Methods for sequencing a polynucleotide template

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

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

a first template strand having a first region and a 5′ phosphate 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, thereby determining the sequence of the first region of the first template strand, wherein each of said reversibly-terminated nucleotides comprises a fluorescent label and a 3′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3′ end of the first polynucleotide template to result in a second polynucleotide template, and wherein said sequential incorporation comprise

(i) incorporating one of said reversibly-terminated 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 reversibly-terminated nucleotides in the 3′ end of said second polynucleotide template, thereby yielding a free 3′ hydroxyl group before another of said reversibly-terminated nucleotides is incorporated into the 3′ end of the second 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) ligating a second self-complementary hairpin polynucleotide linker to the free 3′ hydroxyl group of the second template strand and the 5′ phosphate group of the first template strand, thereby generating a self-complementary, circular polynucleotide template,

(e) cleaving the circular polynucleotide template, thereby yielding a cleaved polynucleotide template comprising 3′ end comprising a second free 3′ hydroxyl group used for initiating sequencing of the second region of the second template strand,

(f) performing a second sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3′ end generated in step (e), thereby determining the sequence of the second region of the second template strand, wherein each of said reversibly-terminated nucleotides comprises a fluorescent label and a 3′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3′ end of the cleaved polynucleotide template, wherein the second sequencing-by-synthesis reaction is carried out using a strand-displacing polymerase enzyme, and wherein said sequential incorporation in step (f) comprises

(i) incorporating one of said reversibly-terminated 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 reversibly-terminated nucleotides in the 3′ end of said cleaved polynucleotide template, thereby yielding a free 3′ hydroxyl group before another of said reversibly-terminated nucleotides is incorporated into the 3′ end of said cleaved polynucleotide template;

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

2. The method of claim 1 , wherein said cleaving the circular polynucleotide template in step (e) comprises contacting the circular polynucleotide template with a nicking endonuclease.

3. The method of claim 2 , wherein the second self-complementary hairpin polynucleotide linker comprises a recognition site for the nicking endonuclease which cleaves at a site before, at or beyond the 3′ end of the second self-complementary hairpin polynucleotide linker of the circular polynucleotide template.

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

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

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

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

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

9. The method of claim 1 , wherein the polynucleotide template in step (a) is directly linked to the surface and the surface is located on a solid support.

10. The method of claim 1 , wherein the extension reaction of step (c) is performed without determining the identity of the unlabeled nucleotide added in step (c).

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

(a) providing a first polynucleotide template immobilized on a surface, said first polynucleotide template comprising a first template strand having a first region and a 5′ phosphate 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, thereby determining the sequence of the first region of the first template strand, wherein each of said reversibly-terminated nucleotides comprises a fluorescent label and a 3′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3′ end of the first polynucleotide template to result in a second polynucleotide template, and wherein said sequential incorporation comprise

(i) incorporating one of said reversibly-terminated 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 reversibly-terminated nucleotides in the 3′ end of said second polynucleotide template, thereby yielding a free 3′ hydroxyl group before another of said reversibly-terminated nucleotides is incorporated into the 3′ end of the second 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) ligating a second self-complementary hairpin polynucleotide linker to the free 3′ hydroxyl group of the second template strand and the 5′ phosphate group of the first template strand, thereby generating a self-complementary, circular polynucleotide template,

(e) cleaving the circular polynucleotide template, thereby yielding a cleaved polynucleotide template comprising a 3′ end comprising a second free 3′ hydroxyl group used for initiating sequencing of the second region of the second template strand, wherein cleaving the circular polynucleotide template comprises contacting the circular polynucleotide template with a first nicking endonuclease and a second nicking endonuclease, wherein the first self-complementary hairpin polynucleotide linker comprises a recognition site for the first nicking endonuclease which directs cleavage by the first nicking endonuclease at a site before, at or beyond the 5′ end of the first self-complementary hairpin linking polynucleotide, and wherein the second self-complementary hairpin polynucleotide linker comprises a recognition site for the second nicking endonuclease which directs cleavage by the second nicking endonuclease at a site before, at or beyond the 3′ end of the second self-complementary hairpin polynucleotide linker,

(f) removing a portion of the first template strand from the cleaved polynucleotide template by denaturation, wherein the portion is between a cleavage site of the first nicking endonuclease and a cleavage site of the second nicking endonuclease of the circular polynucleotide template,

(g) performing a second sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3′ end generated in step (e), thereby determining the sequence of the second region of the second template strand, wherein each of said reversibly-terminated nucleotides comprises a fluorescent label and a 3′ blocking group, the blocking group prevents any further nucleotide incorporation into the 3′ end of the cleaved polynucleotide template, and wherein said sequential incorporation in step (g) comprises

(i) incorporating one of said reversibly-terminated 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 reversibly-terminated nucleotides in the 3′ end of said cleaved polynucleotide template, thereby yielding a free 3′ hydroxyl group before another of said reversibly-terminated nucleotides is incorporated into the 3′ end of said cleaved polynucleotide template; wherein said first template strand ranges in length from 100 nucleotides to 1 kb.

12. The method of claim 11 , wherein the polynucleotide template forms a part of an array.

13. The method of claim 11 , wherein the first sequencing-by-synthesis reaction of step (b) comprises incorporation of 10 to 200 consecutive nucleotides.

14. The method of claim 11 , wherein the second sequencing-by-synthesis reaction of step (f) comprises incorporation of 10 to 200 consecutive nucleotides.

15. The method of claim 11 , wherein the extension reaction of step (c) comprises incorporation of at least 100 consecutive nucleotides.

16. The method of claim 11 , wherein the extension reaction of step (c) comprises incorporation of at least 200 consecutive nucleotides.

17. The method of claim 11 , wherein the polynucleotide template in step (a) is directly linked to the surface and the surface is located on a solid support.

18. The method of claim 11 , wherein the extension reaction of step (c) is performed without determining the identity of the unlabeled nucleotide added in step (c).