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

• US 20050020525A1
• Filed: 01/14/2004
• Published: 01/27/2005
• Est. Priority Date: 02/20/2002
• Status: Abandoned Application

• Current Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated), Icn. Sima Therapeutics
• Original Assignee: Sirna Therapeutics, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Vaish, Narendra, Chen, Tonqian, Morissey, David, Thompson, James, Beigelman, Leonid, McSwiggen, James, Vargeese, Chandra, Zinnen, Shawn, Haeberli, Peter, Usman, Nassim, Jamison, Sharon, Chowrira, Bharat, Macejak, Dennis, Fosnaugh, Kathy, Wang, Weimen, Pavco, Pamela
• Application Number:
  US10/757,803
• Publication Number:
  US 20050020525A1
• Time in Patent Office: Days
• US Class Current: 514/44.A
• 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: A61K 47/544 Phospholipids
• CPC Class Codes: A61K 47/549 Sugars, nucleosides, nucleotides or nucleic acids
• CPC Class Codes: A61K 47/551 one of the codrug's components being a vitamin, e.g. niacinamide, vitamin B3, cobalamin, vitamin B12, folate, vitamin A or retinoic acid
• CPC Class Codes: A61K 47/554 the modifying agent being a steroid plant sterol, glycyrrhetic acid, enoxolone or bile acid
• CPC Class Codes: A61K 47/59 obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
• CPC Class Codes: A61K 47/60 the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
• CPC Class Codes: A61K 47/64 Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent peptidic linkers A61K47/65
• CPC Class Codes: A61K 47/645 Polycationic or polyanionic oligopeptides, polypeptides or polyamino acids, e.g. polylysine, polyarginine, polyglutamic acid or peptide TAT
• CPC Class Codes: A61K 49/0008 Screening agents using (non-human) animal models or transgenic animal models or chimeric hosts, e.g. Alzheimer disease animal model, transgenic model for heart failure
• 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 15/87 Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
• CPC Class Codes: C12N 2310/111 spanning the whole gene, or a large part of it
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/141 MicroRNAs, miRNAs
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/318 where the PO2 is completely replaced, e.g. MMI or formacetal
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/332 Abasic residue
• 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 2310/53 : partially self-complementary or closed

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 double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence is chemically modified in a manner that said second sequence can no longer act as a guide sequence for mediating RNA interference.

2. The siNA molecule of claim 1, wherein said second sequence does not have a terminal 5′

-hydroxyl (5′

-OH) or 5′

-phosphate group.

3. The siNA molecule of claim 1, wherein said second sequence comprises a terminal cap moiety at the 5′

-end of said second sequence.

4. The siNA molecule of claim 1, wherein said second sequence comprises a terminal cap moiety at the 5′

-end and 3′

-end of said second sequence.

5. The siNA molecule of claim 3, wherein said terminal cap moiety is an inverted deoxyabasic moiety.

6. The siNA molecule of claim 4, wherein said terminal cap moiety is an inverted deoxyabasic moiety.

7. The siNA molecule of claim 1, wherein said siNA molecule comprises no ribonucleotides.

8. The siNA molecule of claim 1, wherein said siNA molecule comprises ribonucleotides.

9. The siNA molecule of claim 1, wherein said first sequence and said second sequence each comprise about 19 to about 23 nucleotides, and wherein each said sequence comprises at least about 19 nucleotides that are complementary to the nucleotides of the other strand.

10. The siNA molecule of claim 1, wherein any pyrimidine nucleotides in said second sequence are 2′

-O-methylpyrimidine nucleotides.

11. The siNA molecule of claim 1, wherein any purine nucleotides in said second sequence are 2′

-deoxy purine nucleotides.

12. The siNA molecule of claim 1, wherein any pyrimidine nucleotides in said second sequence are 2′

-deoxy-2′

-fluoro pyrimidine nucleotides.

13. The siNA molecule of claim 1, wherein any pyrimidine nucleotides in said first sequence are 2′

-deoxy-2′

-fluoro pyrimidine nucleotides

14. The siNA molecule of claim 1, wherein any purine nucleotides in said first sequence are 2′

-O-methyl purine nucleotides.

15. The siNA molecule of claim 1, wherein any purine nucleotides in said first sequence comprise 2′

-deoxy-purine nucleotides.

16. The siNA molecule of claim 1, wherein said first sequence comprises a phosphorothioate internucleotide linkage at the 3′

end of said first sequence.

17. A pharmaceutical composition comprising the siNA molecule of claim 1 in an acceptable carrier or diluent.