Cy5 Maleimide (also sold under Sulfo-Cyanine5 Maleimide) is a water-soluble, bright, far-red-fluorescent dye with excitation ideally suited for the 633 nm or 647 nm laser lines. A significant advantage to using long wavelength dyes such as Cy5 or AF 647 dye over other fluorophores is the low autofluorescence of biological specimens in this region of the spectrum.
Maleimide is the most popular sulfhydryl-reactive reactive group for conjugating the dye to a thiol group on a protein, oligonucleotide thiophosphate, or low molecular weight ligand. We do not recommended using Cy5 Maleimide for labeling proteins at high molar ration due significant self-quenching. Cy5 conjugates are only recommended for detection of moderate-to-high abundance targets. For detection of low-abundance biological targets we recommend using AF 647 Maleimide (Alexa Fluor ® 647 analog) or IR 647 (IRDye® 647 analog), which can attached to proteins at high molar ratios without significant self-quenching, enabling brighter conjugates and more sensitive detection.