Antisense oligonucleotides comprising universal and/or degenerate bases

• US 20030045488A1
• Filed: 08/16/2001
• Published: 03/06/2003
• Est. Priority Date: 04/08/1999
• Status: Abandoned Application

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Brown, Bob D., Riley, Timothy A.
• Application Number:
  US09/931,732
• Publication Number:
  US 20030045488A1
• Time in Patent Office: Days
• US Class Current: 514/44
• 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: 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 15/1137 against enzymes viral enzymes C12N15/1131; receptors C12N15/1138
• CPC Class Codes: C12N 2310/18 acting by a non-sequence specific mechanism other than C12N2310/16 or C12N2310/17
• CPC Class Codes: C12N 2310/31 of the backbone
• CPC Class Codes: C12N 2310/319 linked by 2'-5' linkages, i.e. having a free 3'-position
• CPC Class Codes: C12N 2310/331 Universal or degenerate base
• CPC Class Codes: C12N 2310/345 having at least two different backbone modifications
• CPC Class Codes: C12Y 207/11013 Protein kinase C (2.7.11.13)

Abstract

Antisense oligonucleotides containing one or more degenerate and/or universal bases, and one or more modified backbone linkages, and use of these oligonucleotides for cleaving target RNA molecules.

Claims

1. An antisense oligonucleotide comprising at least one non-naturally occurring backbone linkage and between 6 and about 50 bases, wherein at least one of said bases are universal and/or degenerate bases and, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

2. The antisense oligonucleotide of claim 1, wherein no more than about 50% of said bases are universal and/or degenerate bases.

13. A method of cleaving a plurality of target RNA molecules of different sequence, comprising contacting said target RNA molecules with an antisense oligonucleotide according to any one of claims 1-10 in the presence of an RNAse capable of cleaving said target RNA molecules.

14. The method of claim 13, wherein said RNase is selected from the group consisting of RNAse H, RNAse L, and RNAse P.

3. An antisense oligonucleotide comprising a first non-RNase H recruiting region of between 3 and about 15 bases, an RNase H recruiting region of between 3 and about 15 bases, and a second non-RNase H recruiting region, wherein at least one of said bases are universal and/or degenerate bases and, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

4. The antisense oligonucleotide of claim 3, wherein no more than about 50% of said bases are universal and/or degenerate bases.

5. An antisense oligonucleotide comprising a non-RNase H recruiting section and an RNase H recruiting section, wherein at least one of said bases are universal and/or degenerate bases and, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

6. The antisense oligonucleotide of claim 5, wherein no more than about 50% of said bases are universal and/or degenerate bases.

7. An antisense oligonucleotide comprising an RNase L-recruiting region comprising a 2′

-5′

adenosine oligomer, wherein an RNA targeting region of said antisense oligonucleotide comprises at least one universal and/or degenerate bases and, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

8. The antisense oligonucleotide of claim 7, wherein said RNA targeting region comprises no more than about 50% universal and/or degenerate bases.

9. An antisense oligonucleotide comprising an RNase P-recruiting region, wherein an RNA targeting region of said antisense oligonucleotide comprises at least one universal and/or degenerate bases and, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

10. The antisense oligonucleotide of claim 9, wherein said RNA targeting region comprises no more than about 50% universal and/or degenerate bases.

11. A ribozyme comprising an RNA targeting region, which comprises at least one universal and/or degenerate bases, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

12. The ribozyme of claim 11, wherein said RNA targeting region comprises no more than about 50% universal and/or degenerate bases.

15. A method of cleaving a plurality of target RNA molecules of different sequence, comprising contacting said target RNA molecules with a ribozyme according to claims 11 or 12.

16. A method of cleaving a plurality of target RNA molecules of different sequence, comprising contacting said target RNA molecules with an antisense oligonucleotide comprising between 6 and -about 50 bases, wherein said antisense oligonucleotide comprises at least one universal and/or degenerate base and, wherein said antisense oligonucleotide complements at least two RNA molecules of a different sequence.

17. A method for reducing the deleterious effects of an antisense oligonucleotide comprising one or more sequence motifs, comprising replacing one or more bases within said one or more sequence motifs with one or more universal and/or degenerate bases.

18. The method of claim 17, wherein said sequence motif is a CG dinucleotide.

19. The method of claim 17, wherein said sequence motif is a poly-G sequence.