Parallel preparation of high fidelity probes in an array format

1. A method of purifying a set of oligonucleotides, comprising the steps of

a) providing a solid substrate comprising a plurality of ribonucleotides attached thereto at a density of 200 to 2000 pmoles per cm 2 , one said ribonucleotide shown below

wherein PG 1 is protecting group 1, PG 2 is an alkaline resistant protecting group, 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 DMT, B is a naturally or non-naturally occurring base in which the exocyclic amine groups are protected with alkaline labile protecting groups, 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

wherein PG 4 is DMT, 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) deprotecting said set of oligonucleotides while said oligonucleotides are still attached to said substrate by subjecting said oligonucleotides to alkaline conditions, wherein said alkaline conditions remove said alkaline labile protecting groups acting to protect said exocyclic amines and in addition cleave depurinated DNA, leaving a 3′-end of the cleaved depurinated strand attached to the substrate and releasing a truncated fragment;

h) washing the solid support to remove said released truncated fragments and protecting groups, leaving full length oligonucleotides having a DMT group on the 5′-hydroxyl group and truncated oligonucleotides without the 5′-DMT group;

i) 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;

j) transesterifying each of said one or more ribonucleotides to yield said solid substrate having a cyclic ester attached thereto and a mixture of full length oligonucleotides having 5′-DMT groups and free 3′-hydroxyl groups and having the structure

and truncated fragments lacking the DMT group;

k) applying the mixture to hydrophobic oligonucleotide purification resin to isolate only those oligonucleotides having the 5′-DMT group to yield full length oligonucleotides; and

l) removing the 5′-DMT group to provide sets of full length oligonucleotides having both 5′- and 3′-hydroxyl groups.

2. A method according to claim 1 wherein said PG 2 is selected from the group consisting of FPMP, CEE, TBDMS, TOM and a photo labile protective group.

3. A method according to claim 2 wherein said PG 2 is selected from the group consisting of FPMP and CEE.

4. A method according to claim 3 wherein PG 2 is removed with mild acid.

5. A method according to claim 2 wherein said PG 2 is selected from the group consisting of TBDMS and TOM.

6. A method according to claim 5 wherein PG 2 is removed by exposure to fluoride ions.

7. A method according to claim 2 wherein said PG 2 is a photo labile protecting group removed by exposure to electromagnetic radiation of about 310 nm and up.

8. A method according to claim 7 wherein said photolabile protecting group is selected from the group consisting of NNPOC and MBPMOC.