Nucleic acid sequencing using microsphere arrays

• US 20050191698A1
• Filed: 04/14/2005
• Published: 09/01/2005
• Est. Priority Date: 04/20/1999
• Status: Abandoned Application

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Chee, Mark S., Stuelpnagel, John R.
• Application Number:
  US11/107,215
• Publication Number:
  US 20050191698A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface.

Claims

1-21. -21. (canceled)

22. A method of sequencing a plurality of different target nucleic acids, comprising:

(a) providing a population of microspheres distributed at discrete sites on a surface of a substrate,

wherein each discrete site comprises a microsphere attached to a hybridization complex comprising a different target nucleic acid and a primer, and

wherein one or more enzymes used to generate a signal from pyrophosphate is attached at said discrete sites

(b) extending said primer at each of said discrete sites, thereby adding nucleotides complementary to said target nucleic acid and releasing pyrophosphate; and

(c) detecting said pyrophosphate using said one or more enzymes,

thereby sequencing said plurality of target nucleic acids.

23. The method of claim 22, wherein said substrate comprises a fiber optic substrate.

24. The method of claim 23, wherein said discrete sites comprise etched wells.

25. The method of claim 22, wherein said microspheres are non-covalently associated with said discrete sites.

26. The method of claim 22, wherein said discrete sites comprise wells.

27. The method of claim 22, wherein said primer is covalently attached to said microsphere.

28. The method of claim 22, wherein said target sequence is covalently attached to said microspheres.

29. The method of claim 22, wherein said target nucleic acid comprises a PCR amplification product.

30. The method of claim 22, wherein said target nucleic acid comprises genomic DNA.

31. The method of claim 22, wherein said microspheres are randomly distributed at said discrete sites.

32. The method of claim 22, wherein said one or more enzymes comprise sulfurylase.

33. The method of claim 22, wherein said one or more enzymes comprise luciferase.

34. The method of claim 22, wherein said signal comprises an optical signal.

35. The method of claim 22, wherein said signal comprises fluorescence.

36. The method of claim 22, wherein said signal comprises luminescence.

37. The method of claim 22, wherein said one or more enzymes is attached to a microsphere.

38. The method of claim 22, wherein said discrete sites are at a density of 10,000,000 to 2,000,000,000 per cm².

39. The method of claim 22, wherein said discrete sites are at a density of 100,000 to 10,000,000 per cm².

40. The method of claim 22, wherein said discrete sites are at a density of 1,000 to 10,000 per cm².

41. The method of claim 22, wherein said discrete sites are at a density of 10 to 1,000 per cm².

42. The method of claim 22, wherein said nucleotides are deoxyribonucleotides.

43. The method of claim 22, wherein the genome sequence of a human is determined.

44. The method of claim 22, wherein the genome sequence of a bacteria is determined.

45. The method of claim 22, wherein the genome sequence of a virus is determined.