All amidites (xanthene, FAM amidites) have xanthene hydroxyls protected by pivaloyl groups (CH3)3CO to ensure stability of the products during oligonucleotide synthesis. That's why they are colourless or slightly coloured substances. Under standard cleavage and deprotection conditions (ammonia, 2 h at room temperature) xanthene hydroxyls are deprotected and xanthene derivatives give their characteristic fluorescence.
Why my xanthene amidites and supports does not fluoresce?
Xanthene amidites and supports (FAM, TET, HEX, JOE, SIMA, R6G, VIC-derivatives) have data on fluorescence with ~500/530 excitation/emission maxima, but all products are colourless or slightly coloured substances. How is it possible?