Patent ID: 7547775

Claim:
A method of fabricating a plurality of oligonucleotides having free 3′-hydroxyl groups from a high density oligonucleotide array, said method comprising the steps of a) providing a solid substrate comprising a plurality of ribonucleotides attached thereto, one said ribonucleotide shown below wherein PG 1 is protecting group 1, PG 2 is protecting group 2, B is a naturally or non-naturally occurring base, and said ribonucleotide is attached to said substrate through the 5′-hydroxyl group; b) selectively removing PG 1 in pre-selected areas to provide a plurality of free 3′-hydroxyl groups on said ribonucloetide; c) reacting said free 3′-hydroxyl groups with a 2′-deoxyribonucleotide having the structure wherein PG 3 is protecting group 3 and RG is a reactive group to couple said 2′-deoxyribonucleotide to said ribonucleotide to provide the structure d) selectively removing PG 3 from the 5′-hydroxyl of said 2′-deoxyribonucleotide in pre-selected areas to provide a plurality of free 5′-hydroxyl groups; e) reacting said free 5′-hydroxyl groups with an additional 2′-deoxyribonucleotide having the structure to yield a product of the structure f) repeating steps d and e one or more times to provide said oligonucleotides attached to said solid substrate; g) removing PG 2 from one or more of said ribonucleotides to provide a free 2′-hydroxyl group on each of said one or more ribonucleotides; and h) transesterifying each of said one or more ribonucleotides to yield said solid substrate having a cyclic ester attached thereto and free oligonucleotides, each oligonucleotide having a 3′-hydroxyl group and having the structure