it depends a lot on the molecule you are trying to study. your best-case scenario is when the molecule is fluorescent os chromo/fluorogenic or environment-sensitive, and you can do UV or better yet fluorescence emission. CD would be another option, but much worse sensitivity. You can also do displacement assays with EtBr or some other dye... as I said, it depends a lot on your specific case.
See here and references therein: B. S. Reddy, S. M. Sondhi, J. W. Lown, Pharmacol. Ther. 1999, 84, 1–111.
Thanks a lot. M. Vazquez. What we wish to see upon metabolite synthesis by an enzyme, if these reactive metabolites will bind to DNA, and binding efficiency etc.
Microcale thermophoresis is a fantastic technology to study small compound-DNA interactions. It is fast, flexible and consumes low material.
Read about it here http://2bind.de/moleculareinteraction/techniques/
Electrochemical evaluation: of Interraction of DNA with molecularly imprinted polymers.
Article Molecularly Imprinted Polypyrrole for DNA Determination
By the way, we have also used single-molecule fluorescence to study the dynamics of the binding process. Take a look at:
J. Bordello, M.I. Sánchez, M.E. Vázquez, J.L. Mascareñas, W. Al-Soufi, M. Novo, Chem. Eur. J., 2014, (DOI: 10.1002/chem.201404926).
J. Bordello, M.I. Sánchez, M.E. Vázquez, J L. Mascareñas, W. Al-Soufi, M. Novo. Angew. Chem. Int. Ed., 2012, 51, 7541–7544. (DOI: 10.1002/anie.201201099).
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