Transposon end compositions and methods for modifying nucleic acids

• US 9,115,396 B2
• Filed: 07/07/2011
• Issued: 08/25/2015
• 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:
  US13/177,772
• Publication Number:
  US 20110287435A1
• Time in Patent Office: 1,510 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 population of non-selectively amplified linear DNA fragments representative of a target genomic DNA, wherein the ends of each DNA fragment comprise a transposon polynucleotide, wherein the transposon polynucleotide comprises a sequencing tag and a transposon end sequence, wherein the DNA fragments are attached to a surface through capture tags and are obtained using a plurality of transposome complexes for next generation sequencing, wherein

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

and

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

2. The population of claim 1, wherein the transposome complex of (1) comprises two of the first transposon polynucleotide, and the transposome complex of (2) comprises two of the second transposon polynucleotide.

3. The population of claim 1, wherein at least one transposon end sequence is phosphorylated.

4. The population of claim 1, wherein at least one transposon polynucleotide further comprises a detection tag, such that the DNA fragments additionally comprise a detection tag.

5. The population of claim 1, wherein at least one transposon polynucleotide further comprises an address tag, such that the DNA fragments additionally comprise an address tag.

6. The population of claim 1, wherein a transposon polynucleotide further comprises a second sequencing tag, such that the DNA fragments additionally comprise a second sequencing tag.

7. The population of claim 1, wherein at least one transposon polynucleotide further comprises a first amplification tag, such that the DNA fragments additionally comprise a first amplification tag.

8. The population of claim 1, wherein at least one transposon polynucleotide further comprises a transcription promoter sequence, such that the DNA fragments additionally comprise a transcription promoter sequence.

9. The population of claim 1, wherein the capture tags are attached to the surface through annealing sites on the surface.

10. The population of claim 1, wherein the capture tags comprise a first affinity binding molecule bound to a second affinity binding molecule attached to the surface.

11. The population of claim 1, wherein the surface comprises at least a million of the amplified linear DNA fragments.

12. The population of claim 11, wherein at least a million of the amplified linear DNA fragments are different.

13. The population of claim 1, wherein the surface is part of 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 population of claim 1, wherein the non-selectively amplified linear DNA fragments representative of a target genomic DNA are obtained by:

(a) contacting the target genomic DNA with the plurality of transposome complexes, thereby obtaining a plurality of tagged linear DNA fragments;

(b) extending the 3′

ends of the tagged linear DNA fragments; and

(c) non-selectively amplifying the extended tagged linear DNA fragments, thereby obtaining the population of non-selectively amplified linear DNA fragments representative of the target genomic DNA.

14. A library for next generation sequencing comprising a population of non-selectively amplified linear nucleic acid fragments representative of a target nucleic acid and attached through a capture tag to a surface, wherein the ends of each nucleic acid fragment comprise a sequencing tag and a transposon polynucleotide end sequence.

15. The library of claim 14, wherein each end of the nucleic acid fragments comprises the sequencing tag linked to the transposon polynucleotide.

16. The library of claim 14, wherein the capture tag and sequencing tag of at least one nucleic acid fragment comprise the same sequence.

17. The library of claim 14, wherein the transposon polynucleotides comprise the sequencing tags.

18. The library of claim 14, wherein the sequencing tag is selected from the group consisting of SEQ ID NO:

09, SEQ ID NO;

10, SEQ ID NO;

14 and SEQ ID NO;

15.

19. The library of claim 14, wherein the transposon polynucleotides of at least one nucleic acid fragment attached to the surface are different from transposon polynucleotides of other nucleic acid fragments attached to the surface.

20. The library of claim 14, wherein the surface comprises at least a million amplified linear nucleic acid fragments.

21. The library of claim 14, wherein at least a million of the amplified linear nucleic acid fragments are different.

22. The library of claim 14, wherein the surface is part of a substrate selected from the group consisting of a bead, a chip, a slide, a microtiter plate, a tube, a microchannel, and a dipstick.

23. The library of claim 14, wherein the target nucleic acid comprises genomic DNA.

25. The library of claim 14, wherein the population of non-selectively amplified linear nucleic acid fragments representative of a target nucleic acid is obtained by:

(a) contacting the target nucleic acid with a plurality of transposome complexes, thereby obtaining a plurality of tagged linear nucleic acid fragments;

(b) extending the 3′

ends of the tagged linear nucleic acid fragments; and

(c) non-selectively amplifying the extended tagged linear nucleic acid fragments, thereby obtaining the population of non-selectively amplified linear nucleic acid fragments representative of the target nucleic acid.

26. A population of non-selectively amplified linear DNA fragments for next generation sequencing that is representative of the sequences of both strands of a target genomic DNA from which the DNA fragments were generated, wherein both ends of each DNA fragment comprise a transferred transposon end sequence and wherein at least one end of each DNA fragment also comprises a sequencing tag, wherein the DNA fragments are attached to a surface through capture tags and are produced using a plurality of transposome complexes, wherein

(1) at least one transposome complex comprises a transposase and a transposon end sequence comprising a first transferred transposon end oligonucleotide;

and

(2) at least one transposome complex comprises a transposase and a transposon end sequence comprising a second transferred transposon end oligonucleotide.

27. The population of claim 26, wherein the transposase is selected from a Tn5 transposase, a hyperactive Tn5 transposase, and a Mu transposase.