Transposon end compositions and methods for modifying nucleic acids

• US 9,040,256 B2
• Filed: 01/06/2014
• Issued: 05/26/2015
• 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:
  US14/148,463
• Publication Number:
  US 20140162897A1
• Time in Patent Office: 505 Days
• Field of Search: None
• US Class Current: 435/61
• 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 parallel sequencing of a target DNA in a sample, the method comprising:

(a) providing;

(1) a target DNA; and

(2) a plurality of transposome complexes wherein each transposome complex comprises a transposase and two transposon end compositions comprising transposon end sequences;

(b) incubating the target DNA with the plurality of transposome complexes under conditions whereby the target DNA is fragmented into double-stranded DNA fragments comprising a transferred strand from the transposon end compositions joined to the 5′

ends of the double-stranded DNA fragments, thereby generating 5′

-tagged DNA fragments;

(c) extending the 3′

ends of the 5′

-tagged DNA fragments;

(d) non-selectively amplifying the extended 5′

-tagged DNA fragments under conditions that do not intentionally select for or against amplification of particular 5′

-tagged DNA fragments based on their target DNA sequences to generate a representative library of amplified DNA fragments having a population that is representative of the target DNA from which the fragments were generated, wherein each amplified DNA fragment comprises;

(1) a first tag on a 5′

end,

(2) a second tag on a 3′

end, and

(3) a capture tag;

(e) capturing a plurality of the amplified DNA fragments on a surface through the capture tag;

(f) providing a plurality of sequencing primers that anneal to a portion of each captured DNA fragment; and

(g) simultaneously sequencing the captured fragments in a single multiplex format to determine the nucleotide sequences of the DNA fragments captured on the surface in parallel.

2. The method of claim 1, wherein the first and second tags each comprise a tag selected from the group consisting of a transposon end tag, a sequencing tag, an amplification tag, a detection tag, an address tag, a capture tag, a restriction site tag and a transcription promoter.

3. The method of claim 2, wherein the first and second tags comprise transposon end tags.

4. The method of claim 2, wherein the first and second tags comprise amplification tags.

5. The method of claim 2, wherein one or both of the first and second tags comprise an address tag.

6. The method of claim 1, wherein said extending comprises incubating the 5′

-tagged DNA fragments with a DNA polymerase selected from the group consisting of a strand-displacing DNA polymerase and a DNA polymerase having 5′

-to-3′

exonuclease activity.

7. The method of claim 1, wherein (d) further comprises denaturing the amplified DNA fragments to single-stranded DNA fragments.

8. The method of claim 7, wherein said extending comprises incubating the 5′

-tagged DNA fragments with a template-independent DNA polymerase.

9. The method of claim 1, wherein said extending comprises:

incubating the 5′

-tagged DNA fragments with an RNA-dependent DNA polymerase and a terminal tagging oligoribonucleotide comprising a 5′

-portion and 3′

-portion, wherein the 5′

-portion comprises a sequence that is complementary to a portion of the second tag and the 3′

-portion comprises a random sequence of between three and eight nucleotides wherein the 3′

-terminal nucleotide of the random nucleotides is not extendable by a DNA polymerase, under conditions wherein the 3′

ends of the 5′

-tagged single-stranded DNA fragments are extended.

10. The method of claim 1, wherein at least one transposome complex comprises a Tn5 transposase and a Tn5 transposon end composition.

11. The method of claim 1, wherein at least one transposome complex comprises a Mu transposase and a Mu transposon end composition.

12. The method of claim 1, wherein the plurality of transposome complexes comprises two different types of transposome complexes, each different type of transposome complex comprising a different transposase and different transposon end compositions.

13. The method of claim 12, wherein the transposase in one of the transposome complexes is a Tn5 transposase and the transposase in the other transposome complex is a Mu transposase.

14. The method of claim 1, wherein the first tag comprises a capture tag, and wherein the surface for parallel sequencing comprises capture molecules that bind the capture tag.

15. The method of claim 1, wherein the surface comprises at least a million different said captured DNA fragments.

16. The method of claim 1, wherein the target DNA comprises a plurality of different nucleic acids.

17. A method for parallel sequencing of a target DNA comprising:

a) providing a library of linear double-stranded target DNA fragments, each fragment comprising a first end comprising a first transposon end and a first amplification tag domain affixed to a 5′

strand and a 3′

strand comprising a nucleic acid complementary thereto, and a second end comprising a second transposon end and a second amplification tag domain affixed to the 5′

strand and a 3′

strand comprising a nucleic acid complementary thereto, wherein the transposon ends are affixed to the DNA fragments via an in vitro transposition reaction comprising a plurality of transposomes, each transposome comprising a transposase and transposon ends, and wherein the library was generated under conditions that did not intentionally select for or against extension of particular DNA fragments based on their tar et DNA sequences in order to non-selectively generate a representative library of DNA fragments having a population that is representative of the tar et DNA from which the fragments were generated

b) denaturing the library of linear DNA fragments to generate single-stranded DNA fragments,

c) capturing the single-stranded DNA fragments on a substrate under conditions wherein a portion of the fragments are captured on the substrate, and

d) parallel sequencing the captured DNA fragments, wherein the captured DNA fragments are sequenced simultaneously in a single multiplex format.

18. The method of claim 17, wherein the transposon ends or complements thereof further comprise one or more of a capture tag domain, an address tag domain, a sequencing tag domain, and a restriction site tag domain.

19. The method of claim 18, where the transposon ends or complements thereof comprise an address tag domain.

20. The method of claim 17, where denaturing is heat denaturing.

21. The method of claim 18, wherein one or both of the transposon ends or complements thereof comprise a capture tag domain and the substrate comprises capture molecules that bind the capture tag domain.

22. The method of claim 21, wherein the capture molecule is a DNA sequence that is affixed to the substrate.

23. The method of claim 17, wherein the transposase is a Tn5 transposase and the transposon ends are Tn5 transposon ends.

24. The method of claim 17, wherein the transposase is a Mu transposase and the transposon ends are Mu transposon ends.

25. A method of sequencing a target nucleic acid comprising:

(a) contacting the target nucleic acid with a plurality of transposomes, wherein each transposome comprises a transposase and a transposon end sequence, thereby obtaining a plurality of fragmented nucleic acids, each fragmented nucleic acid comprising the transposon end sequence;

(b) extending the 3′

ends of the fragmented nucleic acids;

(c) extending a primer hybridized to the extended 3′

ends of the plurality of fragmented nucleic acids, wherein the primer comprises a capture tag and wherein the extension is under conditions that do not intentionally select for or against extension of particular fragmented nucleic acids based on their target nucleic acid sequences in order to non-selectively generate a representative library of nucleic acid fragments having a population that is representative of the target nucleic acid from which the fragments were generated;

(d) capturing the extended nucleic acids through the capture tag with a plurality of capture probes attached to a surface; and

(e) sequencing simultaneously the captured nucleic acids in a single multiplex format.

26. The method of claim 25, wherein the surface comprises at least a million different captured nucleic acids.

27. The method of claim 25, wherein the target nucleic acid comprises a plurality of different nucleic acids.

28. A method for determining the DNA nucleotide sequence of target DNA, comprising:

(A) non-selectively generating a representative library of di-tagged single-stranded DNA fragments of target DNA for use as templates for parallel DNA sequencing, wherein the combination of all of the di-tagged single-stranded DNA fragments in said library is qualitatively and/or quantitatively representative of the target DNA from which the library was generated, by performing the steps of;

(1) providing;

(a) double-stranded target DNA from one or multiple organisms or sources, wherein said target DNA is selected from the group consisting of genomic DNA, subgenomic DNA, chromosomal DNA, mitochondrial DNA, chloroplast DNA, episomal DNA, cDNA made by reverse transcription of RNA, DNA from an environmental sample and DNA from a clinical or biological specimen; and

(b) a plurality of transposome complexes, each of which comprises a transposase and a transposon end composition comprising a transferred strand oligonucleotide that exhibits a transferred transposon end sequence and, optionally, an arbitrary sequence 5′

of said transferred transposon end sequence, and a non-transferred strand oligonucleotide that exhibits a non-transferred transposon end sequence;

(2) incubating the target DNA with the plurality of transposome complexes under conditions wherein the target DNA is fragmented into double-stranded DNA fragments, each strand of which comprises a transferred strand from a transposon end composition joined to its 5′

end, to which a non-transferred strand oligonucleotide is hybridized, thereby generating a population of annealed 5′

-tagged DNA fragments;

(3) incubating the population of 5′

-tagged DNA fragments with a DNA polymerase such that their 3′

ends are extended under conditions that do not intentionally select for or against extension of particular 5′

-tagged DNA fragments based on their target DNA sequences and that non-selectively generate a representative library of di-tagged single-stranded DNA fragments, each of which exhibits a first tag on its 5′

end and a second tag on its 3′

end, such that the di-tagged single-stranded DNA fragments in said library are qualitatively and/or quantitatively representative of the sequences of both strands of the target DNA from which the di-tagged single-stranded DNA fragments were generated; and

(B) sequencing the target DNA by performing the steps of;

(1) capturing a plurality of at least a million di-tagged single-stranded DNA fragments on a surface through a tag of the di-tagged single-stranded DNA fragments;

(2) providing a plurality of sequencing primers, wherein a primer of said plurality anneals to a portion of each captured di-tagged single-stranded DNA fragment; and

(3) simultaneously parallel sequencing the di-tagged single-stranded DNA fragments captured on the surface in a single multiplex format and analyzing and assembling the nucleotide sequence data for all of the sequenced di-tagged single-stranded DNA fragments, thereby determining the DNA nucleotide sequence of the target DNA.