Sequencing method employing ternary complex destabilization to identify cognate nucleotides

• US 10,633,692 B2
• Filed: 04/02/2019
• Issued: 04/28/2020
• 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:
  US16/372,812
• Publication Number:
  US 20190226012A1
• Time in Patent Office: 392 Days
• 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 for identifying a nucleotide of a nucleic acid, comprising:

(a) providing a solid support that is attached to a primed template nucleic acid molecule, wherein the solid support is in contact with a first reaction mixture that comprises a polymerase and a plurality of different nucleotide types,

wherein the primed template nucleic acid molecule, the polymerase and one of the plurality of different nucleotide types form a stabilized ternary complex on the solid support;

(b) progressively removing nucleotide types of the plurality of different nucleotide types from contact with the primed template nucleic acid molecule on the solid support;

(c) monitoring stability of the ternary complex on the solid support during the progressive removal of the nucleotide types, without incorporating any nucleotide into the primer; and

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

2. The method of claim 1, wherein the progressively removing of step (b) comprises exchanging the first reaction mixture with a second reaction mixture that does not include a first nucleotide type of the plurality of different nucleotide types.

3. The method of claim 2, wherein the monitoring of step (c) comprises observing dissociation of the ternary complex in the second reaction mixture and step (d) comprises identifying the first nucleotide type as the nucleotide that comprises the base complementary to the next base of the template strand.

4. The method of claim 1, further comprising (e) incorporating a nucleotide into the primer of the primed template nucleic acid molecule, thereby forming an extended primed template nucleic acid molecule.

5. The method of claim 4, further comprising repeating steps (a) through (e) using the extended primed template nucleic acid molecule instead of the primed template nucleic acid molecule.

6. The method of claim 4, wherein the nucleotide that is incorporated into the primer of the extended primed template nucleic acid molecule comprises a reversible terminator moiety.

7. The method of claim 6, further comprising removing the reversible terminator moiety from the extended primed template nucleic acid molecule and repeating steps (a) through (e) using the extended primed template nucleic acid molecule instead of the primed template nucleic acid molecule.

8. The method of claim 4, wherein the nucleotide that is incorporated into the primer of the extended primed template nucleic acid molecule is a non-labeled nucleotide.

9. The method of claim 1, wherein the nucleotides in the plurality of different nucleotide types comprise exogenous labels.

10. The method of claim 9, wherein step (c) comprises detecting dissociation of the exogenous labels from the primed template nucleic acid molecule on the solid support.

11. The method of claim 9, wherein each type of nucleotide in the plurality of different nucleotide types is linked to a different type of label.

12. The method of claim 9, wherein the different types of nucleotides in the plurality of different nucleotide types are linked to the same type of label.

13. The method of claim 1, wherein the polymerase comprises an exogenous label and wherein step (c) comprises detecting the exogenous label.

14. The method of claim 13, wherein step (c) comprises detecting dissociation of the exogenous labels from the primed template nucleic acid molecule on the solid support.

15. The method of claim 1, wherein the first reaction mixture comprises cognates for four different base types in the template nucleic acid.

16. The method of claim 1, wherein the solid support is covalently attached to the primed template nucleic acid molecule.