RNA interference mediated inhibition of gene expression using chemically modified short interfering nucleic acid (siNA)

• US 20070004667A1
• Filed: 08/11/2006
• Published: 01/04/2007
• Est. Priority Date: 02/20/2002
• Status: Abandoned Application

• Current Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Original Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Thompson, James, Beigelman, Leonid, Chen, Tongqian, Wang, Weimin, McSwiggen, James, Vargeese, Chandra, Zinnen, Shawn, Haeberli, Peter, Morrissey, David, Usman, Nassim, Jamison, Sharon, Chowrira, Bharat, Macejak, Dennis, Fosnaugh, Kathy, Vaish, Narendra, Pavco, Pamela
• Application Number:
  US11/502,875
• Publication Number:
  US 20070004667A1
• Time in Patent Office: Days
• US Class Current: 514/44.A
• CPC Class Codes: A61K 47/544 Phospholipids
• CPC Class Codes: A61K 47/549 Sugars, nucleosides, nucleotides or nucleic acids
• CPC Class Codes: A61K 47/554 the modifying agent being a steroid plant sterol, glycyrrhetic acid, enoxolone or bile acid
• CPC Class Codes: A61K 9/0019 Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner non-active ingredients are additionally classified in A61K47/00
• CPC Class Codes: C07F 9/65616 containing the ring system having three or more than three double bonds between ring members or between ring members and non-ring members, e.g. purine or analogs
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/317 with an inverted bond, e.g. a cap structure
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/351 Conjugate
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/51 modulating the chemical stability, e.g. nuclease-resistance
• CPC Class Codes: C12N 2330/30 chemically synthesised
• 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

Abstract

The present invention concerns methods and reagents useful in modulating gene expression in a variety of applications, including use in therapeutic, diagnostic, target validation, and genomic discovery applications. Specifically, the invention relates to synthetic chemically modified small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against target nucleic acid sequences. The small nucleic acid molecules are useful in the treatment of any disease or condition that responds to modulation of gene expression or activity in a cell, tissue, or organism.

Claims

1. A chemically synthesized double stranded short interfering RNA (siRNA) molecule comprising a sense strand and an antisense strand having structure:

5. The siRNA molecule of any of claims 1-4, wherein each N, or each N and N, of the antisense strand is complementary to a target RNA sequence.

6. The siRNA molecule of any of claims 1-4, wherein each N, or each N and N, but excluding (N N), of the antisense strand is complementary to a target RNA sequence.

7. The siRNA molecule of any of claims 1-4, wherein (N N) is absent.

8. The siRNA molecule of any of claims 1-4, wherein (N N) of the antisense strand, when present, further comprises a phosphorothioate internucleotide linkage.

9. The siRNA molecule of any of claims 1-4, wherein (N N) of the sense strand, when present, further comprises a phosphorothioate internucleotide linkage.

10. The siRNA molecule of any of claims 1-4, wherein each B is independently selected from the group consisting of deoxyabasic moiety, inverted deoxyabasic moiety, LNA, or inverted nucleotide.

11. The siRNA molecule of claim 7, wherein each B is independently selected from the group consisting of deoxyabasic moiety, inverted deoxyabasic moiety, LNA, or inverted nucleotide.

12. The siRNA molecule of any of claims 1-4, wherein said base-pair is a canonical base pair.

13. The siRNA molecule of any of claims 1-4, wherein said base-pair is a non-canonical base pair.

14. The siRNA molecule of claim 6, wherein the target RNA sequence is a mammalian RNA sequence.

15. The siRNA molecule of claim 6, wherein the target RNA sequence is a viral RNA sequence.

16. The siRNA molecule of claim 15, wherein said viral RNA is selected from the group consisting of hepatitis C virus (HCV), hepatitis B virus (HBV), human immunodeficiency virus (HIV);

respiratory syncytial virus (RSV);

human papilloma virus (HPV); and

herpes simplex virus (HSV).

17. A composition comprising the siRNA molecule of any of claims 1-4 in a carrier or diluent.

18. A cell comprising the siRNA molecule of any of claims 1-4.

2. A chemically synthesized double stranded short interfering RNA (siRNA) molecule comprising a sense strand and an antisense strand having structure:

3. A chemically synthesized double stranded short interfering RNA (siRNA) molecule comprising a sense strand and an antisense strand having structure:

4. A chemically synthesized double stranded short interfering RNA (siRNA) molecule comprising a sense strand and an antisense strand having structure: