Method for sequencing nucleic acid molecules

• US 20080227654A1
• Filed: 02/06/2008
• Published: 09/18/2008
• Est. Priority Date: 05/19/1999
• Status: Abandoned Application

• Current Assignee: Cornell University
• Original Assignee: Cornell University
• Inventors: Craighead, Harold G., Turner, Stephen, Foquet, Mathieu, Korlach, Jonas, Levene, Michael, Webb, Watt W.
• Application Number:
  US12/027,242
• Publication Number:
  US 20080227654A1
• Time in Patent Office: Days
• US Class Current: 506/9
• 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 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2561/113 Real time assay
• CPC Class Codes: C12Q 2561/12 Fluorescence lifetime measurement
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10S 436/805 Optical property
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonuelcotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymeras to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Claims

1. A method of sequencing a target nucleic acid molecule having a plurality of nucleotide bases comprising:

providing a complex of a nucleic acid polymerizing enzyme and the target nucleic acid molecule oriented with respect to each other in a position suitable to add a nucleotide analog at an active site complementary to the target nucleic acid;

providing a plurality of types of nucleotide analogs proximate to the active site, wherein each type of nucleotide analog is complementary to a different nucleotide in the target nucleic acid sequence;

polymerizing a nucleotide analog at an active site, wherein the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid, leaving the added nucleotide analog ready for subsequent addition of nucleotide analogs;

identifying the nucleotide analog added at the active site as a result of said polymerizing; and

repeating said providing a plurality of types of nucleotide analogs, said polymerizing, and said identifying so that the sequence of the target nucleic acid is determined.

2. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is selected from the group consisting of a DNA polymerase, an RNA polymerase, reverse transcriptase, and mixtures thereof.

3. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is a thermostable polymerase.

4. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is a thermodegradable polymerase.

5. A method according to claim 1, wherein the target nucleic acid molecule is selected from the group consisting of double-stranded DNA, single-stranded DNA, single stranded DNA hairpins, DNA/RNA hybrids, RNA with a recognition site for binding of the polymerase, and RNA hairpins.

6. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is bound to the target nucleic acid molecule complex at an origin of replication, a nick or gap in a double-stranded target nucleic acid, a secondary structure in a single-stranded target nucleic acid, a binding site created by an accessory protein, or a primed single stranded nucleic acid.

7. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is provided with one or more accessory proteins to modify its activity.

8. A method according to claim 7, wherein the accessory protein is selected from the group consisting of a single-stranded binding protein, a primase, and helicase.

9. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is processive.

10. A method according to claim 1, wherein the nucleic acid polymerizing enzyme is non-processive.

11. A method according to claim 1, wherein the nucleotide analogs are selected from the group consisting of a ribonucleotide, a deoxyribonucleotide, a modified ribonucleotide, a modified deoxyribonucleotide, a peptide nucleotide, a modified peptide nucleotide, and a modified phosphate-sugar backbone nucleotide.

12. A method according to claim 1 further comprising:

hybridizing an oligonucleotide primer to the target nucleic acid molecule prior to or during said providing a plurality of nucleotide analogs.

13. A method according to claim 12, wherein the oligonucleotide primer comprises nucleotides selected from the group consisting of ribonucleotides, deoxyribonucleotides, modified ribonucleotides, modified deoxyribonucleotides, peptide nucleic acids, modified peptide nucleic acids, and modified phosphate-sugar backbone nucleotides.

14. A method according to claim 1, wherein the nucleotide analogs are provided with a label.

15. A method according to claim 14, wherein the label is selected from the group consisting of chromophores, fluorescent moieties, enzymes, antigens, heavy metals, magnetic probes, dyes, phosphorescent groups, radioactive materials, chemiluminescent moieties, scattering or fluorescent nanoparticles, Raman signal generating moieties, and electrochemical detection moieties.

16. A method according to claim 14, wherein the label is attached to the nucleotide analog at its base, sugar moiety, alpha phosphate beta phosphate, or gamma phosphate.

17. A method according to claim 14, wherein the label is attached to the nucleotide analog with a linker.

18. A method according to claim 14, wherein the label is attached to the nucleotide analog without a linker.

19. A method according to claim 14 further comprising

removing the label from the nucleotide analog during or after said identifying and before said polymerizing many further nucleotide analogs at the active site.

20. A method according to claim 19, wherein said removing is carried out by bleaching the label.

21. A method according to claim 20, wherein said bleaching is carried out by photobleaching with radiation which is adjusted to induce and control label removal.

22. A method according to claim 19, wherein said removing is carried out by cleaving the label from the nucleotide analog.

23. A method according to claim 22, wherein beta- or gamma-labeled nucleotide analogs are enzymatically cleaved.

24. A method according to claim 14, wherein each of the plurality of types of nucleotide analogs have different labels which are distinguished from one another during said identifying.

25. A method according to claim 14, wherein three or less of the plurality of types of nucleotide analogs have a different label.

26. A method according to claim 14, wherein the different types of nucleotide analogs have the same label but are distinguished by different properties due to the presence of base fluorophores, quenched fluorophores, or fluorogenic nucleotide analogs.

27. A method according to claim 1, wherein the nucleic acid polymerizing enzyme carries a label and said identifying is carried out by detecting interaction between the label and the nucleotide analog.

28. A method according to claim 27, wherein the label is a fluorescence resonance energy transfer donor or acceptor.

29. A method according to claim 1, wherein said identifying is carried out by non-optical procedures.

30. A method according to claim 1, wherein said identifying is carried out by optical procedures selected from the group consisting of far-field microspectroscopy, near-field microspectroscopy, evanescent wave or wave guided illumination, nanostructure enhancement, and combinations thereof.

31. A method according to claim 1, wherein said identifying is carried out by utilizing single and/or multiphoton excitation, fluorescence resonance energy transfer, or photoconversion.

32. A method according to claim 1, wherein said identifying is achieved by spectral wavelength discrimination, measurement and separation of fluorescence lifetimes, fluorophore identification and/or background suppression.

33. A method according to claim 32, wherein fluorophore identification and/or background suppression utilizes fast switching between excitation modes and illumination sources, and combinations thereof.

34. A method according to claim 1, wherein said providing a complex comprises:

positioning either (1) an oligonucleotide primer or (2) the target nucleic acid molecule on a support;

hybridizing either (1) the target nucleic acid molecule to the positioned oligonucleotide primer or (2) an oligonucleotide primer to the positioned target nucleic acid molecule, to form a primed target nucleic acid molecule complex; and

providing the nucleic acid polymerizing enzyme on the primed target nucleic acid molecule complex in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site.

35. A method according to claim 34, wherein said hybridizing is carried out by additionally binding the end of the target nucleic acid molecule opposite to that bound to the oligonucleotide primer to a second oligonucleotide primer positioned on the support.

36. A method according to claim 34, wherein the support and either the oligonucleotide primer or the target nucleic acid molecule are bound reversibly or irreversibly with corresponding components of a covalent or non-covalent binding pair selected from the group consisting of an antigen-antibody binding pair, a streptavidin-biotin binding pair, photoactivated coupling molecules, and a pair of complementary nucleic acids.

37. A method according to claim 34, where the oligonucleotide primer is positioned on the support and the target nucleic acid molecule is hybridized to the positioned oligonucleotide primer.

38. A method according to claim 34, wherein the target nucleic acid molecule is positioned on the support and the oligonucleotide primer is hybridized to the positioned target nucleic acid molecule.

39. A method according to claim 1, wherein said providing a complex comprises:

positioning, on a support, a double stranded nucleic acid molecule comprising the target nucleic acid and having a recognition site proximate the active site, and

providing the nucleic acid polymerizing enzyme on the target nucleic acid molecule in a position suitable to move along the target nucleic acid molecule.

40. A method according to claim 1, wherein said providing a complex comprises:

positioning a nucleic acid polymerizing enzyme on a support in a position suitable for the target nucleic acid complex to move relative to the nucleic acid polymerizing enzyme.

41. A method according to claim 40, wherein the support and the nucleic acid polymerizing enzyme are bound reversibly or irreversibly with corresponding components of a covalent or non-covalent binding pair selected from the group consisting of an antigen-antibody binding pair, a streptavidin-biotin binding pair, photoactivated coupling molecules, and a pair of complementary nucleic acids.

42. A method according to claim 1, wherein the nucleic acid polymerizing enzyme or the target nucleic acid is positioned on an adjustable support.

43. A method according to claim 1, wherein the nucleic acid polymerizing enzyme or the target nucleic acid is positioned in a gel with pores.

44. A method according to claim 1, wherein the target nucleic acid and the nucleic acid polymerizing enzyme are positioned on a solid support proximate to each other.

45. A method according to claim 1, wherein said identifying is carried out by reducing background noise resulting from free nucleotide analogs.

46. A method according to claim 45, wherein said identifying comprises:

directing activating radiation to a region substantially corresponding to the active site and

detecting the nucleotide analog polymerized at the active site.

47. A method according to claim 45, wherein said identifying distinguishes nucleotide analogs polymerized at the active site from free nucleotide analogs.

48. A method according to claim 45, wherein said identifying is carried out in a confined region proximate to the active site.

49. A method according to claim 48, wherein said identifying is carried out in a nanostructure.

50. A method according to claim 49, wherein the nanostructure is a punctuate, acicular, or resonant nanostructure which enhances said detecting.

51. A method according to claim 48, wherein nucleotide analogs that are not polymerized at the active site move rapidly through a microstructure to and from the confined region.

52. A method according to claim 51, wherein the microstructure comprises:

a plurality of channels to direct different nucleotide analogs to the confined region and

a discharge channel to permit materials to be removed from the confined region, and the nanostructure comprises;

a housing defining the confined region and constructed to facilitate said identifying.

53. A method according to claim 45, wherein said identifying is carried out by electromagnetic field enhancement with electromagnetic radiation being enhanced proximate to an object with a small radius of curvature adjacent to the active site.

54. A method according to claim 45, wherein said identifying is carried out by near-field illumination of cavities in which the primed target nucleic acid molecule is positioned.

55. A method according to claim 45, wherein said identifying is carried out with optical fibers proximate to the complex.

56. A method according to claim 45, wherein said identifying and said reducing background is carried out by time gated delay of photon detection.

57. A method according to claim 1, wherein said method is carried out by sequencing different target nucleic acid molecules at a plurality of different locations on an array.

58. A method according to claim 1, wherein said method is carried out by simultaneously or sequentially sequencing the same target nucleic acid and combining output from such sequencing.

59. An apparatus suitable for sequencing a target nucleic acid molecule comprising:

a support;

a nucleic acid polymerizing enzyme or oligonucleotide primer suitable to bind to a target nucleic acid molecule, wherein said nucleic acid polymerizing enzyme or said oligonucleotide primer is positioned on said support; and

a microstructure defining a confined region containing said support and said nucleic acid polymerizing enzyme or said oligonucleotide primer and configured to permit labeled nucleotide analogs that are not positioned on the support to move rapidly through the confined region.

60. An apparatus according to claim 59, wherein the microstructure comprises:

a plurality of channels to direct different types of nucleotide analogs to the confined region and

a discharge channel to permit materials to be removed from the confined region and a nanostructure constructed to facilitate identification of nucleotide analogs positioned on the support.

61. An apparatus suitable for sequencing a target nucleic acid molecule comprising:

a support;

a nucleic acid polymerizing enzyme or oligonucleotide primer suitable to hybridize to a target nucleic acid molecule, wherein said nucleic acid polymerizing enzyme or said oligonucleotide primer is positioned on said support;

a housing defining a confined region containing said support and said nucleic acid polymerizing enzyme or said oligonucleotide primer and constructed to facilitate identification of labeled nucleotide analogs positioned on the support; and

optical waveguides proximate to the confined region to focus activating radiation on the confined region and to collect radiation from the confined region.