Gapped 2'-modified oligonucleotides

• US 5,856,455 A
• Filed: 04/21/1997
• Issued: 01/05/1999
• Est. Priority Date: 12/24/1991
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Cook, Phillip Dan
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): VIVLEMORE, TRACY ANN
• Application Number:
  US08/861,306
• Time in Patent Office: 624 Days
• Field of Search: 435/6, 435/325, 435/375, 514/44, 536/23.1, 536/24.3, 536/24.5, 536/24.31, 536/24.32, 935/33, 935/34
• US Class Current: 536/23.1
• 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: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/125 incorporating agents resulting in resistance to degradation

Abstract

Oligonucleotides and other macromolecules are provided that have increased nuclease resistance, substituent groups for increasing binding affinity to complementary strand, and subsequences of 2'"'"'-deoxy-erythro-pentofuranosyl nucleotides that activate RNase H enzyme. Such oligonucleotides and macromolecules are useful for diagnostics and other research purposes, for modulating protein in organisms, and for the diagnosis, detection and treatment of other conditions susceptible to antisense therapeutics.

Claims

1. An oligonucleotide comprising a sequence of nucleotide units wherein:

at least one of said nucleotide units is functionalized to increase nuclease resistance of said oligonucleotide;

at least one of said nucleotide units bears an aminoalkoxy, allyloxy, or imidazolylalkoxy 2'"'"'-substituent group; and

a plurality of said nucleotide units have 2'"'"'-deoxy-erythro-pentofuranosyl sugar moieties, said 2'"'"'-deoxy-erythro-pentofuranosyl nucleotide units being consecutively located in said sequence of nucleotide units.

2. The oligonucleotide of claim 1 wherein each of said nucleotide units is a phosphorothioate or phosphorodithioate nucleotide.

3. The oligonucleotide of claim 1 wherein the 3'"'"' terminal nucleotide unit of said oligonucleotide includes a nuclease resistance modifying group on at least one of the 2'"'"' or the 3'"'"' positions of said nucleotide unit.

4. The oligonucleotide of claim 1 wherein:

a plurality of said nucleotide units bear substituent groups that increases binding affinity of said oligonucleotide to said strand of nucleic acid, said substituent-bearing nucleotides being divided into a first nucleotide unit sub-sequence and a second nucleotide unit sub-sequence; and

said plurality of 2'"'"'-deoxy-erythro-pentofuranosyl nucleotide units is positioned in said sequence of nucleotide units between said first nucleotide unit sub-sequence and said second nucleotide unit sub-sequence.

5. The oligonucleotide of claim 1 wherein:

a plurality of said nucleotide units bear substituent groups that increase binding affinity of said oligonucleotide to said complementary strand of nucleic acid; and

at least a portion of said substituent-bearing nucleotide are consecutively located at one of the 3'"'"' terminus or the 5'"'"' terminus of said oligonucleotide.

6. The oligonucleotide of claim 1 wherein at least five of said nucleotide units have 2'"'"'-deoxy-erythro-pentofuranosyl sugar moieties, said at least five 2'"'"'-deoxy-erythro-pentofuranosyl nucleotide units being consecutively located in said sequence of nucleotide units.

7. The oligonucleotide of claim 1 wherein from one to about eight of said nucleotide units bear a substituent group that increases the binding affinity of said oligonucleotide to said complementary strand, said substituent-bearing nucleotide units being consecutively located in said sequence of nucleotide units.

8. The oligonucleotide of claim 1 wherein:

from one to about eight of said nucleotide units bear a substituent group for increasing the binding affinity of said oligonucleotide to said complementary strand, said substituent-bearing nucleotide units being consecutively located in said sequence of nucleotide units; and

at least five of said nucleotide units have 2'"'"'-deoxy-erythro-pentofuranosyl sugar moieties, said at least five 2'"'"'-deoxy-erythro-pentofuranosyl nucleotide units being consecutively located in said sequence of nucleotide units.

9. The oligonucleotide of claim 1 wherein at least one of said nucleotide units bears an aminoalkoxy 2'"'"'-substituent group.

10. The oligonucleotide of claim 1 wherein at least one of said nucleotide units bears an allyloxy 2'"'"'-substituent group.

11. The oligonucleotide of claim 1 wherein at least one of said nucleotide units bears an imidazolylalkoxy 2'"'"'-substituent group.

13. The oligonucleotide of claim 1 including:

a further plurality of said nucleotides bearing 2'"'"'-substituent groups;

said 2'"'"'-deoxy-erythro-pentofuranosyl nucleotides being positioned in said oligonucleotide between groups of nucleotides having said 2'"'"'-substituent group located thereon.

12. An oligonucleotide comprising a sequence of phosphorothioate nucleotides wherein:

a plurality of said nucleotides bear an aminoalkoxy, allyloxy, or imidazolylalkoxy 2'"'"'-substituent group; and

a plurality of said nucleotides have 2'"'"'-deoxy-erythro-pentofuranosyl sugar moieties.

14. The oligonucleotide of claim 12 wherein said substituent-bearing nucleotides are located at one of the 3'"'"' terminus or the 5'"'"' terminus of said oligonucleotide.

15. The oligonucleotide of claim 12 wherein at least one of said nucleotide units bears an aminoalkoxy 2'"'"'-substituent group.

16. The oligonucleotide of claim 12 wherein at least one of said nucleotide units bears an allyloxy 2'"'"'-substituent group.

17. The oligonucleotide of claim 12 wherein at least one of said nucleotide units bears an imidazolylalkoxy 2'"'"'-substituent group.

18. An oligonucleotide comprising a sequence of phosphorothioate nucleotides wherein:

a first portion of said nucleotides have 2'"'"'-deoxy-2'"'"'-fluoro, 2'"'"'-ethoxy, 2'"'"'-propoxy, 2'"'"'-aminopropoxy or 2'"'"'-allyloxy pentofuranosyl sugar moieties, and

a further portion of said nucleotides have 2'"'"'-deoxy-erythro-pentofuranosyl sugar moieties.

19. The oligonucleotide of claim 18 wherein said first portion of said nucleotides are located at either the 3'"'"' terminus or the 5'"'"' terminus of said oligonucleotide.

20. The oligonucleotide of claim 19 further comprising:

an additional portion of said nucleotides having 2'"'"'-deoxy-2'"'"'-fluoro, 2'"'"'-ethoxy, 2'"'"'-propoxy, 2'"'"'-aminopropoxy or 2'"'"'-allyloxy pentofuranosyl sugar moieties, and said further portion of said nucleotides positioned in said oligonucleotide between said first portion of nucleotides and said additional portion of said nucleotides.

21. The oligonucleotide of claim 18 wherein a first portion of said nucleotides have 2'"'"'-deoxy-2'"'"'-fluoro pentofuranosyl sugar moieties.

22. The oligonucleotide of claim 18 wherein a first portion of said nucleotides have 2'"'"'-ethoxy pentofuranosyl sugar moieties.

23. The oligonucleotide of claim 18 wherein a first portion of said nucleotides have 2'"'"'-propoxy pentofuranosyl sugar moieties.

24. The oligonucleotide of claim 18 wherein a first portion of said nucleotides have 2'"'"'-aminopropoxy pentofuranosyl sugar moieties.

25. The oligonucleotide of claim 18 wherein a first portion of said nucleotides have 2'"'"'-allyloxy pentofuranosyl sugar moieties.

26. An oligonucleotide comprising a sequence of nucleotide units wherein:

at least one of said nucleotide units is functionalized to increase nuclease resistance of said oligonucleotide;

at least one of said nucleotide units bears an aminoalkoxy 2'"'"'-substituent group; and

a plurality of said nucleotide unites have 2'"'"'-deoxy-erythro-pentofuranosyl sugar moieties, said 2'"'"'-deoxy-erythro-pentofuranosyl nucleotide units being consecutively located in said sequence of nucleotide units.