Separation of pyrophosphate release and pyrophosphate detection

• US 8,445,412 B2
• Filed: 02/24/2010
• Issued: 05/21/2013
• Est. Priority Date: 02/25/2009
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Hirschbein, Bernard, Gorpe-Yasar, Filiz
• Primary Examiner(s): Marschel, Ardin
• Assistant Examiner(s): Manteuffel, Richard L
• Application Number:
  US13/203,463
• Publication Number:
  US 20110306521A1
• Time in Patent Office: 1,182 Days
• Field of Search: 506/16, 435/6.1
• US Class Current: 506/16
• CPC Class Codes: C12Q 1/66 involving luciferase
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing.

Claims

1. A method of delaying pyrophosphate detection comprising:

providing a pyrophosphate sequestering agent;

generating pyrophosphate in the presence of said sequestering agent, wherein generating pyrophosphate in the presence of said sequestering agent comprises incorporating a nucleotide or nucleotide analog into a polynucleotide, whereby said pyrophosphate is reversibly sequestered;

releasing said pyrophosphate from said sequestering agent; and

detecting said pyrophosphate.

2. The method of claim 1, wherein said pyrophosphate is reversibly sequestered by adsorption onto said sequestering agent.

3. The method of claim 2, wherein said pyrophosphate sequestering agent comprises a cationic agent.

4. The method of claim 3, wherein said cationic agent comprises an agent selected from the group consisting of a metal ion, a metal salt, a metal oxide, hydroxyapatite, ammonium, a substituted ammonium salt, or a resin or bead comprising ammonium or a substituted ammonium salt.

5. The method of claim 4, wherein said metal ion, metal salt or metal oxide comprises Ti ion or TiO2.

6. The method of claim 2, wherein said pyrophosphate sequestering agent comprises particles or beads.

7. The method of claim 1, wherein releasing the pyrophosphate from said sequestering agent comprises providing a release reagent to said sequestering agent.

8. The method of claim 7, wherein said release reagent comprises an anionic agent.

9. The method of claim 8, wherein said anionic agent comprises an agent selected from the group consisting of oxalic acid, an oxalate salt, sulfamic acid, a sulfamate salt, ethylene diamine tetraacetic acid (EDTA), and ethylene glycol-bis-β

-amino-ethyl ether N, N, N′

, N′

-tetra-acetic acid (EGTA).

10. The method of claim 7, wherein said release reagent comprises phosphate, bisphosphonate, or ATP sulfurylase.

11. The method of claim 10, wherein said ATP sulfurylase is in solution.

12. The method of claim 1, wherein detecting said pyrophosphate comprises providing a pyrophosphate detecting agent.

13. The method of claim 12, wherein said pyrophosphate detecting agent comprises luciferase.

14. The method of claim 13, wherein said pyrophosphate detecting agent further comprises ATP sulfurylase.

15. The method of claim 13, wherein said luciferase is attached to a bead.

16. The method of claim 14, wherein said ATP sulfurylase is attached to a bead.

17. The method of claim 16, wherein said ATP sulfurylase and said luciferase are both attached to the same bead.

18. The method of claim 1, wherein said polynucleotide is attached to a surface.

19. The method of claim 18, wherein said surface comprises a bead or a well.

20. The method of claim 1, further comprising the step of washing said sequestering agent.

21. The method of claim 20, wherein washing comprises adding a washing enzyme to said sequestering agent.

22. The method of claim 21, wherein said washing enzyme is selected from the group consisting of pyrophosphatase, apyrase, alkaline phosphatase and ATP sulfurylase.

23. The method of claim 21, further comprising adding a washing enzyme inhibitor to said sequestering agent.

24. The method of claim 23, wherein said washing enzyme inhibitor is sodium azide.

25. The method of claim 20, wherein said washing step comprises electric-field assisted removal of pyrophosphate from said sequestering agent.

26. A method for sequencing a nucleic acid, said method comprising:

providing nucleotides or nucleotide analogs in the presence of a pyrophosphate sequestering agent and a pyrophosphate detecting agent;

incorporating one or more of said nucleotides or nucleotide analogs into a polynucleotide so as to extend said polynucleotide in the presence of said pyrophosphate sequestering agent, thereby generating sequestered pyrophosphate;

removing said unincorporated nucleotides or nucleotide analogs from the presence of said pyrophosphate detecting agent;

releasing said pyrophosphate from said sequestering agent in the presence of said pyrophosphate detecting agent; and

detecting released pyrophosphate, wherein released pyrophosphate indicates that one or more nucleotides or nucleotide analogs have been incorporated into said polynucleotide.

28. The method of claim 26, wherein said pyrophosphate is reversibly sequestered by adsorption onto said sequestering agent.

29. The method of claim 28, wherein said pyrophosphate sequestering agent comprises a cationic agent.

30. The method of claim 29, wherein said cationic agent comprises an agent selected from the group consisting of a metal ion, a metal salt and a metal oxide.

31. The method of claim 30, wherein said metal ion, metal salt or metal oxide comprises Ti ion or TiO2.

32. The method of claim 28, wherein said sequestering agent comprises particles or beads.

33. The method of claim 26, wherein releasing the pyrophosphate from said sequestering agent comprises providing a release reagent to said sequestering agent.

34. The method of claim 33, wherein said release reagent comprises an anionic agent.

35. The method of claim 33, wherein said release reagent comprises phosphate.

36. The method of claim 26, wherein said pyrophosphate detecting agent comprises luciferase.

37. The method of claim 36, wherein said pyrophosphate detecting agent further comprises ATP sulfurylase.

38. The method of claim 26, wherein said polynucleotide is attached to a surface.

27. A method of modulating the availability of free pyrophosphate during sequencing of a nucleic acid molecule, said method comprising:

combining nucleotides or nucleotide analogs with a nucleic acid template;

incubating the nucleic acid template and said nucleotides or nucleotide analogs together with a polymerase and a pyrophosphate sequestering agent under conditions sufficient to form a polynucleotide complementary to all or a portion of the nucleic acid template, wherein pyrophosphate generated during said incubating is reversibly sequestered by the sequestering agent;

removing from said nucleic acid template the nucleotides or nucleotide analogs that have not been incorporated into the polynucleotide; and

releasing said pyrophosphate from said pyrophosphate sequestering agent by providing a release reagent.

39. The method of claim 27, further comprising providing a pyrophosphate detecting agent, thereby detecting pyrophosphate that is released from said pyrophosphate sequestering agent.

40. The method of claim 27, wherein said pyrophosphate sequestering agent comprises a cationic agent.

41. The method of claim 40, wherein said cationic agent comprises an agent selected from the group consisting of a metal ion, a metal salt and a metal oxide.

42. The method of claim 41 wherein said metal ion, metal salt or metal oxide comprises Ti ion or TiO2.

43. The method of claim 27, wherein said sequestering agent comprises particles or beads.

44. The method of claim 27, wherein said release reagent comprises an anionic agent.

45. The method of claim 27, wherein said release reagent comprises phosphate.

46. The method of claim 27, wherein said pyrophosphate detecting agent comprises luciferase.

47. The method of claim 46, wherein said pyrophosphate detecting agent further comprises ATP sulfurylase.

48. The method of claim 27, wherein said polynucleotide is attached to a surface.