Pacific blue fluorescent dye modification is a post synthesis conjugation to a primary amino group. The amino group can be placed at the 5' and 3' and for internal positions an amino modified base is used, e.g Amino dT C6

Pacific Blue is a UV-excitable, bright blue fluorescent dye used for labeling oligonucleotides excitable by the 405 nm spectral line of blue diode (violet color) laser. Pacific Blue has an absorbance maximum of 410 nm and an emission maximum of 455 nm. Because UV light can photodamage labeled oligos, and many kinds of cells and tissues autofluoresce under UV light, Pacific Blue can only be used in a limited number of applications. Nevertheless, for such applications as nucleic acid microarrays and in situ hybridization, where a blue fluorescent probe provides a easily distinguishable, contrasting color to the green, yellow, orange and red fluorescence produced by longer-wavelength probes, Pacific Blue can be a good choice.