Hydroxymethyl substituted RNA oligonucleotides and RNA complexes

• US 8,314,227 B2
• Filed: 05/21/2008
• Issued: 11/20/2012
• Est. Priority Date: 05/22/2007
• Status: Active Grant

• Current Assignee: Arcturus Therapeutics, Inc. (Arcturus Therapeutics Holdings, Inc.)
• Original Assignee: Marina Biotech, Inc. (Pentair Plc (Ireland))
• Inventors: Wengel, Jesper
• Primary Examiner(s): Angell, Jon E
• Application Number:
  US12/515,403
• Publication Number:
  US 20100056768A1
• Time in Patent Office: 1,644 Days
• Field of Search: 536/24.5
• US Class Current: 536/24.5
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• 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 15/111 General methods applicable to biologically active non-coding 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/31 of the backbone
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/323 modified ring structure
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2320/51 modulating the chemical stability, e.g. nuclease-resistance

Abstract

The present invention is directed to RNA oligonucleotides or complexes of RNA oligonucleotides, denoted herein together as RNA complexes, containing at least one, but optionally more that one, hydroxymethyl substituted nucleotide monomer(s). By a hydroxymethyl substituted nucleotide monomer is understood a nucleotide monomer containing a hydroxymethyl group (that may be unsubstituted, O-substituted for example with a conjugating group, or converted into an optionally substituted or conjugated aminomethyl group). This hydroxymethyl group is not partaking in formation of an internucleotide linkage and is not the hydroxymethyl group (containing the 5′-hydroxy group) of a natural RNA monomer. The RNA complexes of the invention may be useful for therapeutic applications, diagnostic applications or research applications.

Claims

1. An oligonucleotide comprising an acyclic 2′

-3′

-seco-nucleotide monomer wherein the oligonucleotide is an RNA duplex having first and second RNA strands, and wherein the acyclic monomer is monomer D

2. The oligonucleotide of claim 1, each strand comprising from 15 to 40 nucleotide and acyclic monomers.

3. The oligonucleotide of claim 1, each strand comprising from one to five acyclic monomers.

4. The oligonucleotide of claim 1, further comprising a nucleotide analogue selected from the group consisting of 2′

-O-alkyl-RNA monomers, 2′

-amino-DNA monomers, 2′

-fluoro-DNA monomers, PNA monomers, HNA monomers, ANA monomers, FANA monomers, CeNA monomers, ENA monomers, DNA monomers, and INA monomers.

5. The oligonucleotide of claim 1, further comprising one or more 2′

-O-alkyl-RNA nucleotide analogues.

6. The oligonucleotide of claim 1, further comprising a phosphorothioate linkage or a boranophosphate linkage.

7. The oligonucleotide of claim 1, wherein the oligonucleotide is capable of mediating RISC dependent translational repression or degradation of a target nucleotide sequence complementary to a portion of the oligonucleotide.

8. The oligonucleotide of claim 1, comprising a number of base pairs from 14 to 26 base pairs.

9. The oligonucleotide of claim 1 comprising at least one overhang.

10. The oligonucleotide of claim 1, comprising an overhang of from 1 to 14 nucleotides.

11. The oligonucleotide of claim 1 comprising at least one 3′

-overhang.

12. The oligonucleotide of claim 1, comprising at least one 3′

-overhang of from 1 to 14 nucleotides.

13. The oligonucleotide of claim 1 comprising at least one blunt end.

14. The oligonucleotide according to claim 1, comprising a nucleotide sequence that is complementary to a target nucleotide sequence.

15. The oligonucleotide according to claim 1, having reduced off-target effects as compared to an identical oligonucleotide with natural RNA monomers instead of acyclic monomers.

16. The oligonucleotide according to claim 1, wherein the oligonucleotide has increased or prolonged potency for gene silencing as compared to an identical oligonucleotide with natural RNA monomers instead of acyclic monomers.

17. The oligonucleotide according to claim 1, wherein the oligonucleotide has improved stability towards enzymatic degradation as compared to an identical oligonucleotide with natural RNA monomers instead of acyclic monomers.

18. The oligonucleotide according to claim 1, wherein the oligonucleotide has reduced immune stimulation as compared to an identical oligonucleotide with natural RNA monomers instead of acyclic monomers.

19. The oligonucleotide according to claim 1, wherein one of the strands is a discontinuous passenger strand.

20. An oligonucleotide comprising an acyclic 2′

-3′

-seco-nucleotide monomer wherein the oligonucleotide is a microRNA, and wherein the acyclic monomer is monomer D

21. An oligonucleotide comprising an acyclic 2′

-3′

-seco-nucleotide monomer wherein the oligonucleotide is a single-stranded RNA targeting a microRNA, and wherein the acyclic monomer is monomer D

22. An oligonucleotide comprising an acyclic 2′

-3′

-seco-nucleotide monomer wherein the oligonucleotide is a steric block RNA-binding RNA, and wherein the acyclic monomer is monomer D