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Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay
Ruel E McKnight1, Aaron B Gleason, James A Keyes
1Department of Chemistry, State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA. mcknight@geneseo.edu
Abstract:
A topoisomerase I DNA unwinding assay has been used to determine the relative DNA-binding affinities of a model pair of homologous naphthalene diimides. Binding affinity data were corroborated using calorimetric (ITC) and spectrophotometric (titration and T(m)) studies, with substituent size playing a significant role in binding. The assay was also used to investigate the mode of binding adopted by several known DNA-binding agents, including SYBR Green and PicoGreen. Some of the compounds exhibited unexpected binding modes.
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