Sulfo-Cy3-SE is widely used in biological research for labeling proteins, peptides, and other biomolecules. It is particularly valuable in fluorescence microscopy and flow cytometry due to its bright fluorescence and photostability. This dye is commonly employed in immunofluorescence assays to visualize and track specific proteins or cellular components. It is also utilized in protein-protein interaction studies, where it helps in identifying binding partners and understanding molecular pathways. Additionally, Sulfo-Cy3-SE is used in nucleic acid labeling for applications like fluorescence in situ hybridization (FISH) to detect and localize specific DNA or RNA sequences. Its water-soluble nature makes it suitable for labeling in aqueous environments without requiring organic solvents, ensuring minimal disruption to biological systems.