Methods and apparatus for nucleic acid sequencing by signal stretching and data integration

• US 20070231795A1
• Filed: 09/22/2005
• Published: 10/04/2007
• Est. Priority Date: 06/17/2002
• Status: Active Grant

• Current Assignee: Intel Corporation
• Original Assignee: Intel Corporation
• Inventors: Su, Xing
• Granted Patent: US 8,574,892 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: Y10S 977/853 Biological sample

Abstract

The methods and apparatus 100 disclosed herein concern DNA sequencing. In some embodiments of the invention, the methods comprise measuring the distance between labeled nucleotides 220, such as nucleotides labeled with bulky groups. The methods may further comprise placing identical template DNA 200 into four reaction chambers 110, 120, 130, 140, each containing a different labeled nucleotide precursor, synthesizing complementary strands 230, 240, 250 and detecting labeled nucleotides 220. The distances between labeled nucleotides 220 may be used to construct 450 distance maps 310, 320, 330, 340 for each type of labeled nucleotide 220. The distance maps 310, 320, 330, 340 may be aligned 520 to obtain a nucleic acid sequence 210. Overlapping data analysis and frequency analysis may be used to construct 450 the distance maps 310, 320, 330, 340 and non-overlapping data analysis may be used to align 520 the distance maps into a sequence 210.

Claims

1-30. -30. (canceled)

31. A nucleic acid sequencing apparatus comprising:

at least four reaction chambers configured to hold template nucleic acid, a synthetic reagent, a primer and labeled nucleotide precursor in an aqueous environment producing labeled nucleic acid with labeled nucleotides;

one or more nanopores in each of the reaction chambers, each nanopore being sized to allow the passing of the labeled nucleic acid and labeled nucleotides; and

a detection unit configured to detect the labeled nucleotides passing through the nanopores.

32. The apparatus of claim 31, wherein each reaction chamber contains a different nucleotide precursor.

33. The apparatus of claim 31, wherein the nucleotide precursor is selected from the group consisting of deoxyadenosine-5′

-triphosphate (dATP), deoxyguanosine-5′

-triphosphate (dGTP), deoxycytosine-5′

-triphosphate (dCTP) and deoxythymidine-5′

-triphosphate (dTTP) and deoxyuridine-5′

-triphosphate (dUTP).

34. The apparatus of claim 31, wherein the nanopores are between 1 nm and 10 mn in diameter.

35. The apparatus of claim 31, further comprising an information processing and control system operably coupled to the detection unit and configured to record a distance between labeled nucleotides as they pass through the nanopores.

36. The apparatus of claim 31, wherein each reaction chamber further includes a surface configured to attach the template nucleic acid.

37. The apparatus of claim 31, further comprising one or more fluid channels operably coupled to the reaction chambers.

38. The apparatus of claim 37, wherein the one or more fluid channels includes waste port.

39. The apparatus of claim 37, wherein the one or more fluid channels includes a template loading port.

40. The apparatus of claim 37, further comprising a molecular dispenser operably coupled to the one or more fluid channels.

41. A nucleic acid sequencing apparatus comprising:

a first reaction chamber containing labeled deoxyadenosine-5′

-triphosphate (dATP);

a second reaction chamber containing labeled deoxycytosine-5′

-triphosphate (dCTP);

a third reaction chamber containing labeled deoxythymidine-5′

-triphosphate (dTTP);

a fourth reaction chamber containing labeled deoxyuridine-5′

-triphosphate (dUTP);

wherein each of the reaction chambers are designed to hold template nucleic acid, a synthetic reagent, a primer and nucleotide precursors in an aqueous environment producing labeled nucleic acid with labeled nucleotides;

one or more fluid channels operably coupled to the reaction chambers; and

one or more nanopores in each of the reaction chambers, each nanopore being sized to allow the passing of the labeled nucleotide through the nanopores.

42. The apparatus of claim 41, further comprising a detection unit operably coupled to the nanopores and configured to detect the labeled nucleotides passing through the nanopores.

43. The apparatus of claim 42, further comprising an information processing and control system operably coupled to the detection unit and configured to record a distance between labeled nucleotides as they pass through the nanopores.

44. The apparatus of claim 41, wherein the nanopores are between 1 nm and 10 nm in diameter.

45. The apparatus of claim 41, wherein each reaction chamber further includes a surface configured to attach the template nucleic acid.

46. The apparatus of claim 41, wherein the one or more fluid channels includes waste port.

47. The apparatus of claim 41, wherein the one or more fluid channels includes a template loading port.

48. The apparatus of claim 41, further comprising a molecular dispenser operably coupled to the one or more fluid channels.

49. The apparatus of claim 41, wherein the reaction chambers are made of a transparent material.

50. The apparatus of claim 41, wherein the reaction chambers are made on a single integrated chip.