Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay.
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.
McKnight
Ruel E
RE
Department of Chemistry, State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA. mcknight@geneseo.edu
Gleason
Aaron B
AB
Keyes
James A
JA
Sahabi
Sadia
S
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
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