Patent ID: 7060443

Claim:
A method for determining the amount of depurination of oligonucleotides synthesized on a substrate by spatially directed oligonucleotide synthesis in a 5′ to 3′ direction comprising the steps of: a) providing a substrate having a surface with linkers having an active site for oligonucleotide synthesis, the linkers being resistant to cleavage under cleavage conditions; b) synthesizing an ensemble of sequence-specific oligonucleotides in a 5′ to 3′ direction in an area of the substrate, the oligonucleotides having active sites for attaching a detectable label; c) attaching a detectable label to the oligonucleotides in the ensemble; d) exposing the ensemble to a test condition; e) exposing the ensemble to cleavage conditions that cause cleavage of depurinated oligonucleotides; and f) determining the amount of detectable label in the area, wherein said amount of detectable label is a determination of the amount of depurination.