Sequencing method for rapid identification and processing of cognate nucleotide pairs

• US 10,428,378 B2
• Filed: 07/19/2017
• Issued: 10/01/2019
• Est. Priority Date: 08/15/2016
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Omniome, Inc.
• Inventors: Iyidogan, Pinar, Vijayan, Kandaswamy
• Primary Examiner(s): Wilder, Cynthia B
• Application Number:
  US15/654,406
• Publication Number:
  US 20180044715A1
• Time in Patent Office: 804 Days
• CPC Class Codes: C12Q 1/00 Measuring or testing processes involving enzymes, nucleic acids or microorganisms measuring or testing apparatus with condition measuring or sensing means, e.g. colony counters, C12M1/34; Compositions therefor; Processes of preparing such compositions
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6813 Hybridisation assays
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2565/133 conformational analysis
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2565/628 being a surface plasmon resonance spectrometer
• CPC Class Codes: G01N 2001/4038 electric methods, e.g. electromigration, electrophoresis, ionisation
• CPC Class Codes: G01N 21/45 using interferometric methods; using Schlieren methods
• CPC Class Codes: G01N 27/447 using electrophoresis

Abstract

Provided are methods and systems for reducing the time needed for sequencing nucleic acids. The approach relies on detecting formation of nucleotide-specific ternary complexes comprising a polymerase (e.g., a DNA polymerizing enzyme), a primed template nucleic acid molecule, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide, as well as the subsequent next correct nucleotide from a cycle of examining four different nucleotides without requiring chemical incorporation of any nucleotide into the primer.

Claims

1. A method of determining the identity of first and second correct nucleotides respectively comprising bases complementary to the next two bases of a template strand immediately downstream of a primer of a primed template nucleic acid molecule, said method comprising the steps of:

(a) conducting a plurality of cycles of contacting a first primed template nucleic acid molecule with a reaction mixture comprising a polymerase and, for each cycle, a different test nucleotide, and removing any polymerase and nucleotide that may have bound to the first primed template nucleic acid molecule,

wherein the polymerase does not incorporate any of the different test nucleotides into the primer of the first primed template nucleic acid molecule during any of the plurality of cycles;

(b) measuring, for the cycles in step (a), signals indicating the magnitudes of formation of stabilized ternary complexes comprising binding of the first primed template nucleic acid molecule to the polymerase and the different test nucleotides; and

(c) determining the identities of the first correct nucleotide downstream of the primer, and the second correct nucleotide downstream of the primer using the measured signals from step (b), wherein the test nucleotide associated with the highest magnitude of stabilized ternary complex formation is identified as the first correct nucleotide downstream of the primer, and the test nucleotide associated with the second-highest magnitude of stabilized ternary complex formation is identified as the second correct nucleotide downstream of the primer.

2. The method of claim 1, wherein the primer of the first primed template nucleic acid molecule is an extendable primer that does not comprise a reversible terminator moiety attached to its 3′

terminal nucleotide.

3. The method of claim 2, wherein the reaction mixture comprises either a divalent non-catalytic metal ion that inhibits polymerase-mediated incorporation, or a trivalent non-catalytic metal ion that inhibits polymerase-mediated incorporation.

4. The method of claim 2, wherein the plurality of cycles in step (a) comprises four cycles.

5. The method of claim 2, further comprising the step of

(d) incorporating a reversible terminator nucleotide comprising a reversible terminator moiety into the first primed template nucleic acid molecule to produce a first blocked primed template nucleic acid molecule.

6. The method of claim 5, further comprising the step of

(e) removing the reversible terminator moiety from the first blocked primed template nucleic acid molecule to produce a first de-blocked primed template nucleic acid molecule.

7. The method of claim 6, further comprising repeating steps (a)-(c) using the first de-blocked primed template nucleic acid molecule in place of the first primed template nucleic acid molecule.

8. The method of claim 6, further comprising the steps of:

(f) incorporating a reversible terminator nucleotide comprising a reversible terminator moiety into the first de-blocked primed template nucleic acid molecule to produce a second blocked primed template nucleic acid molecule; and

(g) removing the reversible terminator moiety from the second blocked primed template nucleic acid molecule to produce a second de-blocked primed template nucleic acid molecule.

9. The method of claim 8, further comprising repeating steps (a)-(c) using the second de-blocked primed template nucleic acid molecule in place of the first primed template nucleic acid molecule.

10. The method of claim 9, wherein step (c) occurs after all of steps (a)-(b) and (d)-(g) have been performed.

11. The method of claim 5, wherein none of the different test nucleotides comprises an exogenous fluorescent label.

12. The method of claim 11, wherein each of the different test nucleotides is a different native nucleotide.

13. The method of claim 5, wherein the polymerase does not comprise an exogenous fluorescent label, and wherein step (b) does not comprise measuring any fluorescent signal from the polymerase.

14. The method of claim 1, wherein the first primed template nucleic acid molecule is a first blocked primed template nucleic acid molecule, and wherein the primer of the first blocked primed template nucleic acid molecule comprises a reversible terminator moiety that blocks phosphodiester bond formation.

15. The method of claim 14, wherein the reaction mixture comprises a catalytic metal ion.

16. The method of claim 14, wherein the plurality of cycles in step (a) comprises four cycles.

17. The method of claim 14, further comprises the steps of:

(d) removing the reversible terminator moiety from the primer of the first blocked primed template nucleic acid molecule to produce a first de-blocked primer; and

(e) incorporating a reversible terminator nucleotide comprising a reversible terminator moiety into the first de-blocked primer to produce a second blocked primed template nucleic acid molecule.

18. The method of claim 17, wherein steps (a)-(c) are repeated using the second blocked primed template nucleic acid molecule in place of the first blocked primed template nucleic acid molecule.

19. The method of claim 17, further comprising, after step (e), the steps of

(f) removing the reversible terminator moiety from the second blocked primed template nucleic acid molecule to produce a second de-blocked primer;

and

(g) incorporating a reversible terminator nucleotide comprising a reversible terminator moiety into the second de-blocked primer to produce a third blocked primed template nucleic acid molecule.

20. The method of claim 19, wherein steps (a)-(c) are repeated using the third blocked primed template nucleic acid molecule in place of the first blocked primed template nucleic acid molecule.

21. The method of claim 20, wherein step (c) occurs after all of steps (a)-(b) and (d)-(g) have been performed.

22. The method of claim 17, wherein none of the different test nucleotides comprises an exogenous fluorescent label.

23. The method of claim 22, wherein each of the different test nucleotides is a different native nucleotide.

24. The method of claim 17, wherein the polymerase does not comprise an exogenous fluorescent label, and wherein step (b) does not comprise measuring any fluorescent signal from the polymerase.

25. The method of claim 14, wherein the reversible terminator moiety that blocks phosphodiester bond formation is a 3′

-ONH₂ moiety.

26. A method of determining the identity of first and second correct nucleotides respectively comprising bases complementary to the next two bases of a template strand immediately downstream of a primer in a primed template nucleic acid molecule, said method comprising the steps of:

(a) conducting a plurality of cycles of

contacting a first primed template nucleic acid molecule with a reaction mixture comprising a polymerase and, for each cycle, a different pair of test nucleotides, and

removing any polymerase and nucleotide that may have bound to the first primed template nucleic acid molecule,

wherein the polymerase does not incorporate any of the different test nucleotides into the primer of the first primed template nucleic acid molecule during any of the four cycles;

(b) measuring, for the cycles in step (a), signals indicating the magnitudes of formation of stabilized ternary complexes comprising binding of the first primed template nucleic acid molecule to the polymerase and the test nucleotides among the different pairs of test nucleotides; and

(c) determining the identities of the first correct nucleotide downstream of the primer, and the second correct nucleotide downstream of the primer using the measured signals from step (b), wherein the test nucleotide associated with the highest magnitude of stabilized ternary complex formation is identified as the first correct nucleotide downstream of the primer, and the test nucleotide associated with the second-highest magnitude of stabilized ternary complex formation is identified as the second correct nucleotide downstream of the primer.

27. The method of claim 26,

wherein the first primed template nucleic acid molecule comprises a primer with a reversible terminator moiety that blocks phosphodiester bond formation.