Clonal amplification of nucleic acid on solid surface with template walking

• US 10,233,488 B2
• Filed: 09/26/2016
• Issued: 03/19/2019
• Est. Priority Date: 12/17/2010
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Li, Bin, Lao, Kai Qin, O'Neil, Jennifer, Kunkel, Jennifer, Haley, Kellie, Kasinskas, Rachel, Ma, Zhaochun, Brzoska, Pius
• Primary Examiner(s): Priest, Aaron A
• Application Number:
  US15/276,713
• Publication Number:
  US 20170067098A1
• Time in Patent Office: 904 Days
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/46 involving cholinesterase
• 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 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6846 Common amplification features
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• 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 2521/507 Recombinase
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2537/1376 Displacement by an enzyme
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

Novel methods of generating a localized population of immobilized clonal amplicons on a support are provided.

Claims

1. A method for amplifying a plurality of nucleic acid templates, comprising:

a) providing a plurality of forward primers immobilized on a support, wherein the plurality of forward primers includes a first forward primer and a second forward primer, wherein the plurality of forward primers share at least 90% sequence identity, and wherein the distances between the first forward primer and the second forward primer on the support is not more than twice the length of the first forward primer;

b) providing a nucleic acid reverse strand from the plurality of nucleic acid templates, wherein the nucleic acid reverse strand includes a forward primer-binding sequence that can hybridize to any one of the plurality of forward primers;

c) hybridizing the first forward primer to the forward primer-binding sequence on the nucleic acid reverse strand;

d) generating a first extended forward strand by primer extension of the first forward primer using the nucleic acid reverse strand as a template, wherein at least 85% of the first extended forward strand residues are complementary to the nucleic acid reverse strand residues;

e) performing a walking step, wherein the walking step comprises denaturing at least a portion of the forward primer-binding sequence of the nucleic acid reverse strand from the first forward primer and hybridizing the second forward primer to the forward primer-binding sequence on the nucleic acid reverse strand, wherein a portion of the nucleic acid reverse strand is hybridized to the first extended forward strand;

f) generating a second extended forward strand by primer extension of the second forward primer using the nucleic acid reverse strand as a template, wherein at least 85% of the second extended forward strand residues are complementary to the nucleic acid reverse strand residues; and

g) amplifying the plurality of nucleic acid templates simultaneously in a single continuous liquid phase, by performing one or more amplification cycles comprising steps (e) - (f) under isothermal conditions to form a plurality of clonal nucleic acid populations, wherein the second forward primer of step (e) of an amplification cycle acts as the first forward primer of step (e) of a subsequent amplification cycle, and wherein at least 50% of the nucleic acid strands or their complements in each clonal nucleic acid population are at least 75% identical.

2. The method of claim 1, wherein the support comprises only primers having sequences that are substantially identical to the plurality of forward primers.

3. The method of claim 1, wherein step (e) comprises:

denaturing all of the forward primer-binding sequence on the nucleic acid reverse strand from the first extended forward strand and hybridizing the forward primer-binding sequence to the second forward primer.

4. The method of claim 1, wherein at least 60% of the bases of the plurality of forward primers are adenine, thymine or uracil, or are complementary to adenine, thymine or uracil.

5. The method of claim 1, wherein primer extension of the second forward primer using the nucleic acid reverse strand as a template results in displacing the first extended forward strand that is hybridized to the nucleic acid reverse strand.

6. The method of claim 1, further comprising:

hybridizing the forward primer-binding sequence on the nucleic acid reverse strand to a third forward primer of the plurality of forward primers, wherein a portion of the nucleic acid reverse strand is also hybridized to the first or second extended forward strand.

7. The method of claim 6, wherein the hybridizing the forward primer-binding sequence on the nucleic acid reverse strand to a third forward primer comprises:

denaturing all of the forward primer-binding sequence on the nucleic acid reverse strand from the second extended forward strand and re-hybridizing the forward primer-binding sequence to the third forward primer.

8. The method of claim 7, further comprising:

generating a third extended forward strand by primer extension of the third forward primer using the nucleic acid reverse strand as a template, wherein at least 85% of the second extended forward strand residues are complementary to the nucleic acid reverse strand residues.

9. The method of claim 5, further comprising:

a) hybridizing a first reverse primer to a reverse primer-binding sequence on the first or second extended forward strand, by denaturing at least a portion of the reverse primer-binding sequence on the first or second extended forward strand from the nucleic acid reverse strand, wherein the first reverse primer is a soluble primer;

b) extending the first reverse primer using the first or second extended forward strand as a template; and

c) generating an extended reverse strand wherein at least 85% of the extended reverse strand residues are complementary to the first or second extended forward strand residues.

10. The method of claim 1, wherein the amplifying is carried out by adjusting the isothermal conditions to a temperature range between 45°

C. and 80°

C.

11. The method of claim 1, wherein the forward primers in the plurality of forward primers are immobilized adjacent to each other in a continuous lawn on the support.

12. The method of claim 1, wherein the plurality of nucleic acid templates is produced by taking a plurality of input nucleic acid sequences and appending a first universal adaptor sequence onto the ends of at least one input nucleic acid sequence, and wherein the first universal adaptor sequence hybridizes to the immobilized forward primers.

14. The method of claim 9, further comprising subjecting the extended forward strands and the extended reverse strands to a sequencing reaction.

15. The method of claim 10, wherein at least 50% of the nucleic acid reverse strands are hybridized to forward strands at all times during the amplifying.

16. The method of claim 10, wherein the amplifying is carried out using a polymerase that is active at a temperature at or above 45°

C.

17. The method of claim 16, wherein the amplifying is carried out by maintaining the temperature at a range of between 45°

C. and 70°

C.

18. The method of claim 16, wherein the amplifying is carried out by maintaining the temperature at or around 50°

C., 55°

C., 60°

C., 65°

C., or 70°

C. for between 10 and 120 minutes.

19. The method of claim 1, wherein the amplifying is carried out by adjusting the isothermal conditions to a temperature that is higher than the T_m of all forward primers but lower than the T_m of the nucleic acid reverse strands.

20. The method of claim 12, wherein the forward primers are separated from each other on the support by a distance that is shorter than the length of the universal adapter.

13. The method of 1, wherein individual clonal nucleic acid populations are immobilized within or on a different support from other amplified populations.