Preparation of nucleic acid templates for solid phase amplification

• US 8,168,388 B2
• Filed: 11/24/2006
• Issued: 05/01/2012
• Est. Priority Date: 11/25/2005
• Status: Active Grant

• Current Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Inventors: Gormley, Niall Anthony, Boutell, Jonathan Mark, Turcatti, Gerardo, Barnes, Colin Lloyd
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US12/085,508
• Publication Number:
  US 20100041561A1
• Time in Patent Office: 1,985 Days
• Field of Search: 435/91.1, 435/91.2, 435/6.12
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

The invention relates to a method of preparing template constructs for solid-phase nucleic acid amplification and to use of the templates in methods of solid-phase nucleic acid amplification. The method involves carrying out two ligation reactions: (a) a ligation reaction in which the first end of one or more target polynucleotide molecules are ligated to surface-bound adaptor polynucleotide molecules, and (b) a ligation reaction in which solution-phase adaptor polynucleotide molecules are ligated to the second end of said target polynucleotide molecules, in order to produce one or more template constructs attached to a solid support.

Claims

1. A method of preparing nucleic acid template constructs for solid-phase nucleic acid amplification which comprises performing the following ligation reactions a) and b):

a) a ligation reaction in which the first end of one or more target polynucleotide molecules of unknown sequence are ligated to surface-bound adaptor polynucleotide molecules; and

b) a ligation reaction in which solution-phase adaptor polynucleotide molecules are ligated to the second end of said target polynucleotide molecules of unknown sequence;

thereby producing one or more template constructs attached to a solid support, wherein each of said template constructs comprises a target polynucleotide molecule of unknown sequence ligated to a surface-bound adaptor polynucleotide molecule and a solution-phase polynucleotide molecule, and wherein the target polynucleotide molecules are not digested with a cleavage reagent prior to step a).

2. A method according to claim 1 wherein ligation reaction a) is carried out before ligation reaction b).

3. A method according to claim 2 wherein the target polynucleotide molecules are fully or partially double stranded.

4. A method according to claim 3 wherein the surface-bound adaptor polynucleotide molecules are duplexes.

5. A method according to claim 4 which further comprises, prior to ligation reaction a), a step of annealing two single stranded polynucleotide molecules to form the surface-bound adaptor duplexes.

6. A method according to claim 5 wherein said annealing step is carried out in free solution to form adaptor duplexes which are attached to the solid support prior to ligation reaction a) to form surface-bound adaptor duplexes.

7. A method according to claim 5 wherein each surface-bound adaptor duplex is formed by annealing a complementary oligonucleotide to an amplification primer attached to the solid support.

8. A method according to claim 1 wherein the solution-phase adaptor polynucleotide molecules used in ligation reaction b) are duplexes.

9. A method according to claim 1 wherein the solid support has attached thereto a plurality of forward and/or reverse amplification primers.

10. A method according to claim 9 wherein the amplification primers attached to the solid support all contain identical template-specific nucleotide sequences.

11. A method according to claim 10 wherein the amplification primers attached to a solid support are all of identical structure and identical nucleotide sequence.

12. A method according to claim 9 wherein all the forward amplification primers attached to the solid support are of identical nucleotide sequence and structure and all the reverse amplification primers attached to the solid support are of identical nucleotide sequence and structure but the forward and reverse amplification primers are of different nucleotide sequence.

13. A method according to claim 1 wherein the target polynucleotides are all of identical nucleotide sequence.

14. A method according to claim 1 wherein the template constructs comprise a mixture of target polynucleotides of different nucleotide sequence.

15. A method according to claim 14 wherein the target polynucleotides are fragments of genomic DNA.

16. A method according to claim 15 wherein the target polynucleotides are fragments of human genomic DNA.

17. A method according to claim 14, wherein the mixture of target polynucleotides of different nucleotide sequence is a whole genome library of genomic DNA fragments.

18. A method according to claim 1 wherein the solution-phase adaptor and/or the surface-bound adaptor includes a sequence of nucleotides which permits annealing of a sequencing primer.

19. A method of amplifying nucleic acid template constructs by solid-phase nucleic acid amplification comprising:

preparing template constructs for solid-phase amplification comprising one or more templates to be amplified using the method according to claim 1 and carrying out a solid-phase nucleic acid amplification reaction wherein said template constructs are amplified.

20. A method according to claim 19 wherein said template constructs are amplified by solid-phase amplification using forward and reverse amplification primers.

21. A method according to claim 20 wherein the forward and reverse amplification primers are all attached to the same solid support to which the target constructs are attached.

22. A method according to claim 20 wherein the reverse amplification primers are attached to the same solid support to which the template constructs are attached and the forward amplification primers are present in free solution in the amplification reaction.

23. A method of nucleic acid sequencing which comprises amplifying one or more nucleic acid template constructs using a method as defined in claim 19 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.

24. The method of claim 23, wherein the sequencing reaction comprises sequencing-by-synthesis.

25. The method of claim 19, wherein the template constructs comprise a whole genome library of genomic DNA fragments.

26. The method of claim 1, wherein the target polynucleotide molecules are blunt ended.

27. The method of claim 20, wherein the adaptors comprise universal primer binding sites.

28. The method of claim 27, wherein the forward and reverse amplification primers bind to the universal primer binding sites.

29. The method of claim 28, wherein the forward and reverse amplification primers comprise different sequences.

30. The method of claim 28, wherein one of the amplification primers is attached to the solid support comprising the template constructs.

31. The method of claim 19, wherein the amplification reaction comprises amplifying the template constructs using a single primer.

32. The method of claim 1, further comprising fragmenting a nucleic acid molecule prior to step a) to produce the target polynucleotide molecules of step a).