Binding DNA to an SMCC linker (NHS ester) involves a two-step process:

1. Activation of the SMCC linker with NHS ester

2. Reaction of the activated SMCC linker with the amine group of DNA.

Here are some tips to help you with the process:

1. Use fresh NHS ester: NHS ester is highly susceptible to hydrolysis, which reduces its efficiency. Use fresh NHS ester and keep it at -20°C when not in use.

2. Maintain a pH of 7-9: The reaction works best at a pH range of 7-9. Make sure to adjust the pH of your buffer to this range before starting the reaction.

3. Work with high-quality DNA: DNA purity and quality are critical for the success of this reaction. Use high-quality DNA, free of any impurities that might interfere with the reaction.

4. Optimize reaction conditions: Vary the reaction time and concentration of the SMCC linker and DNA to find the optimal conditions for your specific experiment.

5. Purify the reaction product: Once the reaction is complete, purify the product to remove any unreacted SMCC linker or NHS ester. Gel filtration or dialysis are common methods for purification.

6. Characterize the product: Verify the success of the reaction by characterizing the product using techniques like UV-Vis spectroscopy, gel electrophoresis, or MALDI-TOF mass spectrometry.

7. Store the product correctly: Store the product at -20°C until use. Avoid repeated freeze-thaw cycles, as this can damage the DNA.

Overall, careful optimization of the reaction conditions and purification of the product are crucial for the success of the SMCC linker-DNA conjugation.