Patent ID: 7846660

Claim:
A method for synthesizing different oligonucleotides in the same feature on a substrate for a microarray, the method comprising the steps of: providing the substrate for manufacturing the microarray, the substrate having a plurality features comprising photo-labile first protecting groups formed on its surface, exposing at least one feature to light for a period of time sufficient to cleave only a portion of the photo-labile first protecting groups to leave a first unprotected area of the at least one feature; coupling a non-photosensitive second protecting group to the first unprotected area; further exposing the at least one feature to light for a period of time to cleave the photo-labile first protecting groups from the at least one feature to leave a second unprotected area of the at least one feature; building a first group of oligonucleotides in the second unprotected area using an amidite having a protecting group at its 5′ position; capping the first group of oligonucleotides with a capping compound that is not photo-labile; removing the second protecting group from the at least one feature to unprotect the first area; and building a second group of oligonucleotides in the first unprotected area using an amidite having a protecting group at its 3′ position, such that the at least one feature comprises both 3′-5′-oriented oligonucleotides and 5′-3′-oriented oligonucleotides attached to the substrate surface.