title: Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay.
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.
authors.affiliation: Department of Chemistry, State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA. mcknight@geneseo.edu
authors.forename: Ruel E
authors.initials: RE
authors.lastname: McKnight
authors.forename: Aaron B
authors.initials: AB
authors.lastname: Gleason
authors.forename: James A
authors.initials: JA
authors.lastname: Keyes
authors.forename: Sadia
authors.initials: S
authors.lastname: Sahabi
mesh_terms: D052160:Benzothiazoles; D002151:Calorimetry; D004247:DNA / Q000187:drug effects* / Q000378:metabolism*; D004265:DNA Helicases; D004264:DNA Topoisomerases, Type I; D003959:Diamines; D005456:Fluorescent Dyes; D007094:Imides / Q000494:pharmacology; D007364:Intercalating Agents / Q000494:pharmacology; D008970:Molecular Weight; D009281:Naphthalenes / Q000494:pharmacology; D009930:Organic Chemicals; D010957:Plasmids / Q000737:chemistry / Q000187:drug effects; D011804:Quinolines
chemical_list: D052160:Benzothiazoles; D003959:Diamines; D005456:Fluorescent Dyes; D007094:Imides; D007364:Intercalating Agents; D009281:Naphthalenes; D009930:Organic Chemicals; C099476:PicoGreen; D011804:Quinolines; C098022:SYBR Green I; D004247:DNA; D004265:DNA Helicases; D004264:DNA Topoisomerases, Type I