Method of preparing libraries of template polynucleotides

• US 8,563,478 B2
• Filed: 04/20/2010
• Issued: 10/22/2013
• Est. Priority Date: 11/01/2005
• Status: Active Grant

• Current Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Inventors: Gormley, Niall Anthony, Smith, Geoffrey Paul, Bentley, David, Rigatti, Roberto, Luo, Shujun
• Primary Examiner(s): BOESEN, CHRISTIAN C
• Application Number:
  US12/799,172
• Publication Number:
  US 20100273662A1
• Time in Patent Office: 1,281 Days
• Field of Search: None
• US Class Current: 506/26
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2525/313 Branched oligonucleotides
• CPC Class Codes: C12Q 2565/525 characterised by the capture oligonucleotide being double stranded
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention relates to a method for preparing a library of template polynucleotides and use thereof in methods of solid-phase nucleic acid amplification. More specifically, the invention relates to a method for preparing a library of template polynucleotides that have common sequences at their 5′ ends and at their 3′ ends.

Claims

1. A method of generating a library of different polynucleotide molecules, the method comprising:

(a) providing a plurality of different target polynucleotide duplexes;

(b) providing identical polynucleotide adapters, wherein each adapter comprises a double-stranded annealed region and a mismatched region;

(c) ligating the double-stranded annealed regions of the identical polynucleotide adapters to both ends of the different target polynucleotide duplexes to form adapter-target constructs, and

(d) annealing a single universal primer species to the mismatched regions of the adapter-target constructs and extending the primer to form extension products complementary to both strands of the adapter-target constructs,

wherein the extension products comprise nucleic acid sequences that differ from the nucleic acid sequences of either strand of the adapter-target constructs and the extension products collectively provide a library of different template polynucleotide molecules which have common sequences at their 5′

ends and common sequences at their 3′

ends;

wherein the polynucleotide adapters are forked adapters formed by annealing of partially complementary first and second polynucleotide strands; and

wherein a sequence of 5 or more consecutive nucleotides at 3′

end of the first strand of the forked adapters is complementary to a sequence of 5 or more consecutive nucleotides the 5′

end of the second strand of the forked adapters such that a double-stranded region of 5 or more consecutive base pairs is formed by annealing of the two strands.

2. The method of claim 1, wherein the annealing and extending in step (d) comprises:

i) annealing a single universal primer species to the mismatched regions of each of the adapter-target constructs, ii) extending the primer species by sequential addition of nucleotides to form extension products complementary to at least one strand of each of the adapter-target constructs, and iii) subjecting the products obtained in step ii) to denaturing conditions, thereby separating the extension products from strands of the adapter-target constructs.

3. The method of claim 1, wherein a sequence of at least 10 consecutive nucleotides at the 5′

end of the first strand of the forked adapters and a sequence of at least 10 consecutive nucleotides at the 3′

end of the second strand of the forked adapters are not complementary such that an unmatched region of at least 10 consecutive nucleotides on each strand remains in single stranded form when the double-stranded region is annealed.

4. The method of claim 1, wherein the different target polynucleotide duplexes are fragments of genomic DNA.

5. The method of claim 1, further comprising carrying out a solid-phase nucleic acid amplification reaction wherein said library of different template polynucleotide molecules is amplified on a solid-phase surface.

7. The method of claim 1, further comprising determining the sequence of at least a part of the different target polynucleotide duplexes in the library of different template polynucleotide molecules.

8. The method of claim 1, further comprising a step of purifying the extension products from the adapter-target constructs.

9. The method of claim 1, wherein the providing a plurality of different target polynucleotide duplexes comprises fragmenting a complex polynucleotide sample.

10. The method of claim 9, wherein the library of different template polynucleotide molecules comprises sequences of the whole complex polynucleotide sample.

11. The method of claim 10, wherein the complex polynucleotide sample comprises genomic DNA.

12. The method of claim 5, wherein amplification is carried out using a single surface bound primer.

13. The method of claim 5, further comprising carrying out a sequencing reaction to determine the sequence of at least a part of at least one amplified polynucleotide molecule.

16. The method of claim 1, further comprising amplifying the library of different polynucleotide molecules on a solid support.

6. A method of generating a library of different polynucleotide molecules, the method comprising:

(a) providing a plurality of different target polynucleotide duplexes;

(b) providing identical polynucleotide adapters, wherein each adapter comprises a double-stranded annealed region and a mismatched region;

(c) ligating the double-stranded annealed regions of the identical polynucleotide adapters to both ends of the different target polynucleotide duplexes to form adapter-target constructs, and

(d) annealing a single universal primer species to the mismatched regions of the adapter-target constructs and extending the primer to form extension products complementary to both strands of the adapter-target constructs;

wherein the extension products comprise nucleic acid sequences that differ from the nucleic acid sequences of either strand of the adapter-target constructs and the extension products collectively provide a library of different template polynucleotide molecules which have common sequences at their 5′

ends and common sequences at their 3′

ends;

wherein the single universal primer species comprises a non-hybridizing tail sequence at the 5′

end whereby the single primer species is extended to generate extension products that comprise the tail sequence or a complementary sequence thereof; and

further comprising carrying out a solid-phase nucleic acid amplification reaction wherein the library of different template polynucleotide molecules is amplified, wherein the library of different template polynucleotide molecules is amplified by solid-phase PCR using forward and reverse amplification primers and solid-phase PCR is carried out using amplification primers capable of annealing to the tail sequence of the extension products or the complementary sequence thereof.

14. A method of generating a library of different polynucleotide molecules, the method comprising:

(a) providing a plurality of different target polynucleotide duplexes;

(b) providing identical polynucleotide adapters, wherein each adapter comprises a double-stranded annealed region and a mismatched region;

(c) ligating the double-stranded annealed regions of the identical polynucleotide adapters to both ends of the different target polynucleotide duplexes to form adapter-target constructs, and

(d) annealing a single universal primer species to the mismatched regions of the adapter-target constructs and extending the primer to form extension products complementary to both strands of the adapter-target constructs;

wherein the extension products comprise nucleic acid sequences that differ from the nucleic acid sequences of either strand of the adapter-target constructs and the extension products collectively provide a library of different template polynucleotide molecules which have common sequences at their 5′

ends and common sequences at their 3′

ends;

wherein the library of different polynucleotide molecules is used to prepare a clustered array of nucleic acid colonies on a solid support.

15. The method of claim 14, further comprising carrying out a sequencing reaction to determine the sequence of the nucleic acid colonies.

17. A method of generating a library of different polynucleotide molecules, the method comprising:

(a) providing a plurality of different target polynucleotide duplexes;

(b) providing identical polynucleotide adapters, wherein each adapter comprises a double-stranded annealed region and a mismatched region;

(c) ligating the double-stranded annealed regions of the identical polynucleotide adapters to both ends of the different target polynucleotide duplexes to form adapter-target constructs, and

(d) annealing a single universal primer species to the mismatched regions of the adapter-target constructs and extending the primer to form extension products complementary to both strands of the adapter-target constructs,

wherein the extension products comprise nucleic acid sequences that differ from the nucleic acid sequences of either strand of the adapter-target constructs and the extension products collectively provide a library of different template polynucleotide molecules which have common sequences at their 5′

ends and common sequences at their 3′

ends;

further comprising carrying out a solid-phase nucleic acid amplification reaction wherein said library of different template polynucleotide molecules is amplified on a solid-phase surface;

wherein the solid-phase surface is a solid support; and

wherein the solid support is selected from the group consisting of latex beads, dextran beads, polystyrene, polypropylene surface, polyacrylamide gel, gold surfaces, glass surfaces and silicon wafers.

18. The method of claim 17, wherein the solid support comprises a glass surface.

19. The method of claim 17, wherein the solid support comprises latex beads.

20. The method of claim 17, wherein the solid support comprises dextran beads.

21. The method of claim 17, wherein the solid support comprises polystyrene.

22. The method of claim 17, wherein the solid support comprises a polypropylene surface.

23. The method of claim 17, wherein the solid support comprises a polyacrylamide gel.

24. The method of claim 17, wherein the solid support comprises a gold surface.

25. The method of claim 17, wherein the solid support comprises a silicon wafer.