Sulfo-Cy3 NHS ester is a sulphonated CY3 derivative and fluorophore dye with an Ex/Em of 550/570 nm. Sulfo-Cy3 NHS ester is an amine-reactive fluorescent probe commonly employed for labelling nucleic acids and proteins.

Reference for the usage of CY3-SE:
1. Protein Preparation
It is recommended to prepare the protein (antibody) solution at a concentration of 2 mg/mL, with a pH of 8.5 ± 0.5. If the pH is below 8.0, adjust it using 1 M sodium bicarbonate.
Note: If the protein concentration is below 2 mg/mL, the labeling efficiency will significantly decrease. For optimal labeling efficiency, the recommended final protein concentration range is 2–10 mg/mL. The protein buffer must not contain primary amines (e.g., Tris or glycine) or ammonium ions, as these will affect labeling efficiency.
2. Dye Preparation
Dissolve CY3-SE dye in anhydrous DMSO to prepare a 10 mg/mL stock solution—Aliquot and store at -20°C or -80°C, protected from light.
3. Dye Quantity Calculation
The required amount of CY3-SE dye for the labeling reaction depends on the quantity of protein to be labeled. The optimal molar ratio of CY3-SE dye to protein is approximately 10.
Example: If the protein to be labeled is 500 μL of 2 mg/mL IgG (MW = 150,000), dissolve 1 mg of CY3-SE dye in 100 μL DMSO. The required volume of CY3-SE is 4.88 μL, calculated as follows:
1) mmol (IgG) = mg/mL (IgG) × mL (IgG) / MW (IgG) = 2 mg/mL × 0.5 mL / 150,000 mg/mmol = 6.7 × 10⁻⁶ mmol
2) mmol (CY3-SE) = mmol (IgG) × 10 = 6.7 × 10⁻⁶ mmol × 10 = 6.7 × 10⁻⁵ mmol
3) μL (CY3-SE) = mmol (CY3-SE) × MW (CY3-SE) / mg/μL (CY3-SE) = 6.7 × 10⁻⁵ mmol × 727.84 mg/mmol / 0.01 mg/μL = 4.88 μL (CY3-SE)
4. Labeling Reaction
Slowly add the corresponding volume of 10 mg/mL CY3-SE dye to 0.5 mL of the protein sample solution. Mix gently, then briefly centrifuge to collect the sample at the bottom of the reaction tube. Incubate the reaction tube in the dark at room temperature with gentle shaking for 60 minutes, inverting the tube several times every 10–15 minutes.
5. Protein Purification
Purify the dye-protein conjugate using an appropriate method.