleoside linkage that is more stable to degradation than is a phosphodiester linkage.

3. The composition of claim 2 wherein said modified internucleoside linkage of said compound is phosphorothioate.

4. The composition of claim 3 wherein each internucleoside linkage of said compound is phosphorothioate.

5. The composition of claim 1 wherein said compound comprises four to twelve consecutive nucleosides each having a 2′

-hydroxyl-pentofuranosyl sugar moiety.

6. The composition of claim 5 wherein said compound comprises five to nine consecutive nucleosides each having a 2′

-hydroxyl-pentofuranosyl sugar moiety.

7. The composition of claim 1 wherein said compound comprises at least two nucleoside subunits with 2′

modifications.

8. The composition of claim 7 wherein the 2′

modifications of said compound are fluoro, C₁-C₂₀ alkoxy, C₁-C₉ aminoalkoxy, allyloxy, imidazolylalkoxy or polyethylene glycol.

9. The composition of claim 8 wherein at least one 2′

modification of said compound is 2′

-O-methoxyethyl.

10. The composition of claim 8 wherein at least one 2′

modification of said compound is 2′

-O-methyl.

11. The composition of claim 8 wherein at least one 2′

modification of said compound is 2′

-fluoro.

12. The composition of claim 1 wherein the modified nucleoside subunits of said compound are located at the 3′

terminus or 5′

terminus of the compound.

13. The composition of claim 1 wherein said compound comprises nucleoside subunits with 2′

-hydroxyl-pentofuranosyl sugar moieties positioned between two segments of modified nucleoside subunits.

14. The composition of claim 1 wherein said compound is 100% complementary to said target RNA.

15. The composition of claim 1 wherein said compound is 17 to 20 nucleoside subunits in length.

16. A composition comprising a pharmaceutically acceptable diluent or carrier and a single-stranded oligomeric compound, wherein said compound:

is 15 to 25 nucleoside subunits in length;

is specifically hybridizable with a preselected target RNA;

comprises at least one sugar modification; and

comprises a plurality of nucleoside subunits with 2′

-hydroxyl pentofuranosyl sugar moieties.

17. The composition of claim 16 wherein said sugar modification increases resistance of said compound to single-stranded nucleases or increases affinity of said compound to said target RNA.

18. The composition of claim 16 wherein at least one sugar modification is a 2′

-substituted sugar modification.

19. The composition of claim 16 wherein at least one sugar modification is a 2′

-alkoxy sugar modification.

20. The composition of claim 16 wherein at least one sugar modification is a 2′

-methoxy sugar modification.

21. The composition of claim 16 wherein at least one sugar modification is a 2′

-fluoro sugar modification.

22. The composition of claim 16 wherein at least one sugar modification is a 2′

-O-methoxyethyl sugar modification.

23. The composition of claim 16 wherein said compound further comprises at least one modified internucleoside linkage.

24. The method of claim 23 wherein said modified internucleoside linkage is a phosphorothioate.

25. The method of claim 24 wherein each internucleoside linkage of said compound is phosphorothioate.

26. The composition of claim 16 wherein said compound is 100% complementary to said target RNA.

27. The composition of claim 16 wherein said compound is 17 to 20 nucleoside subunits in length.