Methods and transposon nucleic acids for generating a DNA library

1. An in vitro method for fragmenting DNA, comprising:

a) forming a plurality of transposon complexes by contacting

(i) a plurality of modified transposon end sequences, with

(ii) a plurality of MuA transposase enzymes,

wherein the plurality of modified transposon end sequences are double-stranded nucleic acids having a double-stranded region and a 5′ overhang region, and comprise top and bottom nucleic acid strands, and have MuA R1 and MuA R2 sequences that bind an MuA transposase enzyme, wherein the top or bottom nucleic acid strand contains a recognition sequence that is recognized by a methylation-dependent restriction endonuclease, wherein the recognition sequence includes a 5-methylcytosine, and wherein the recognition sequence is located in the double-stranded region, and wherein the restriction endonuclease enzyme can cleave the top and bottom nucleic acid strands outside of the recognition sequence to generate an overhang end;

b) contacting the plurality of transposon complexes with a plurality of target DNA molecules;

c) incubating the plurality of transposon complexes and the plurality of target DNA molecules under conditions suitable for transposition of the transposon complexes into the target DNA molecules and for fragmenting the target DNA to produce a plurality of fragmented DNA molecules having both ends joined to the modified transposon end sequence, wherein the modified transposon end sequences that are joined to the fragmented DNA molecules include the methylation-dependent restriction endonuclease recognition sequence that includes the 5-methylcytosine; and

d) producing a plurality of cleaved DNA fragments by contacting the plurality of fragmented DNA molecules with the methylation-dependent restriction endonuclease enzyme.

2. The method of claim 1 , wherein the cleaved DNA fragments comprise overhang ends.

3. The method of claim 1 , further comprising: amplifying the fragmented DNA molecules by contacting the fragmented DNA molecules with a plurality of oligonucleotide primers having sequences that are complementary to at least a portion of the modified transposon end sequence under conditions suitable for nucleic acid amplification.

4. The method of claim 1 , wherein the fragmented DNA molecules that are joined at both ends to the modified transposon end sequence contains a gap on both strands.

5. The method of claim 4 , further comprising filling in the gap on both strands with a DNA polymerase having 5′ to 3′ exonuclease activity or having strand displacement activity.

6. The method of claim 1 , further comprising denaturing the plurality of fragmented DNA molecules to produce a plurality of single-stranded fragmented DNA.

7. The method of claim 6 , further comprising immobilizing the plurality of single-stranded fragmented DNA to a support.

8. The method of claim 1 , further comprising sequencing the plurality of fragmented DNA molecules with a high throughput sequencing reaction.

9. The method of claim 7 , further comprising sequencing the plurality of single-stranded fragmented DNA with a high throughput sequencing reaction.

10. The method of claim 3 , wherein the oligonucleotide primers are tailed primers containing an amplification sequence tag, a sequencing tag, a detection tag, or an identification tag.

11. A plurality of fragmented DNA molecules produced by the method of claim 1 .

12. The method of claim 1 , wherein the top or bottom nucleic acid strand which contains the recognition sequence that is cleavable with the methylation-dependent restriction endonuclease enzyme comprises the sequence according to SEQ ID NO:6 or 9.

13. The method of claim 1 , wherein the methylation-dependent restriction endonuclease enzyme comprises SgeI.