Thermoelectric method of sequencing nucleic acids

• US 8,043,814 B2
• Filed: 07/31/2008
• Issued: 10/25/2011
• Est. Priority Date: 07/31/2007
• Status: Active Grant

• Current Assignee: Eric Guilbeau
• Original Assignee: Eric Guilbeau
• Inventors: Guilbeau, Eric J.
• Primary Examiner(s): Horlick; Kenneth R.
• Assistant Examiner(s): Tung; Joyce
• Application Number:
  US12/183,729
• Publication Number:
  US 20090036317A1
• Time in Patent Office: 1,181 Days
• Field of Search: 435/6, 435/91.2, 435/6.12
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention relates to a novel thermoelectric method for determining the sequence of nucleotides on a nucleic acid molecule through use of a thermopile and/or sequencing reagents flowing under the conditions of laminar flow. The methods disclosed herein involve the measurement of the heat generated by a deoxynucleotide incorporation event that can be accomplished without the need to control the temperature of any of a thermopile'"'"'s junctions.

Claims

1. A method of sequencing a nucleic acid comprising:

(a) exposing a primer-hybridized nucleic acid template to a liquid flowing under conditions of laminar flow, wherein the primer comprises a 3′

end, and

(b) while the liquid continues flowing under conditions of laminar flow, measuring heat generated or a temperature difference, if any, associated with incorporation of a known deoxynucleoside triphosphate into the 3′

end of the primer, and either

(1) upon measuring heat generated or a temperature difference, identifying the nucleotide of the template that is complementary to the known deoxynucleoside triphosphate incorporated into the primer, or

(2) upon failing to measure heat generated or a temperature difference, eliminating the possibility that the nucleotide that is complementary to the known deoxynucleoside triphosphate is present in the template at the 3′

end of the primer,

wherein ambient temperature fluctuations are not controlled.

2. The method of claim 1, further comprising obtaining the primer-hybridized nucleic acid template.

19. The method of claim 1, wherein the liquid comprises a polymerase and a known deoxynucleoside triphosphate.

3. A method of sequencing a nucleic acid comprising:

(a) exposing a primer-hybridized nucleic acid template to a liquid comprising a polymerase and a known deoxynucleoside triphosphate; and

(b) measuring heat generated or difference in temperature, if any, as detected by a thermopile comprising at least one measuring junction and at least one reference junction, wherein each reference junction is not maintained at a constant temperature, and either

(1) upon measuring heat generated or a temperature difference, identifying the nucleotide of the template that is complementary to the known deoxynucleoside triphosphate incorporated into the primer, or

(2) upon failing to measure heat generated or a temperature difference, eliminating the possibility that the nucleotide that is complementary to the known deoxynucleoside triphosphate is present in the template at the 3′

end of the primer.

4. The method of claim 3, wherein the thermopile is a thin-film thermopile or a bulk thermopile.

22. The method of claim 3, wherein the method is employed in the absence of a reaction chamber of a finite volume.

23. The method of claim 3, wherein ambient temperature fluctuations are not controlled.

24. The method of claim 3, wherein the method is employed in the absence of a reaction chamber of a finite volume, and wherein ambient temperature fluctuations are not controlled.

5. A method of sequencing a nucleic acid comprising:

(a) obtaining a primer-hybridized nucleic acid template, wherein the primer comprises a 3′

end;

(b) exposing the template to a liquid flowing under conditions of laminar flow, wherein the liquid comprises a polymerase and a known deoxynucleoside triphosphate;

(c) while the liquid continues flowing under conditions of laminar flow, measuring heat generated or difference in temperature, if any, as detected by at least one thin-film thermopile comprising at least one first junction and at least one second junction,

wherein each first junction is a measuring junction and each second junction is a reference junction, wherein each reference junction is not maintained at a constant temperature, and

wherein the heat generated or the difference in temperature between the first and second junctions indicates incorporation of the known deoxynucleoside triphosphate into the 3′

end of the primer; and

either

(d) upon measuring heat or a difference in temperature, identifying the nucleotide of the template that is complementary to the known deoxynucleoside triphosphate incorporated into the primer, or

(e) upon failing to measure heat or a difference in temperature, eliminating the possibility that the nucleotide that is complementary to the known deoxynucleoside triphosphate is present in the template at the 3′

end of the primer.

6. The method of claim 5, wherein the primer-hybridized nucleic acid template is bound to a support.

7. The method of claim 6, wherein the support comprises a glass bead, a polymer bead, a glass microscope slide cover slip, a polymer microscope slide cover slip, a glass microscope slide, a polymer microscope slide, a DNA microarray fabrication glass support, a paramagnetic bead, a glass plate, or any combination thereof.

8. The method of claim 5, wherein the polymerase is selected from the group consisting of DNA polymerase I, DNA polymerase II, DNA polymerase III, Taq polymerase, T7 polymerase, T4 polymerase, Klenow polymerase and an exonuclease-deficient polymerase.

9. The method of claim 8, wherein the polymerase is an exonuclease-deficient polymerase.

10. The method of claim 5, wherein the known deoxynucleoside triphosphate is selected from the group consisting of dATP, dTTP, dGTP and dCTP, dATPα

S, and a tagged deoxynucleoside triphosphate.

11. The method of claim 5, wherein the thin-film thermopile comprises at least 60 junction pairs.

12. The method of claim 11, wherein the thin-film thermopile comprises a material that provides an output of up to about 7.14 microvolts/milli-degree centigrade temperature difference.

13. The method of claim 5, wherein the thin-film thermopile comprises an electrically conductive metal.

14. The method of claim 5, wherein the thin-film thermopile is a bismuth/antimony thin thermopile or silicon/aluminum thin-film thermopile optionally doped with boron.

15. The method of claim 5, wherein the difference in temperature is between about 10⁻

4 and about 10<sup>−

5</sup> Kelvin.

16. The method of claim 5, wherein the liquid further comprises a pyrophosphatase.

17. The method of claim 16, wherein the difference in temperature is between about 10⁻

4 and about 10<sup>−

5</sup> Kelvin.

18. The method of claim 5, further comprising repeating steps (b)-(e) at least once.

25. The method of claim 5, wherein the method is employed in the absence of a reaction chamber of a finite volume.

26. The method of claim 5, wherein ambient temperature fluctuations are not controlled.

27. The method of claim 5, wherein the method is employed in the absence of a reaction chamber of a finite volume, and wherein ambient temperature fluctuations are not controlled.

20. A method of sequencing a nucleic acid comprising:

(a) exposing a primer-hybridized nucleic acid template to a liquid flowing under conditions of laminar flow, wherein the primer comprises a 3′

end, and

(b) while the liquid continues flowing under conditions of laminar flow, measuring heat generated or a temperature difference, if any, associated with incorporation of a known deoxynucleoside triphosphate into the 3′

end of the primer, and either

(1) upon measuring heat generated or a temperature difference, identifying the nucleotide of the template that is complementary to the known deoxynucleoside triphosphate incorporated into the primer, or

(2) upon failing to measure heat generated or a temperature difference, eliminating the possibility that the nucleotide that is complementary to the known deoxynucleoside triphosphate is present in the template at the 3′

end of the primer,

wherein the method is employed in the absence of a reaction chamber of a finite volume, and wherein ambient temperature fluctuations are not controlled.

28. The method of claim 20, wherein the liquid comprises a polymerase and a known deoxynucleoside triphosphate.

29. The method of claim 20, further comprising obtaining the primer-hybridized nucleic acid template.

21. A method of sequencing a nucleic acid comprising:

(a) exposing a primer-hybridized nucleic acid template to a liquid flowing under conditions of laminar flow, wherein the primer comprises a 3′

end, and

(b) while the liquid continues flowing under conditions of laminar flow, measuring heat generated or a temperature difference, if any, associated with incorporation of a known deoxynucleoside triphosphate into the 3′

end of the primer, and either

(1) upon measuring heat generated or a temperature difference, identifying the nucleotide of the template that is complementary to the known deoxynucleoside triphosphate incorporated into the primer, or

(2) upon failing to measure heat generated or a temperature difference, eliminating the possibility that the nucleotide that is complementary to the known deoxynucleoside triphosphate is present in the template at the 3′

end of the primer,

wherein the method is employed in the absence of a reaction chamber of a finite volume, wherein ambient temperature fluctuations are not controlled, and wherein a reference junction temperature of a thermopile is not maintained.

30. The method of claim 21, wherein the liquid comprises a polymerase and a known deoxynucleoside triphosphate.

31. The method of claim 21, further comprising obtaining the primer-hybridized nucleic acid template.