Chemical labeling of an oligonucleotide array. Four sets of 25-base oligonucleotides were synthesized in triplicate on standard epoxysilane-modified glass slides using the 1:1 3MP:MGN solvent system, printing phosphoramidites before tetrazole. Each oligonucleotide contained from 1 to 10 guanosine residues. Alexa-594 dye was conjugated to the guanine bases using the instructions included in the ULYSIS kit (Molecular Probes), and the slide was scanned on the ScanArray using 10 μm resolution at standard laser and PMT settings. Fluorescence intensity was determined using the Dapple spot-finding program. (a) Laser scan of the array. The spots surrounding the experimental Alexa-labeled spots are standard gridding spots that are prehybridized to a control Cy5-labeled oligonucleotide, and are included on all arrays to facilitate grid placement and as a check on virtual well formation. (b) Fluorescence intensity from Dapple output graphed against the number of dGMP residues in the molecule. A good linear fit is observed (r2 = 0.99) and shows fluorescence intensity to be proportional to guanine content between four and 10 bases.