Methods for sequencing a polynucleotide template

1. A method for pairwise sequencing of a polynucleotide template, the method comprising:

(a) providing a polynucleotide template immobilized on a surface, said polynucleotide template comprising

a first template strand having a first region, wherein the first template strand lacks a 5 ′ phosphate group or comprises a blocked 5 ′ phosphate group such that the first template strand is not capable of being ligated to a free 3 ′ hydroxyl group, and

a first self-complementary hairpin polynucleotide linker comprising a loop region and a stem region, wherein the 5 ′ end of one strand of the stem region is linked to the 3 ′ end of said first template strand and the 3 ′ end of the other strand of the stem region comprises a first free 3 ′ hydroxyl group used for initiating sequencing of the first region of the first template strand,

(b) performing a first sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3 ′ end of said first self-complementary hairpin polynucleotide linker, thereby determining the sequence of the first region of the first template strand, wherein each of said nucleotides comprises a fluorescent label and a 3 ′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3 ′ end of the polynucleotide template, and wherein said sequential incorporation comprise

(i) incorporating one of said nucleotides into the first free 3 ′ hydroxyl group and detecting a fluorescent signal generated from the fluorescent label using a CCD camera or other fluorescence detection means, and

(ii) cleaving the fluorescent label and the 3 ′ blocking group from said one of said nucleotides in the 3 ′ end of said polynucleotide template, thereby yielding a free 3 ′ hydroxyl group before another of said nucleotides is incorporated into the 3 ′ end of said polynucleotide template,

(c) adding an unlabeled nucleotide to the free 3 ′ hydroxyl group in the last nucleotide added in step (b) and performing an extension reaction in the presence of different unlabeled nucleotides, thereby generating a second template strand having a free 3 ′ hydroxyl group, wherein the second template strand is complementary to the full length of said first template strand and comprises a second region,

(d) forming a ligation product by ligating a second self-complementary hairpin polynucleotide linker having a free 3 ′ hydroxyl group to the free 3 ′ hydroxyl group of the second template strand, whereby the free 3 ′ hydroxyl group of the second self-complementary hairpin polynucleotide linker provides a second free 3 ′ hydroxyl group used for initiating sequencing of the second region of the second template strand, and

(e) performing a second sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3 ′ end of the second self-complementary hairpin polynucleotide linker of said ligation product using a strand-displacing polymerase, thereby generating an extended complementary strand and determining the sequence of the second region of the second template strand, wherein each of said nucleotides comprises a fluorescent label and a 3 ′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3 ′ end of said ligation product the extended complementary strand, and wherein said sequential incorporation after step (d) comprises

(i) incorporating one of said nucleotides into the second free 3 ′ hydroxyl group and detecting a fluorescent signal generated from the fluorescent label using a CCD camera or other fluorescence detection means, and

(ii) cleaving the fluorescent label and the 3 ′ blocking group from said one of said nucleotides in the 3 ′ end of said ligation product,

thereby yielding a free 3 ′ hydroxyl group before another of said nucleotides is incorporated into the 3 ′ end of said ligation product;

wherein the first template strand ranges in length from 100 nucleotides to 1 kb.

2. The method of claim 1 , wherein the polynucleotide template forms part of an array.

3. The method of claim 1 , wherein the first sequencing-by-synthesis reaction of step (b) comprises incorporation of 10 to 200 consecutive nucleotides.

4. The method of claim 1 , wherein the second sequencing-by-synthesis reaction of step (e) comprises incorporation of 10 to 200 consecutive nucleotides.

5. The method of claim 1 , wherein the extension reaction of step (c) comprises incorporation of at least 100 consecutive nucleotides.

6. The method of claim 1 , wherein the extension reaction of step (c) comprises incorporation of at least 200 consecutive nucleotides.

7. The method of claim 1 , wherein the polynucleotide template is directly linked to the surface of a solid support.

8. The method of claim 1 , wherein the extension reaction of step (c) is performed without determining the identities of the unlabeled nucleotides added in step (c).

9. A method for pairwise sequencing of a polynucleotide template, the method comprising:

(a) providing a polynucleotide template immobilized on a surface, said polynucleotide template comprising

a first template strand having a first region, and

a first self-complementary hairpin polynucleotide linker comprising a loop region and a stem region, wherein the 5 ′ end of one strand of the stem region is linked to the 3 ′ end of said first template strand and the 3 ′ end of the other strand of the stem region comprises a first free 3 ′ hydroxyl group used for initiating sequencing of the first region of the first template strand,

(b) performing a first sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3 ′ end of said first self-complementary hairpin polynucleotide linker, thereby determining the sequence of the first region of the first template strand, wherein each of said nucleotides comprises a fluorescent label and a 3 ′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3 ′ end of the polynucleotide template, and wherein said sequential incorporation comprise

(i) incorporating one of said nucleotides into the first free 3 ′ hydroxyl group and detecting a fluorescent signal generated from the fluorescent label using a CCD camera or other fluorescence detection means, and

(ii) cleaving the fluorescent label and the 3 ′ blocking group from said one of said n nucleotides in the 3 ′ end of said polynucleotide template, thereby yielding a free 3 ′ hydroxyl group before another of said nucleotides is incorporated into the 3 ′ end of said polynucleotide template,

(c) adding an unlabeled nucleotide to the free 3 ′ hydroxyl group in the last nucleotide added in step (b) and performing an extension reaction in the presence of different unlabeled nucleotides, thereby generating a second template strand having a free 3 ′ hydroxyl group, wherein the second template strand is complementary to the full length of said first template strand and comprises a second region,

(d) forming a ligation product by ligating a second self-complementary hairpin polynucleotide linker having a free 3 ′ hydroxyl group to the free 3 ′ hydroxyl group of the second template strand, whereby the free 3 ′ hydroxyl group of the second self-complementary hairpin polynucleotide linker provides a second free 3 ′ hydroxyl group used for initiating sequencing of the second region of the second template strand,

(e) producing a truncated ligation product by removing a portion of the first template strand from said ligation product, and

(f) performing a second sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3 ′ end of the second self-complementary hairpin polynucleotide linker of said truncated ligation product, thereby generating an extended complementary strand and determining the sequence of the second region of the second template strand, wherein each of said nucleotides comprises a fluorescent label and a 3 ′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3 ′ end of said truncated ligation product, and wherein said sequential incorporation after step (d) comprises

(i) incorporating one of said nucleotides into the second free 3 ′ hydroxyl group and detecting a fluorescent signal generated from the fluorescent label using a CCD camera or other fluorescence detection means, and

(ii) cleaving the fluorescent label and the 3 ′ blocking group from said one of said nucleotides in the 3 ′ end of said truncated ligation product, thereby yielding a free 3 ′ hydroxyl group before another of said nucleotides is incorporated into the 3 ′ end of said truncated ligation product;

wherein the first template strand ranges in length from 100 nucleotides to 1 kb.

10. The method of claim 9 , wherein the portion of the first template strand is removed by cleavage of the polynucleotide template of said ligation product with a nicking endonuclease followed by denaturation of said truncated ligation product and the portion of the first template strand is located upstream of the cleavage site of said nicking endonuclease.

11. The method of claim 9 , wherein the first self-complementary hairpin polynucleotide linker comprises a recognition site for a nicking endonuclease which directs a cleavage by the nicking endonuclease at a site before, at or beyond the 5 ′ end of the first self-complementary hairpin polynucleotide linker.

12. The method of claim 9 , wherein the polynucleotide template forms part of an array.

13. The method of claim 9 , wherein the first sequencing-by-synthesis reaction of step (b) comprises incorporation of 10 to 200 consecutive nucleotides.

14. The method of claim 9 , wherein the second sequencing-by-synthesis reaction of step (e) comprises incorporation of 10 to 200 consecutive nucleotides.

15. The method of claim 9 , wherein the extension reaction of step (c) comprises incorporation of at least 100 consecutive nucleotides.

16. The method of claim 9 , wherein the extension reaction of step (c) comprises incorporation of at least 200 consecutive nucleotides.

17. The method of claim 9 , wherein the polynucleotide template is directly linked to the surface of a solid support.

18. The method of claim 9 , wherein the extension reaction of step (c) is performed without determining the identities of the unlabeled nucleotides added in step (c).