Stabilized nucleic acid dark quencher-fluorophore probes

• US 8,674,094 B2
• Filed: 07/28/2011
• Issued: 03/18/2014
• Est. Priority Date: 04/01/2008
• Status: Active Grant

• Current Assignee: HSB Corporate Trust Company (UK) Limited
• Original Assignee: Biosearch Technologies Incorporated
• Inventors: Cook, Ronald M., Lyttle, Matt
• Primary Examiner(s): BARKER, MICHAEL P
• Application Number:
  US13/193,517
• Publication Number:
  US 20110282041A1
• Time in Patent Office: 964 Days
• Field of Search: None
• US Class Current: 544/243
• CPC Class Codes: C07D 219/04 with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to carbon atoms of the ring system
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/073 with 2-deoxyribosyl as the saccharide radical
• CPC Class Codes: C09B 31/02 Disazo dyes
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

Abstract

The present invention provides a new class of solids supports for synthesis of modified oligomers of nucleic acids, and nucleic acid probes that have a format expediently synthesized on the new supports. Exemplary solid supports include at least one quencher bound through a linker to the solid support. Various exemplary embodiments include a moiety that stabilizes a duplex, triplex or higher order aggregation (e.g., hybridization) of nucleic acids of which the oligomer of the invention is a component. Other components of the solid support include moieties that stabilize aggregations of nucleic acids, e.g., intercalators, minor groove binding moieties, bases modified with a stabilizing moiety (e.g., alkynyl moieties, and fluoroalkyl moieties), and conformational stabilizing moieties, such as those described in commonly owned U.S. Patent Application Publication No. 2007/0059752.

Claims

1. A nucleic acid oligomer, wherein said nucleic acid oligomer is prepared by a method comprising:

coupling a monomeric nucleic acid to an acceptor nucleomonomer or an acceptor oligomer,

wherein said monomeric nucleic acid is of the formula;

2. The nucleic acid oligomer according to claim 1, wherein said linker is a member selected from a single covalent bond, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl.

3. The nucleic acid oligomer according to claim 1, wherein R^d is a nucleic acid protecting group.

4. The nucleic acid oligomer according to claim 3, wherein said nucleic acid protecting group is dimethoxytrityl.

5. The nucleic acid oligomer according to claim 1, wherein R^c is

6. The nucleic acid oligomer according to claim 1, wherein said monomeric nucleic acid is of a formula selected from:

7. The nucleic acid oligomer according to claim 1, wherein

8. The nucleic acid oligomer according to claim 1, wherein said quencher is of a structure according to Formula (III):

14. The nucleic acid oligomer according to claim 1, wherein said nucleic acid oligomer is a probe.

15. The nucleic acid oligomer according to claim 14, wherein said probe is selected from molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes, light up probes, invader detection probes, and taqman probes.

9. A nucleic acid oligomer, wherein said nucleic acid oligomer is prepared by a method comprising:

coupling a monomeric nucleic acid to an acceptor nucleomonomer or an acceptor oligomer,

wherein said monomeric nucleic acid is of the formula;

21. The nucleic acid oligomer according to claim 9, wherein said linker is a member selected from a single covalent bond, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl.

22. The nucleic acid oligomer according to claim 9, wherein R^d is a nucleic acid protecting group.

23. The nucleic acid oligomer according to claim 22, wherein said nucleic acid protecting group is dimethoxytrityl.

24. The nucleic acid oligomer according to claim 9, wherein R^c is

25. The nucleic acid oligomer according to claim 9, wherein said monomeric nucleic acid is of a formula selected from:

26. The nucleic acid oligomer according to claim 9, wherein Q-L⁴ is:

27. The nucleic acid oligomer according to claim 9, wherein said nucleic acid oligomer is a probe.

28. The nucleic acid oligomer according to claim 27, wherein said probe is selected from molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes, light up probes, invader detection probes, and taqman probes.

10. A nucleic acid oligomer, wherein said nucleic acid oligomer is prepared by a method comprising:

coupling a monomeric nucleic acid to an acceptor nucleomonomer or an acceptor oligomer,

wherein said monomeric nucleic acid is of the formula;

16. The nucleic acid oligomer according to claim 10, wherein v is 1.

29. The nucleic acid oligomer according to claim 10, wherein said linker is a member selected from a single covalent bond, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl.

30. The nucleic acid oligomer according to claim 10, wherein R^d is a nucleic acid protecting group.

31. The nucleic acid oligomer according to claim 30, wherein said nucleic acid protecting group is dimethoxytrityl.

32. The nucleic acid oligomer according to claim 10, wherein R^c is

33. The nucleic acid oligomer according to claim 10, wherein said monomeric nucleic acid is of a formula selected from:

34. The nucleic acid oligomer according to claim 10, wherein Q-L⁴ is:

35. The nucleic acid oligomer according to claim 10, wherein said nucleic acid oligomer is a probe.

36. The nucleic acid oligomer according to claim 35, wherein said probe is selected from molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes, light up probes, invader detection probes, and taqman probes.

11. A nucleic acid oligomer, wherein said nucleic acid oligomer is prepared by a method comprising:

coupling a monomeric nucleic acid to an acceptor nucleomonomer or an acceptor oligomer,

wherein said monomeric nucleic acid is of the formula;

12. The nucleic acid oligomer according to claim 11, wherein said monomeric nucleic acid is of the formula:

13. The nucleic acid oligomer according to claim 11, wherein said monomeric nucleic acid is of the formula:

17. The nucleic acid oligomer according to claim 11, wherein said quencher is of the structure:

18. The nucleic acid oligomer according to claim 11, wherein said quencher is of the structure:

19. The nucleic acid oligomer according to claim 11, wherein said quencher is of the structure:

37. The nucleic acid oligomer according to claim 11, wherein said linker is a member selected from a single covalent bond, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl.

38. The nucleic acid oligomer according to claim 11, wherein R^d is a nucleic acid protecting group.

39. The nucleic acid oligomer according to claim 38, wherein said nucleic acid protecting group is dimethoxytrityl.

40. The nucleic acid oligomer according to claim 11, wherein R^c is

41. The nucleic acid oligomer according to claim 11, wherein said monomeric nucleic acid is of a formula selected from:

42. The nucleic acid oligomer according to claim 11, wherein Q-L⁴ is:

43. The nucleic acid oligomer according to claim 11, wherein said nucleic acid oligomer is a probe.

44. The nucleic acid oligomer according to claim 43, wherein said probe is selected from molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes, light up probes, invader detection probes, and taqman probes.

20. A nucleic acid oligomer, wherein said nucleic acid oligomer is prepared by a method comprising:

coupling a monomeric nucleic acid to an acceptor nucleomonomer or an acceptor oligomer,

wherein said monomeric nucleic acid is of the formula;

45. The nucleic acid oligomer according to claim 20, wherein said linker is a member selected from a single covalent bond, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl.

46. The nucleic acid oligomer according to claim 20, wherein R^d is a nucleic acid protecting group.

47. The nucleic acid oligomer according to claim 46, wherein said nucleic acid protecting group is dimethoxytrityl.

48. The nucleic acid oligomer according to claim 20, wherein R^c is

49. The nucleic acid oligomer according to claim 20, wherein said monomeric nucleic acid is of a formula selected from:

50. The nucleic acid oligomer according to claim 20, wherein Q-L⁴ is:

51. The nucleic acid oligomer according to claim 20, wherein said nucleic acid oligomer is a probe.

52. The nucleic acid oligomer according to claim 51, wherein said probe is selected from molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes, light up probes, invader detection probes, and taqman probes.