Propargyl substituted nucleoside compounds and methods

• US 8,835,625 B2
• Filed: 05/11/2012
• Issued: 09/16/2014
• Est. Priority Date: 12/23/2003
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Rosenblum, Barnett, Jeon, Geun-sook, Khan, Shaheer
• Primary Examiner(s): Crane, Lawrence E
• Application Number:
  US13/470,181
• Publication Number:
  US 20120309953A1
• Time in Patent Office: 858 Days
• Field of Search: None
• US Class Current: 536/26.26
• CPC Class Codes: C07H 19/00 Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/02 with ribosyl as saccharide radical
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical

Abstract

Disclosed, among other things, are compounds having the structure

wherein X comprises a bond or a linker, LABEL comprises at least one detectable label, W₁ taken alone is —H or —OH, W₂ is —OH or a non-extendable moiety, W₃ when taken alone is —H or when taken together with W₁ is —CH₂—O—, and W₄ is OH, monophosphate, diphosphate, or triphosphate. Also disclosed are labeled polynucleotide compounds and methods of use thereof.

Claims

1. A compound having a structure of Formula III:

2. The compound of claim 1, wherein W₁ is H.

3. The compound of claim 1, wherein W₂ is selected from the group consisting of H, azido, amino, fluoro, chloro and methoxy.

4. The compound of claim 1, wherein W₁ is OH.

5. The compound of claim 1, wherein W₂ is OH.

6. The compound of claim 1, wherein W₄ is selected from the group consisting of monophosphoryl, diphosphoryl and triphosphoryl.

7. The compound of claim 1, wherein W₄ is triphosphoryl.

8. The compound of claim 1, wherein LABEL is selected from the group consisting of a fluorescent dye, an energy transfer dye, a quencher, and biotin.

9. The compound of claim 1, wherein LABEL is a fluorescent dye selected from the group consisting of a rhodamine dye, a fluorescein dye, a rhodol dye, a cyanine dye, a phthalocyanine dye and a squaraine dye.

10. The compound of claim 1, wherein the fluorescent dye is a fluorescein dye, a rhodamine dye or an energy transfer dye.

11. The compound of claim 1, wherein LABEL is an energy transfer dye which is a donor dye covalently attached to an acceptor dye, wherein either the donor dye or the acceptor dye is covalently attached to the linker, and the acceptor dye is capable of absorbing light emitted by the donor dye.

12. The compound of claim 11, wherein the donor dye is selected from the group consisting of a fluorescein dye and a rhodamine dye.

13. The compound of claim 11, wherein the acceptor dye is selected from the group consisting of a rhodamine dye, a fluorescein dye, a cyanine dye and a non-fluorescent quencher.

14. The compound of claim 1, wherein X is the linker and is selected from the group consisting of diradicals having a structure of one of the following formulae:

15. The compound of claim 14, wherein the further linker is a diradical selected from the group consisting of:

16. The compound of claim 1, wherein X is the linker and is selected from the group consisting of diradicals having a structure selected from the group consisting of:

17. The compound of claim 16, wherein the further linker is a diradical selected from the group consisting of:

18. The compound of claim 1, wherein X is the linker and is selected from the group consisting of diradicals selected from the group consisting of:

19. The compound of claim 1, wherein X is the linker and is selected from the group consisting of diradicals, having an amine terminus and an opposite terminus, selected from group consisting of:

20. A compound having a structure of Formula III:

21. The compound of claim 20, wherein LABEL is selected from the group consisting of a fluorescent dye, an energy transfer dye, a quencher and biotin.

22. The compound of claim 20, wherein LABEL is an energy transfer dye which is a donor dye covalently attached to an acceptor dye, wherein either the donor dye or the acceptor dye is covalently attached to the linker, and the acceptor dye is capable of absorbing light emitted by the donor dye.

23. A compound having a structure of Formula III:

24. The compound of claim 23, wherein W₁ is H.

25. The compound of claim 23, wherein W₂ is selected from the group consisting of H, azido, amino, fluoro, chloro and methoxy.

26. The compound of claim 23, wherein W₁ is OH.

27. The compound of claim 23, wherein W₂ is OH.

28. The compound of claim 23, wherein W₄ is selected from the group consisting of monophosphoryl, diphosphoryl and triphosphoryl.

29. The compound of claim 23, wherein W₄ is triphosphoryl.

30. The compound of claim 23, wherein LABEL is selected from the group consisting of a fluorescent dye, an energy transfer dye, a quencher, and biotin.

31. The compound of claim 23, wherein LABEL is a fluorescent dye selected from a group consisting of a rhodamine dye, a fluorescein dye, a rhodol dye, a cyanine dye, a phthalocyanine dye and a squaraine dye.

32. The compound of claim 23, wherein the fluorescent dye is a fluorescein dye, a rhodamine dye or an energy transfer dye.

33. The compound of claim 23, wherein LABEL is an energy transfer dye consisting of a donor dye covalently attached to an acceptor dye, wherein either the donor dye or the acceptor dye is covalently attached to the linker, and the acceptor dye is capable of absorbing light emitted by the donor dye.

34. The compound of claim 23, wherein the donor dye is a fluorescein dye or a rhodamine dye.

35. The compound of claim 23, wherein the acceptor dye is a rhodamine dye, a fluorescein dye, a cyanine dye or a non-fluorescent quencher.

36. The compound of claim 23, wherein X is a linker, and the linker is a diradical having a structure of one of the following formulae:

37. The compound of claim 36, wherein the further linker is a diradical selected from the group consisting of:

38. The compound of claim 23, wherein X is a linker, and the linker is a diradical having a structure selected from the group consisting of:

39. The compound of claim 23, wherein X is a linker and the linker is a diradical selected from the group consisting of:

40. The compound of claim 23, wherein X is a linker, and the linker is a diradical, having an amine terminus and an opposite terminus, selected from group consisting of:

41. A compound having a structure of Formula III:

42. The compound of claim 41, wherein LABEL is selected from the group consisting of a fluorescent dye, an energy transfer dye, a quencher, and biotin.

43. The compound of claim 41, wherein LABEL is an energy transfer dye consisting of a donor dye covalently attached to an acceptor dye, wherein either the donor dye or the acceptor dye is covalently attached to the linker, and the acceptor dye is capable of absorbing light emitted by the donor dye.