The Alexa Fluor® 647 dyes, used to label nucleotides, are compatible with commonly used microarray scanners, and provide greater signal correlation (R2) valuesthan the spectrally similar Cy™3 and Cy™5 dye pair, improving the resolution of two-color microarray gene expression assays to 1.3-fold changes in expression. The exceptionally bright and photostable Alexa Fluor® dyes are also essentially insensitive tob pH and are highly water soluble.