Figure 2

Scan image of 4-plex microarray used for coupling studies. Coupling yield based on up to four sets of coupling parameters (or in a separate experiment, different phosphoramidites) were determined on single microarrays. The labels A, C, G, and T/U can refer to the four amidites, but in this scan only NPPOC-dT was used with four different sets of coupling parameters. The numbers at the top and bottom label the length of the experimental oligonucleotide, which is synthesized after a thymidine 15mer linker. Each numerical label is associated with four features, labeled in white in the top left corner: Cy3-labeled n-mer (a), unlabeled n-mer (b), Cy3-labeled 1-mer (c), and unlabeled 1-mer (d). The normalized intensity I of each n-mer is calculated as [I(a)-I(b)]/[I(c)-I(d)]. The data from this array is given in Table 2, Array 4. The 0-mer features are the result of coupling from a phosphoramidite port on the synthesizer containing pure acetonitrile and are used to calibrate the capping efficiency. Spot intensities are uniformly high due to high coupling efficiency.