Cyanine 3-dUTP can replace TTP in reactions in which it serves as a substrate for E. coli DNA polymerase (holoenzyme and Klenow fragment), T4 and Taq DNA polymerases, reverse transcriptase (from AMV and M-MuLV) and terminal transferase. Fluorescently labeled probes can be prepared with this fluorescent nucleotide by a variety of methods including nick translation, cDNA labeling and 3’-end labeling. Probes generated by these methods are suitable for use for the identification of specific sequences by in situ hybridization procedures on fixed cells and tissues by direct fluorescence detection. Cyanine 3-dUTP can also be used for multicolor fluorescence labeling.