Asymmetric adapter library construction

1. A method of producing an asymmetrically tagged nucleic acid fragment, said method comprising:

i) ligating an adapter to each end of a double-stranded nucleic acid fragment, wherein said adapter comprises:

(a) a first and a second nucleic acid strand associated with each other via one or more complementary domains, said adapter having a first end and a second end;

(b) one or more region of substantial non-complementarity between said first and second nucleic acid strands;

(c) a ligation site positioned on said first end of said adapter configured to allow ligation of said adapter to said double stranded nucleic acid fragment; and

(d) a hairpin structure positioned on the 3′ strand on said second end of said adaptor, said hairpin structure producing a nucleic acid synthesis self-priming site; and

ii) performing a first round of nucleic acid synthesis initiated from said self-priming site using a nucleotide polymerase, thereby producing an asymmetrically tagged nucleic acid fragment.

2. The method of claim 1 , wherein said nucleotide polymerase is selected from the group consisting of: a RNA polymerase, a mesophilic DNA polymerase, a reverse transcriptase, and a thermophilic DNA polymerase.

3. The method of claim 1 , wherein in said region of substantial non-complementarity, said first and/or second nucleic acid strands comprise one or more of the following: a unique identifier (UID), an RNA polymerase promoter region, a primer binding site, a restriction enzyme site, and a recombination site.

4. The method of claim 1 , wherein said adaptor comprises an RNA polymerase promoter region adjacent to said hairpin structure or within the duplex region of said hairpin structure.

5. The method of claim 4 , wherein said RNA promoter region is oriented such that RNA polymerization proceeds toward said hairpin structure.

6. The method of claim 1 , wherein said double-stranded nucleic acid fragment is produced by digesting a parent double-stranded nucleic acid sample with a restriction enzyme and polishing the ends of the resultant restriction enzyme fragments to create ends compatible with said ligation site of said adapter.

7. The method of claim 1 , wherein said method further comprises isolating one strand of said asymmetrically tagged nucleic acid fragment.

8. The method of claim 7 , wherein said isolating comprises treating said asymmetrically tagged nucleic acid fragment with an exonuclease selected to digest only one strand of said asymmetrically tagged nucleic acid fragment.

9. A nucleic acid adapter comprising:

(a) a first and a second nucleic acid strand associated with each other via one or more complementary domains, said adapter having a first end and a second end;

(b) one or more region of substantial non-complementarity between said first and second nucleic acid strands;

(c) a ligation site positioned on said first end of said adapter configured to allow ligation of said adapter to a double stranded nucleic acid fragment; and

(d) a hairpin structure positioned on the 3′ strand on said second end of said adaptor, said hairpin structure producing a nucleic acid synthesis self-priming site.

10. The adapter of claim 9 , wherein said region of substantial non-complementarity in said first or second nucleic acid strand comprises one or more of the following: a unique identifier (UID), an RNA polymerase promoter region, a primer binding site, a restriction enzyme site, and a recombination site.

11. The adapter of claim 9 , wherein said adaptor comprises an RNA polymerase promoter region adjacent to said hairpin structure or within the duplex region of said hairpin structure.

12. The method of claim 1 , wherein said adapter comprises one or more wobble base pair positioned in said one or more complementary domains such that said resultant asymmetrically tagged nucleic acid fragment comprises a restriction enzyme recognition and/or cut site at only one end.

13. The method of claim 12 , wherein said one or more wobble base pair is positioned within said ligation site.

14. The method of claim 12 , wherein said method further comprises:

digesting said asymmetrically tagged nucleic acid fragment with a restriction enzyme specific for said restriction enzyme recognition and/or cut site; and

ligating a second, different adapter to said digested fragment, said second adapter having a ligation site compatible with the digested end of said fragment.

15. The adapter of claim 9 , wherein said adapter further comprises one or more wobble base pair positioned in said one or more complementary domains within a restriction enzyme recognition and/or cut site in said adapter.

16. The method of claim 1 , wherein said adapter further comprises a cleavable linker in the loop region of said hairpin structure.

17. The adapter of claim 9 , wherein said adapter further comprises a cleavable linker in the loop region of said hairpin structure.