Methods for sequencing a polynucleotide template

1. A method for sequencing a first region and a second region of a polynucleotide template, the method comprising:

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

a single polynucleotide strand having a first region and a second region, said first region and said second region separated by at least 50 nucleotides, and

a 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 polynucleotide 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 polynucleotide strand,

(b) performing a first sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3′ end of said polynucleotide template, thereby determining the sequence of the first region of the polynucleotide 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 polynucleotide template, and wherein said sequential incorporation comprises

(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 the 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 an extension product having a second free 3′ hydroxyl group used for initiating sequencing of the second region of the polynucleotide strand, and

(d) performing a second sequencing-by-synthesis reaction comprising sequential incorporation of different complementary reversibly-terminated nucleotides into the 3′ end of the extension product generated in step (c), thereby determining the sequence of the second region of the polynucleotide 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 polynucleotide template, and wherein said sequential incorporation after step (c) 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 extension product, thereby yielding a free 3′ hydroxyl group before another of said nucleotides is incorporated into the 3′ end of said extension product;

wherein said polynucleotide 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 (d) 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 step (c) is performed without determining the identities of the nucleotides of the extension product.

9. The method of claim 1 , wherein said unlabeled nucleotides in step (c) comprise dUTP such that the extension product comprises one or more uracil bases, and wherein step (c) further comprises contacting the extension product with a uracil DNA glycosylase to cleave said one or more uracil bases in the extension product, thereby generating the second free 3′ hydroxyl group.