Sulfo-Cyanine5 amine is widely used in bioconjugation for labeling biomolecules such as antibodies, peptides, and nucleic acids. Its high water solubility makes it ideal for biological applications performed in aqueous environments, reducing the need for organic solvents. The amine-reactive form allows efficient coupling to carboxyl groups via EDC chemistry or to other activated esters, enabling stable linkage in probe synthesis.

It is commonly employed in fluorescence-based imaging techniques, including fluorescence microscopy and flow cytometry, due to its strong absorbance and emission in the far-red region (~650 nm excitation, ~670 nm emission), which minimizes background autofluorescence from biological samples. Its sulfo group enhances cell membrane impermeability, making it suitable for labeling extracellular targets or cell-surface receptors.

Additionally, Sulfo-Cyanine5 amine is used in developing diagnostic assays and in vivo imaging probes where low nonspecific binding and high signal-to-noise ratios are critical. It is also applied in multiplex assays when combined with other fluorophores due to minimal spectral overlap with green and yellow dyes.