Conformational probes and methods for sequencing nucleic acids

• US 9,862,998 B2
• Filed: 04/19/2016
• Issued: 01/09/2018
• Est. Priority Date: 06/18/2010
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: He, Molly, Chen, Cheng-Yao, Kool, Eric, Ronaghi, Mostafa, Previte, Michael, Pantoja, Rigo
• Primary Examiner(s): HORLICK, KENNETH R
• Application Number:
  US15/132,662
• Publication Number:
  US 20160298186A1
• Time in Patent Office: 630 Days
• Field of Search: 435 911
• 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 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2563/125 the label being enzymatic, i.e. proteins, and non proteins, such as nucleic acid with enzymatic activity
• CPC Class Codes: C12Q 2565/1015 labels being on the same oligonucleotide
• CPC Class Codes: C12Q 2565/133 conformational analysis

Abstract

This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Claims

1. A method of determining a sequence of nucleotides for a nucleic acid sample, comprising

providing an array of nucleic acid templates, wherein the nucleic acid templates comprise nucleotide sequence fragments of the nucleic acid sample, and wherein the nucleotide sequence fragments comprise a universal sequence to form tailed fragments;

contacting the array of nucleic acid templates with conformationally labeled polymerases and at least four different nucleotide species under conditions, wherein the conformationally labeled polymerases comprise a finger domain and a thumb domain, wherein the conformationally labeled polymerases catalyze sequential addition of the nucleotide species to form nucleic acid complements of the nucleic acid templates, wherein the different nucleotide species comprise at least one non-natural nucleotide analog, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species;

detecting a series of the conformational signal changes from the conformationally labeled polymerase under the conditions and at individual locations of the array; and

determining the sequence of nucleotides for the nucleic acid sample by determining the rates or time durations for the conformational signal changes at the individual locations of the array, wherein the determining comprises distinguishing at least 5 fold difference between the rate or time duration for the conformational signal changes of the at least one non-natural nucleotide analog and the other different nucleotide species that are added to form the nucleic acid complements of the nucleic acid templates to determine the sequence of nucleotides for the nucleic acid sample.

2. The method of claim 1, wherein the at least one non-natural nucleotide analog lacks probes that are detected in the method.

3. The method of claim 1, wherein the providing the array comprises amplifying portions of the nucleic acid sample to produce the nucleotide sequence fragments.

4. The method of claim 1, wherein the tailed fragments are hybridized to oligonucleotides attached to the array and wherein the oligonucleotides are complementary to the universal sequence.

5. The method of claim 1, further comprising

contacting the array of nucleic acid templates with conformationally labeled exonucleases under conditions wherein the conformationally labeled exonucleases catalyze sequential removal of nucleotide species from the nucleic acid templates, wherein the sequential removal of each different nucleotide species produces a conformational signal change from each of the conformationally labeled exonucleases and wherein the rate or time duration for the conformational signal change is distinguishable for at least one different nucleotide species that is removed;

detecting a series of changes in the signal from the conformationally labeled exonuclease under the conditions and at the individual locations of the array; and

determining the rates or time durations for the changes in the signal for the series of changes in the signal from the conformationally labeled exonuclease.

6. The method of claim 5, wherein the rate or time duration for the conformational signal change is distinguishable for only one of four different nucleotide species that are removed.

7. The method of claim 5, wherein the rates or time durations for the conformational signal change are distinguishable for four of four different nucleotide species that are removed.

8. The method of claim 5, wherein the at least one different nucleotide species that is removed comprises a modified alpha-phosphate moiety.

9. The method of claim 8, wherein the modified alpha-phosphate moiety comprises a moiety other than oxygen covalently attached to the alpha phosphate.

10. The method of claim 1, wherein the nucleotide species comprise at least four different non-natural nucleotide analogs.

11. The method of claim 1, wherein the conformationally labeled polymerases each comprise an optical probe.

12. The method of claim 11, wherein the conformational signal change comprises a change in wavelength or intensity from the optical probe.

13. The method of claim 11, wherein the optical probe comprises a fluorophore.

14. The method of claim 11, wherein the conformationally labeled polymerases each comprise a pair of optical probes.

15. The method of claim 14, wherein the conformational signal change comprises increased FRET from the pair of optical probes, decreased FRET from the pair of optical probes, increased fluorescence quenching from the pair of optical probes or decreased fluorescence quenching from the pair of optical probes.

16. The method of claim 1, wherein the at least one non-natural nucleotide species comprise at least one caged nucleotide.

17. The method of claim 1, wherein the at least one non-natural nucleotide analog comprises a reversible terminator moiety.

18. The method of claim 1, wherein the nucleic acid templates are individually resolved from each other.

19. The method of claim 1, wherein the nucleic acid templates are present in colonies and individual colonies comprise a plurality of templates that are the same species.

20. The method of claim 19, wherein the method comprises determining a sequence of nucleotides for a plurality of templates present in colonies.

21. The method of claim 1, wherein a probe is attached to the finger domain of the conformationally labeled polymerases.

22. The method of claim 1, wherein a probe is attached to the thumb domain of the conformationally labeled polymerases.

23. The method of claim 1, wherein the conformational signal change comprises increased or decreased FRET between a probe that is attached to the finger domain and a probe that is attached to the thumb domain.