Transposon end compositions and methods for modifying nucleic acids

• US 9,080,211 B2
• Filed: 10/24/2009
• Issued: 07/14/2015
• 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:
  US12/605,337
• Publication Number:
  US 20100120098A1
• Time in Patent Office: 2,089 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

The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5′-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5′- and 3′-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5′-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3′-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next-generation sequencing.).

Claims

1. A method for generating and sequencing a library of DNA fragments having first and second tag sequences, comprising:

(a) providing a target DNA;

(b) providing a plurality of transposome complexes, wherein

(1) at least one transposome complex comprises a hyperactive Tn5 transposase and at least a first polynucleotide comprising a Tn5-type transposon end sequence and a first tag sequence; and

(2) at least one transposome complex comprises a hyperactive Tn5 transposase and at least a second polynucleotide comprising a Tn5-type transposon end sequence and a second tag sequence;

wherein the transposome complexes of (1) and (2) comprise different sequences;

(c) incubating the target DNA and transposome complexes under conditions whereby multiple transposon end sequences and associated tag sequences are inserted into the target DNA and the target DNA is fragmented into a multitude of double-stranded DNA fragments comprising one of the first or the second polynucleotides attached to each 5′

end of the DNA fragments;

(d) non-selectively amplifying the double-stranded DNA fragments; and

(e) sequencing the DNA fragments simultaneously in a single multiplex format.

2. The method of claim 1, wherein the transposome complex of (1) comprises two of the first polynucleotides, and the transposome complex of (2) comprises two of the second polynucleotides.

3. The method of claim 1, wherein a transposome complex comprises a single polynucleotide that forms a hairpin.

4. The method of claim 3, wherein the hairpin comprises a cleavable site, and (c) further comprises cleaving the cleavable sites of a DNA fragment, thereby generating a DNA fragment having a fantail.

5. The method of claim 1, wherein (c) further comprises incubating the DNA fragments with a strand-displacing DNA polymerase under conditions whereby 3′

ends of the DNA fragments are extended.

6. The method of claim 1, wherein (c) further comprises incubating the library of DNA fragments with a DNA polymerase having 5′

-to-3′

exonuclease activity, under conditions whereby 3′

ends of the DNA fragments are extended.

7. The method of claim 1, wherein (c) further comprises incubating the library of DNA fragments with a ligase and a DNA polymerase lacking both strand-displacing and 5′

-to-3′

exonuclease activities, under conditions whereby single-stranded gaps in the DNA fragments are filled in.

8. The method of claim 1, wherein (c) further comprises incubating the library of DNA fragments with a ligase and a ligation oligonucleotide, under conditions whereby single-stranded gaps in the DNA fragments are filled in.

9. The method of claim 1, wherein at least one tag sequence comprises a first sequencing tag, and (e) further comprises contacting a first sequencing primer comprising a portion corresponding to the first sequencing tag with the DNA fragments.

10. The method of claim 9, wherein a tag sequence comprises a second sequencing tag and (e) further comprises contacting a second sequencing primer comprising a portion corresponding to the second sequencing tag with the DNA fragments.

11. The method of claim 1, wherein at least one tag sequence comprises a first amplification tag, and (d) comprises contacting a DNA polymerase and a first primer having a portion corresponding to the first amplification tag with the DNA fragments.

12. The method of claim 11, wherein a tag sequence comprises a second amplification tag, and (d) comprises contacting a second primer having a portion corresponding to the second amplification tag with the DNA fragments.

13. The method of claim 11, wherein the non-selectively amplifying is selected from the group consisting of a strand-displacement amplification reaction, a rolling circle amplification reaction, a loop-mediated amplification reaction, and PCR.

14. The method of claim 1, wherein at least one tag sequence comprises a restriction site.

15. The method of claim 1, wherein at least one tag sequence comprises a transcription promoter sequence, and (d) comprises performing transcription-mediated amplification with the DNA fragments.

16. The method of claim 1, wherein at least one tag sequence comprises an address tag to identify sequences for each sample.

17. The method of claim 1, wherein at least one tag sequence comprises a capture tag, and (e) further comprises providing a surface having an annealing site for the capture tag.

18. The method of claim 17, wherein the capture tag is a first affinity binding molecule and (e) further comprises providing a surface to which a second affinity binding molecule is attached.

19. The method of claim 1, wherein at least one tag sequence comprises a detection tag.

20. The method of claim 19, wherein the detection tag has a sequence that facilitates detection of the DNA fragment.

21. The method of claim 1, wherein (e) further comprises capturing the DNA fragments on a surface.

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

23. The method of claim 21, wherein the surface is on a substrate selected from the group consisting of:

a bead, a chip, a slide, a microtiter plate, a tube, a microchannel, and a dipstick.

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

25. The method of claim 1, wherein (c) comprises extending the 3′

ends of the DNA fragments.

26. A method for generating and sequencing a library of DNA fragments having first and second tag sequences, comprising:

(a) providing a target DNA;

(b) providing a plurality of transposome complexes, wherein

(1) at least one transposome complex comprises a hyperactive Tn5 transposase and at least a first polynucleotide comprising a Tn5-type transposon end sequence and a first tag sequence; and

(2) at least one transposome complex comprises a hyperactive Tn5 transposase and at least a second polynucleotide comprising a Tn5-type transposon end sequence and a second tag sequence;

wherein the transposome complexes of (1) and (2) exhibit different sequences;

(c) incubating the target DNA and transposome complexes under conditions whereby multiple transposon ends and associated tag sequences are inserted into the target DNA and the target DNA is fragmented into a multitude of double-stranded DNA fragments that exhibit one of the first or the second tag sequences attached to each 5′

end of the DNA fragments;

(d) joining a tag to the 3′

ends of the DNA fragments from step (c) to generate a library of di-tagged DNA fragments, each exhibiting a 5′

first or second tag sequence and a 3′

tag sequence,

(e) non-selectively amplifying the library of di-tagged DNA fragments; and

(f) sequencing the di-tagged DNA fragments simultaneously in a single multiplex format.