CY5 is mainly soluble in organic solvents, such as DMSO, DMF, etc. Sulfonated CY5 is not only soluble in these organic solvents, but also in water. This is because the molecular structure of sulfonated CY5 contains sulfonic acid groups, which enhance the hydrogen bonding between it and water molecules, thus making it soluble in water.

Due to its high fluorescence stability and brightness, CY5 is often used to label proteins, nucleic acids and other biomolecules. Sulfonated CY5, on the other hand, is more commonly used for biomarkers in aqueous solutions, such as intracellular fluorescent labeling, and its excellent water solubility makes it perform better in these applications.