Sequencing method employing ternary complex destabilization to identify cognate nucleotides

• US 10,294,514 B2
• Filed: 04/28/2017
• Issued: 05/21/2019
• Est. Priority Date: 04/29/2016
• 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:
  US15/581,828
• Publication Number:
  US 20170314064A1
• Time in Patent Office: 753 Days
• Field of Search: 435 61
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• 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 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2527/137 Concentration of a component of medium
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2565/133 conformational analysis
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, 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 without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.

Claims

1. A method of identifying a nucleotide comprising a base complementary to the next base of a template strand immediately downstream of a primer in a primed template nucleic acid molecule, said method comprising the steps of:

(a) providing a blocked primed template nucleic acid molecule comprising a reversible terminator moiety that precludes the 3′

-terminus of the blocked primed template nucleic acid molecule from participating in phosphodiester bond formation;

(b) contacting the blocked primed template nucleic acid molecule with a first reaction mixture that comprises a polymerase, and a plurality of different nucleotide molecules,

whereby a stabilized ternary complex forms, said stabilized ternary complex comprising one of the plurality of different nucleotide molecules;

(c) contacting the stabilized ternary complex with a second reaction mixture that comprises at least one of the different nucleotide molecules and that does not comprise a first nucleotide molecule of the plurality of different nucleotide molecules;

(d) monitoring interaction of the polymerase and the blocked primed template nucleic acid molecule in contact with the second reaction mixture to detect any of the stabilized ternary complex remaining after step (c); and

(e) identifying the nucleotide that comprises the base complementary to the next base of the template strand using results from step (d).

2. The method of claim 1, further comprising the step of:

(f) removing the reversible terminator moiety from the blocked primed template nucleic acid molecule after step (d).

3. The method of claim 2, wherein step (e) comprises determining either that:

(i) the first nucleotide molecule in step (c) comprises the base complementary to the next base of the template strand if the stabilized ternary complex dissociates in step (d), or

(ii) the first nucleotide molecule in step (c) does not comprise the base complementary to the next base of the template strand if the stabilized ternary complex is retained in step (d).

4. The method of claim 3, wherein the polymerase of the first reaction mixture comprises an exogenous fluorescent label.

5. The method of claim 3, wherein the plurality of different nucleotide molecules in the first reaction mixture is either a plurality of different native nucleotide molecules, or a plurality of different fluorescently labeled nucleotide molecules.

6. The method of claim 5, wherein the first reaction mixture further comprises a catalytic metal ion.

7. The method of claim 5, wherein the first reaction mixture does not comprise non-catalytic metal ions that inhibit phosphodiester bond formation by the polymerase of the first reaction mixture, and wherein the first reaction mixture further comprises a catalytic metal ion.

8. The method of claim 3, wherein step (a) comprises incorporating, with a polymerase, a reversible terminator nucleotide at the 3′

-end of the primer of the primed template nucleic acid molecule, whereby there is produced the blocked primed template nucleic acid molecule comprising the reversible terminator moiety that precludes the 3′

-terminus of the blocked primed template nucleic acid molecule from participating in phosphodiester bond formation.

9. The method of claim 8, further comprising, after step (a) and before step (b), a step of contacting the blocked primed template nucleic acid molecule with the polymerase of the first reaction mixture in the absence the plurality of different nucleotide molecules.

10. The method of claim 8, wherein the second reaction mixture comprises the same polymerase that is present in the first reaction mixture.

11. The method of claim 8, further comprising, after step (a) and before step (b), the step of contacting the blocked primed template nucleic acid molecule with the polymerase of the first reaction mixture in the absence of the plurality of different nucleotide molecules.

12. The method of claim 11, wherein the first reaction mixture further comprises a catalytic metal ion.

13. The method of claim 11, wherein the second reaction mixture comprises the same polymerase that is present in the first reaction mixture.

14. The method of claim 8, further comprising repeating steps (b)-(e) a plurality of times.

15. The method of claim 14, wherein the polymerase used in step (a) and the polymerase of the first reaction mixture in step (b) are different types of polymerase enzymes.

16. The method of claim 14, wherein the polymerase of the first reaction mixture comprises an exogenous fluorescent label.

17. The method of claim 14, wherein the plurality of different nucleotide molecules in the first reaction mixture is either a plurality of different native nucleotide molecules, or a plurality of different fluorescently labeled nucleotide molecules.

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

19. The method of claim 14, wherein the first reaction mixture does not comprise non-catalytic metal ions that inhibit phosphodiester bond formation by the polymerase of the first reaction mixture.

20. The method of claim 14, wherein step (f) is performed before step (e).

21. The method of claim 14, wherein the second reaction mixture comprises the same polymerase that is present in the first reaction mixture.

22. A method of identifying a nucleotide comprising a base complementary to the next base of a template strand immediately downstream of a primer in a primed template nucleic acid molecule, said method comprising:

(a) providing the primed template nucleic acid molecule;

(b) contacting the primed template nucleic acid molecule with a first reaction mixture that comprises a polymerase and a plurality of different nucleotide molecules,

whereby a stabilized ternary complex forms, said stabilized ternary complex comprising one of the plurality of different nucleotide molecules;

(c) contacting the primed template nucleic acid molecule, after step (b), with a second reaction mixture that comprises at least one of the different nucleotide molecules and that does not comprise a first nucleotide molecule of the plurality of different nucleotide molecules;

(d) monitoring interaction of the polymerase and the primed template nucleic acid molecule in the second reaction mixture, without incorporating any nucleotide into the primer, to detect any of the stabilized ternary complex remaining after step (c); and

(e) identifying the nucleotide that comprises the base complementary to the next base of the template strand using results from step (d).

24. The method of claim 22, wherein the plurality of different nucleotide molecules comprises a plurality of different unlabeled nucleotide molecules.

25. The method of claim 24, wherein the polymerase of the first reaction mixture comprises an exogenous fluorescent label producing a detectable signal that is substantially unchanged in the presence or absence of the next correct nucleotide.

26. The method of claim 24, wherein the first reaction mixture comprises four different types of native nucleotide molecules, and the second reaction mixture does not comprise one of the four different types of native nucleotide molecules.

27. The method of claim 24, wherein the first reaction mixture comprises two different types of native nucleotide molecules, and the second reaction mixture does not comprise one of the two different types of native nucleotide molecules.

28. The method of claim 24, further comprising an incorporation step that comprises removing any of the plurality of different nucleotide molecules remaining in contact with the primed template nucleic acid after step (d), contacting the primed template nucleic acid with a third reaction mixture that comprises a polymerase and at least one reversible terminator, and then incorporating a single reversible terminator into the primer.

29. The method of claim 28, wherein the polymerase of the first reaction mixture and the polymerase of the third reaction mixture are different types of DNA polymerase, and wherein the polymerase of the first reaction mixture comprises an exogenous detectable label.

30. The method of claim 22, further comprising an incorporation step that comprises removing any of the plurality of different nucleotide molecules remaining in contact with the primed template nucleic acid after step (d), contacting the primed template nucleic acid with a third reaction mixture that comprises a polymerase and a nucleotide, and then incorporating the nucleotide of the third reaction mixture into the primer.

31. The method of claim 22, further comprising an incorporation step that comprises removing any of the plurality of different nucleotide molecules remaining in contact with the primed template nucleic acid after step (d), contacting the primed template nucleic acid with a third reaction mixture that comprises a polymerase and at least one reversible terminator, and then incorporating a single reversible terminator into the primer.

32. The method of claim 30, further comprising repeating each of steps (b)-(e) and the incorporation step.

33. The method of claim 31, wherein the polymerase of the first reaction mixture and the polymerase of the third reaction mixture are different types of DNA polymerase.

34. The method of claim 22, wherein after step (b) and before step (c) there is a step (b)(i) that comprises monitoring interaction of the primed template nucleic acid molecule with the polymerase in the first reaction mixture, without incorporating any nucleotides molecule into the primer, to detect any of the stabilized ternary complex that formed in step (b).

23. A method of identifying a nucleotide comprising a base complementary to the next base of a template strand immediately downstream of a primer in a primed template nucleic acid molecule, said method comprising:

(a) providing the primed template nucleic acid molecule;

(b) contacting the primed template nucleic acid molecule with a first reaction mixture that comprises a polymerase, but does not comprise any nucleotide, whereby a binary complex forms;

(c) contacting the binary complex with a second reaction mixture that comprises a plurality of different nucleotide molecules, whereby a stabilized ternary complex forms if one of the plurality of different nucleotide molecules comprises the base complementary to the next base of the template strand;

(d) detecting, without incorporating any nucleotide into the primer, any of the stabilized ternary complex that may have formed;

(e) contacting the primed template nucleic acid molecule, after step (d), with a third reaction mixture that comprises at least one of the different nucleotide molecules and that does not comprise a first nucleotide molecule of the plurality of different nucleotide molecules;

(f) detecting, without incorporating any nucleotide into the primer, any of the stabilized ternary complex remaining after step (e); and

(g) identifying the nucleotide that comprises the base complementary to the next base of the template strand using results from both of detecting steps (d) and (f).

35. The method of claim 23, further comprising an incorporation step that comprises first replacing the third reaction mixture in contact with the primed template nucleic acid molecule with a fourth reaction mixture that comprises a polymerase and at least one reversible terminator, and then incorporating the at least one reversible terminator into the primer.

36. The method of claim 23, wherein step (g) comprises determining either that

(i) the first nucleotide molecule comprises the base complementary to the next base of the template strand if the stabilized ternary complex was detected in step (d) but was not detected in step (f), or

(ii) the first nucleotide molecule does not comprise the base complementary to the next base of the template strand if the stabilized ternary complex was detected in both of steps (d) and (f), or

(iii) the first reaction mixture does not comprise the nucleotide comprising the base complementary to the next base of the template strand if the stabilized ternary complex was not detected in at least one of steps (d) and (f).

37. The method of claim 36, further comprising an incorporation step that comprises first replacing the third reaction mixture in contact with the primed template nucleic acid molecule with a fourth reaction mixture that comprises a polymerase and at least one reversible terminator, and then incorporating the at least one reversible terminator into the primer.

38. The method of claim 36, wherein steps (b)-(f) are repeated a plurality of times.

39. The method of claim 36, wherein the primed template nucleic acid molecule of step (a) is immobilized to a surface.

40. The method of claim 36, wherein detecting steps (d) and (f) comprise optical detection.

41. The method of claim 39, wherein step (c) comprises replacing the first reaction mixture with the second reaction mixture by flowing the second reaction mixture over the primed template nucleic acid molecule that is immobilized to the surface.

42. The method of claim 39, wherein step (c) comprises replacing the first reaction mixture with the second reaction mixture by physically moving the primed template nucleic acid molecule that is immobilized to the surface from the first reaction mixture to the second reaction mixture.