Compositions and methods for synthesis of high fidelity oligonucleotides

1. A method for synthesizing high fidelity target oligonucleotides, the method comprising:

a. providing an array comprising a plurality of nucleic acids, each nucleic acid having a sequence comprising a template oligonucleotide sequence and a primer binding sequence, wherein the template oligonucleotide sequence is a reverse complement of the target oligonucleotide;

b. releasing the plurality of nucleic acids from the array;

c. circularizing the plurality of nucleic acids;

d. providing a primer, wherein the primer comprises a sequence complementary to the primer binding sequence, a restriction enzyme recognition site and self-complementary termini, under conditions promoting annealing of the primer to the primer binding sites;

e. amplifying the circularized nucleic acids in a rolling-circle amplification reaction using the primer, thereby forming single-stranded tandem nucleic acid sequences;

f. promoting hairpin formation of the primer wherein the restriction enzyme recognition site is formed within a double-stranded portion of the hairpin;

g. removing the primer binding sequences of the single-stranded tandem nucleic acid sequences by enzymatic cleavage using a suitable restriction enzyme; and

h. isolating the target oligonucleotides.

2. The method of claim 1 wherein in the step of releasing the plurality of nucleic acids is released in a pool.

3. The method according to claim 1 wherein the plurality of nucleic acids is immobilized on the array by their 3′ terminus.

4. The method according to claim 1 wherein the plurality of nucleic acids is synthesized on the array in a 3′-5′ direction.

5. The method according to claim 1 wherein the plurality of nucleic acids is synthesized on the array in a 5′-3′ direction.

6. The method according to claim 1 wherein the primer binding sequence is at least 100 bps long.

7. The method according to claim 1 wherein in the step of providing the array, the array comprises a plurality of template oligonucleotides and the primer binding sequence is ligated to each of the plurality of the template oligonucleotides.

8. The method according to claim 1 wherein, in the step of providing the array, the array comprises a porous reaction layer coupled to a phosphorylation reagent.

9. The method according to claim 1 wherein the primer binding site is 3′ or 5′ of the template oligonucleotide sequence.

10. The method according to claim 1 wherein the plurality of nucleic acids is phosphorylated at the 3′ end and wherein the step of releasing further comprises dephosphorylating the 3′ end of the nucleic acids and phosphorylating the 5′ end of the nucleic acids.

11. The method according to claim 1 wherein the step of circularizing is in the presence of a ligase.

12. The method according to claim 1 further comprising purifying the target oligonucleotides.

13. The method according to claim 1 wherein the primers contain dT-biotin and wherein, in the step of isolating, the oligonucleotides are purified using streptavidin beads.

14. The method of claim 1 wherein in step (a) the plurality of nucleic acids is synthesized on an array.