Methods of nucleic acid amplification and sequencing

• US 20090117621A1
• Filed: 07/20/2006
• Published: 05/07/2009
• Est. Priority Date: 07/20/2005
• Status: Abandoned Application

• Current Assignee: Solexa Ltd. (Illumina Incorporated)
• Original Assignee: Solexa Ltd. (Illumina Incorporated)
• Inventors: Boutell, Jonathan Mark, Earnshaw, David James, Schroth, Gary Paul, Cox, Anthony James, Smith, Geoffrey Paul
• Application Number:
  US11/989,171
• Publication Number:
  US 20090117621A1
• Time in Patent Office: Days
• US Class Current: 435/91.200
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides

Abstract

The invention relates to a method of amplifying one or more nucleic acid templates on a solid support in a nucleic acid amplification reaction, for example by solid-phase PCR using one or more amplification primers attached to the solid support. The method is characterised in that the amplification primers used comprise a template-specific portion which is a sequence of at least 26 consecutive nucleotides and are not capable of annealing to target regions in the template under conditions of the amplification reaction. The method is particularly useful for amplifying human genomic DNA.

Claims

1. A method of amplifying one or more nucleic acid templates on a solid support which comprises:

a) bringing into contact the following components under conditions which permit a nucleic acid amplification reaction;

i) a solid support,

ii) a plurality of forward and reverse amplification primers, wherein the solid support is provided with the forward and/or reverse amplification primers immobilised thereon, and

iii) one or more nucleic acid templates to be amplified comprising at the 3′

end a primer-binding sequence which is a sequence of nucleotides capable of annealing to the forward amplification primers and at the 5′

end a primer-binding sequence which is a sequence of nucleotides the complement of which is capable of annealing to the reverse amplification primers; and

b) carrying out a nucleic acid amplification reaction whereby said template(s) is/are amplified with said forward and reverse amplification primers,

characterised in that the amplification primers immobilised on the solid support comprise a template-specific portion which is a sequence of at least 26 consecutive nucleotides capable of annealing to a primer binding sequence in the template or the complement thereof and that the forward and reverse primers are not capable of annealing to any part of the template other than their respective primer binding sequences during the nucleic acid amplification reaction.

2. The method according to claim 1 wherein the one or more templates to be amplified each include a target sequence located between the two primer binding sequences, each said target sequence representing a fragment of the full sequence of a nucleic acid sample of interest, and the forward and reverse primers are selected based on knowledge of the full sequence of the nucleic acid sample of interest so as not to be capable of annealing to any part of the template other than their respective primer binding sequences during the nucleic acid amplification reaction.

3. The method according to claim 2 wherein the nucleic acid sample of interest is genomic DNA.

4. The method according to claim 3 wherein the nucleic acid sample of interest is human genomic DNA.

5. The method according to claim 4 wherein the nucleic acid sample of interest represents from 50% to 100% of the complete human genome.

6. The method according to claim 1 wherein the nucleic acid template(s) is/are produced by providing one or more target nucleic acid molecules to be amplified and adding thereto at the 3′

end a first adaptor polynucleotide comprising a primer binding sequence capable of annealing to the forward amplification primers and at the 5′

end a second adaptor polynucleotide comprising a primer binding sequence the complement of which is capable of annealing to the reverse amplification primers.

7. The method according to claim 6 wherein a plurality of templates to be amplified in a single amplification reaction are produced by providing a plurality of target nucleic acid molecules of different sequence and adding thereto at the 3′

end a first universal adaptor polynucleotide comprising a sequence of nucleotides capable of annealing to the forward amplification primers and at the 5′

end a second universal adaptor polynucleotide comprising a sequence of nucleotides the complement of which is capable of annealing to the reverse amplification primers.

8. The method according to claim 7 wherein the plurality of target nucleic acid molecules of different sequence are genomic DNA fragments.

9. The method according to claim 8 wherein the genomic DNA fragments are human genomic DNA fragments.

10. The method according to claim 9 wherein the sequences of the template-specific portions in the forward and reverse amplification primers are selected such that any sequence of 20 consecutive nucleotides in either template-specific portion is at least 2 bases different to any 20-mer in either strand of the human genome.

11. The method according to claim 1 wherein both the forward and reverse amplification primers comprise a template-specific portion which is a sequence of at least 26 consecutive nucleotides.

12. The method according to claim 11 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of at least 30 consecutive nucleotides.

13. The method according to claim 12 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of at least 35 consecutive nucleotides.

14. The method according to claim 11 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of less than 50 consecutive nucleotides.

15. The method according to claim 14 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of from 30 to 45 consecutive nucleotides.

16. The method according to claim 15 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of from 35 to 40 consecutive nucleotides.

17. The method according to claim 16 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of 35 consecutive nucleotides

18. The method according to claim 1 wherein the forward and/or the reverse amplification primers immobilised on the solid support additionally comprise a linker portion which is not capable of annealing to the template to be amplified or the complement thereof.

19. The method according to claim 18 wherein the linker portion is a sequence of nucleotides which is not capable of annealing to the template to be amplified or the complement thereof.

20. The method according to claim 19 wherein the linker portion consists of from 1 to 20 consecutive nucleotides.

21. The method according to claim 20 wherein the linker portion consists of from 1 to 10 consecutive nucleotides

22. The method according to claim 20 wherein the linker portion consists of thymidine nucleotides.

23. The method according to claim 18 wherein the linker portion comprises a non-nucleotide chemical moiety.

24. The method according to claim 1 wherein in step a) the solid support is provided with both the forward and reverse amplification primers immobilised thereon.

25. The method according to claim 24 wherein in step a) the solid support is provided with both the forward and reverse amplification primers and the nucleic acid template to be amplified immobilised thereon, the template being attached to the solid support at the 5′

end.

26. The method according to claim 1 wherein the forward and reverse primers are identical.

27. The method according to claim 1 wherein the solid support is a solid supported polyacrylamide hydrogel.

29. The method of nucleic acid sequencing which comprises amplifying one or more nucleic acid templates using a method as defined in claim 1 and carrying out a sequencing reaction to determine the sequence of the whole or a part of at least one amplified nucleic acid strand produced in the amplification reaction.

28. (canceled)

30. A solid support having immobilised thereon a plurality of forward and/or reverse amplification primers, characterised in that said forward and/or reverse amplification primers comprise a template-specific portion capable of annealing to the template or the complement thereof which is a sequence of at least 26 consecutive nucleotides.

31. The solid support according to claim 30 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of at least 30 consecutive nucleotides.

32. The solid support according to claim 31 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of at least 35 consecutive nucleotides.

33. The solid support according to claim 30 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of less than 50 consecutive nucleotides.

34. The solid support according to claim 31 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of from 30 to 45 consecutive nucleotides.

35. The solid support according to claim 34 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of from 35 to 40 consecutive nucleotides.

36. The solid support according to claim 35 wherein the template-specific portion in the forward and/or reverse amplification primers is a sequence of 35 consecutive nucleotides

37. The solid support according to claim 30 wherein the forward and/or the reverse amplification primers immobilised on the solid support additionally comprise a linker portion which is not capable of annealing to the template to be amplified or the complement thereof.

38. The solid support according to claim 37 wherein the linker portion is a sequence of nucleotides which is not capable of annealing to the template to be amplified or the complement thereof.

39. The solid support according to claim 38 wherein the linker portion consists of from 1 to 20 consecutive nucleotides.

40. The solid support according to claim 39 wherein the linker portion consists of from 1 to 10 consecutive nucleotides

41. The solid support according to claim 39 wherein the linker portion consists of thymidine nucleotides.

42. The solid support according to claim 37 wherein the linker portion comprises a non-nucleotide chemical moiety.

43. The solid support according to claim 30 wherein the forward and reverse primers are identical.

44. (canceled)