Sulfo-Cy3 DBCO is widely used in bioorthogonal chemistry for labeling and imaging biomolecules in live cells and biological systems. Its key application lies in copper-free click chemistry, where it reacts selectively and efficiently with azide-functionalized molecules without the need for toxic copper catalysts. This makes it ideal for labeling cell surface glycans, proteins, and nucleic acids in living systems with minimal background and high sensitivity.

The sulfo group enhances water solubility and reduces nonspecific binding, allowing for clean and efficient conjugation in aqueous environments. Sulfo-Cy3 DBCO is commonly used in fluorescence microscopy, flow cytometry, and in vivo imaging due to its bright red fluorescence and excellent photostability. It is also employed in multiplex labeling experiments when combined with other fluorophores, enabling simultaneous tracking of multiple biomolecular targets. Its bioorthogonal reactivity and optical properties make it a powerful tool for studying dynamic biological processes in real time.