Alexa Fluor® 647 dye for labeling nucleotides is compatible with commonly used microarray scanners and provides excellent signal correlation (R2) values are greater than those of the spectrally similar Cy™3 and Cy™5 dye pairs and improve the resolution of two-color microarray gene expression experiments, reaching 1.3-fold expression changes. Extra bright and photostable Alexa Fluor® dyes are also virtually insensitive to pH and highly water-soluble.