Transposon end compositions and methods for modifying nucleic acids

• US 9,085,801 B2
• Filed: 06/05/2012
• Issued: 07/21/2015
• Est. Priority Date: 10/24/2008
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Epicentre Technologies Corporation (Illumina Incorporated)
• Inventors: Grunenwald, Haiying Li, Caruccio, Nicholas, Jendrisak, Jerome, Dahl, Gary
• Primary Examiner(s): BERTAGNA, ANGELA MARIE
• Application Number:
  US13/489,204
• Publication Number:
  US 20130196860A1
• Time in Patent Office: 1,141 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• 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 1/6855 Ligating adaptors
• 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 2535/122 Massive parallel sequencing

Abstract

Compositions of transposome complexes for generating DNA fragments with specific 5′- and 3′-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.

Claims

1. A method for sequencing a target DNA, comprising:

(a) incubating the target DNA with transposome complexes comprising

(1) a transposase and

(2) a first polynucleotide comprising

(i) a 3′

portion comprising a transposon end sequence, and

(ii) a first tag comprising a first sequencing tag,

under conditions whereby the target DNA is fragmented, and the 3′

transposon end sequence of the first polynucleotide is transferred to the 5′

ends of the fragments, thereby producing double-stranded fragments wherein the 5′

ends are tagged with the first tag, and there is a single-stranded gap at the 3′

ends of the 5′

-tagged strands;

(b) incubating the fragments with a nucleic acid modifying enzyme under conditions whereby a second tag is attached to the 3′

ends of the 5′

-tagged strands;

(c) amplifying the fragments by providing a polymerase and an amplification primer comprising a capture tag and a sequence complementary to a portion of the second tag, thereby generating amplified fragments having capture tags, the first tag at the 5′

ends and the second tag at the 3′

ends, wherein the amplification is non-selective such that a population of amplified fragments representative of the target DNA is generated;

(d) capturing the amplified fragments to a surface through the capture tags; and

(e) simultaneously sequencing the captured amplified fragments on the surface in a single multiplex format by providing first sequencing primers comprising a portion corresponding to the first sequencing tag, extending the first sequencing primers, and detecting the identity of nucleotides adjacent to the first sequencing tags.

3. The method of claim 1, wherein the second tag comprises a second sequencing tag, and the sequencing further comprises:

annealing second sequencing primers complementary to the second sequencing tags; and

extending the second sequencing primers by incorporating nucleotides and detecting the identity of the incorporated nucleotides.

5. The method of claim 1 or 2, wherein the nucleic acid modifying enzyme in step (b) is a strand-displacing DNA polymerase.

6. The method of claim 1 or 2, wherein the nucleic acid modifying enzyme in step (b) is a DNA polymerase having 5′

-to-3′

exonuclease activity.

7. The method of claim 1 or 2, wherein the nucleic acid-modifying enzyme in step (b) comprises a ligase and DNA polymerase lacking both strand-displacing and 5′

-to-3′

exonuclease activities to fill in the single-stranded gap.

8. The method of claim 1 or 2, wherein the nucleic acid-modifying enzyme in step (b) is a ligase and step (b) further comprises providing a ligation oligonucleotide.

9. The method of claim 8, wherein the ligation oligonucleotide has a 5′

-phosphate group, a random sequence, and a 3′

portion comprising the second tag.

10. The method of claim 1 or 2, wherein step (b) comprises denaturing the fragments obtained in step (a) and incubating the fragments with a terminal transferase.

11. The method of claim 1 or 2, wherein step (b) comprises incubating the library of DNA fragments with a DNA polymerase and a terminal tagging oligonucleotide.

12. The method of claim 1 or 2, wherein step (b) comprises incubating the library of DNA fragments with a ssDNA ligase.

13. The method of claim 1 or 2, wherein the target DNA is incubated in step (a) with transposomes comprising different sequences.

14. The method of claim 13, wherein one transposome comprises two of the first polynucleotide.

15. The method of claim 1 or 2, wherein a transposome comprises a single polynucleotide that forms a hairpin.

16. The method of claim 15, wherein the hairpin comprises a cleavable site, and the method further comprises cleaving the cleavable site, thereby generating a DNA fragment having a fantail.

17. The method of claim 1 or 2, wherein the first polynucleotide comprises an address tag to identify the source of the fragment.

18. The method of claim 1 or 2, wherein the transposome comprises a Tn5 transposase.

19. The method of claim 1, wherein the surface comprises at least a million captured fragments.

20. The method of claim 1, wherein at least a million captured fragments are different.

2. A method for sequencing a target DNA, comprising:

(a) incubating the target DNA with transposome complexes comprising

(1) a transposase and

(2) a first polynucleotide comprising

(i) a 3′

portion comprising a transposon end sequence, and

(ii) a first tag comprising an amplification tag,

under conditions whereby the target DNA is fragmented, and the 3′

transposon end sequence of the first polynucleotide is transferred to the 5′

ends of the fragments, thereby producing double-stranded fragments, wherein the 5′

ends are tagged with the first tag, and wherein there is a single-stranded gap at the 3′

ends of the 5′

-tagged strands;

(b) incubating the fragments with a nucleic acid modifying enzyme under conditions whereby a second tag is attached to the 3′

ends of the 5′

-tagged strands;

(c) non-selectively amplifying the fragments by providing a polymerase and an amplification primer comprising

(i) a sequence complementary to the second tag,

(ii) a first sequencing tag, and

(iii) a capture tag;

thereby generating a population of amplified fragments having capture tags, the first tag at the 5′

ends and a second tag at the 3′

ends, wherein the amplification is under conditions such that a population of amplified fragments representative of the target DNA is generated;

(d) capturing the amplified fragments on a surface through the capture tags; and

(e) simultaneously sequencing the captured fragments on the surface in a single multiplex format by providing first sequencing primers comprising a portion corresponding to the first sequencing tag, extending the first sequencing primers, and detecting the identity of nucleotides adjacent to the first sequencing tags.

4. The method of claim 2, wherein the second tag comprises a second sequencing tag, and the sequencing further comprises:

annealing second sequencing primers complementary to the second sequencing tags; and

extending the second sequencing primers by incorporating nucleotides and detecting the identity of the incorporated nucleotides.

21. A method of sequencing a target nucleic acid, comprising:

(a) contacting the target nucleic acid with a plurality of transposomes, each transposome comprising;

(1) a transposase, and

(2) a polynucleotide comprising a tag and a transposon end sequence

under conditions whereby a plurality of linear nucleic acid fragments of the target nucleic acid is obtained, each fragment comprising the tag attached to the 5′

end;

(b) extending the 3′

ends of the fragments;

(c) non-selectively amplifying the fragments with primers that anneal to the extended 3′

ends of the fragments and comprise a capture tag, thereby generating a population of amplified fragments representative of the target nucleic acid;

(d) binding the amplified fragments to a surface by hybridizing the capture tags to a plurality of capture probes attached to the surface; and

(e) simultaneously sequencing the captured fragments on the surface in a single multiplex format to determine the nucleotide sequence of the target nucleic acid.

22. The method of claim 21, wherein the surface comprises at least a million captured fragments.

23. The method of claim 22, wherein the at least a million captured fragments are different.

24. The method of claim 21, wherein a substrate selected from the group consisting of a bead, chip, slide, microtiter plate, tube, microchannel, and dipstick comprises the surface.