Enthalpy measurements for sequencing of a nucleic acid sample

• US 10,337,059 B2
• Filed: 09/21/2015
• Issued: 07/02/2019
• Est. Priority Date: 12/20/2006
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Esfandyarpour, Hesaam, Ronaghi, Mostafa
• Primary Examiner(s): Bertagna, Angela M.
• Application Number:
  US14/860,553
• Publication Number:
  US 20160186252A1
• Time in Patent Office: 1,380 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2527/119 pH
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)

Abstract

The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.

Claims

1. A method for sequencing a nucleic acid sample, comprising:

(a) providing a plurality of nucleic acid molecules and a polymerase in one or more thermally isolated chambers among a plurality of thermally isolated chambers that each has a volume of less than 0.1 μ

L, wherein each of said plurality of nucleic acid molecules comprises (i) a nucleic acid sequence of a single-stranded nucleic acid template derived from said nucleic acid sample, and (ii) a primer hybridized thereto, which primer comprises a hairpin formed by self-hybridization of said single-stranded nucleic acid template or a single-stranded oligonucleotide that has sequence complementarity with said single-stranded nucleic acid template;

(b) providing a plurality of nucleotides of a single species in said one or more thermally isolated chambers comprising said plurality of nucleic acid molecules;

(c) detecting an enthalpy change in said one or more thermally isolated chambers comprising said plurality of nucleic acid molecules, wherein said enthalpy change is associated with incorporation of one or more nucleotides of said plurality of nucleotides of said single species by said polymerase into a nucleic acid strand growing from said primer, wherein said nucleic acid strand has sequence complementarity with said single-stranded nucleic acid template; and

(d) repeating (b) and (c) to obtain a sequence of said single-stranded nucleic acid template.

2. The method of claim 1, wherein (d) comprises repeating (b) and (c) with nucleotides of a different species than said single species.

3. The method of claim 1, further comprising, prior to (d), removing unincorporated nucleotides from said one or more thermally isolated chambers comprising said plurality of nucleic acid molecules.

4. The method of claim 1, wherein each of said plurality of nucleic acid molecules is immobilized to a support.

5. The method of claim 4, wherein said support comprises a particle.

6. The method of claim 5, wherein said particle comprises metal.

7. The method of claim 5, wherein said particle is magnetic.

8. The method of claim 1, wherein said enthalpy change is detected by one or more sensors.

9. The method of claim 8, wherein said one or more sensors comprise a heat sensor.

10. The method of claim 9, wherein said heat sensor is selected from the group consisting of a calorimeter, a thermocouple, a thermometer, and an infrared (IR) sensor.

11. The method of claim 8, wherein a sensor of said one or more sensors is positioned adjacent to a surface of a given one of said plurality of thermally isolated chambers.

12. The method of claim 8, wherein a sensor of said one or more sensors extends into a given one of said plurality of thermally isolated chambers.

13. The method of claim 1, further comprising measuring a pH change in said one or more thermally isolated chambers, wherein said pH change is associated with said incorporation of said one or more nucleotides of said single species by said polymerase into said primer of said plurality of nucleic acid molecules.

14. The method of claim 13, wherein said pH change is measured via a potential difference between a reference electrode and a measuring electrode.

15. The method of claim 1, wherein different chambers among said plurality of thermally isolated chambers comprise nucleic acid templates that differ in sequence between different chambers.

16. The method of claim 1, wherein said plurality of thermally isolated chambers are comprised in a substrate comprising one or more fluid channels in fluid communication with said plurality of thermally isolated chambers.

17. The method of claim 1, wherein said enthalpy change is detected in the absence of detecting a dye or label.

18. The method of claim 1, further comprising generating said plurality of nucleic acid molecules from said single-stranded nucleic acid template via clonal amplification.

19. The method of claim 1, wherein a given one of said plurality of thermally isolated chambers comprises a well.

20. The method of claim 1, wherein said primer comprises said hairpin formed by self-hybridization of said single-stranded nucleic acid template.

21. The method of claim 1, wherein said primer comprises said single-stranded oligonucleotide that has sequence complementarity with said single-stranded nucleic acid template.