DNA affinity binding studies using a fluorescent dye displacement technique: the dichotomy of the binding site.
We have observed a number of discrepancies and contradictions in the use of a fluorescent intercalator displacement assay in surveying the binding affinities of dinuclear polypyridyl ruthenium(II) complexes with DNA. By a modification of the assay using the fluorescent minor-groove binder 4',6-diamidino-2-phenylindole, rather than intercalating dyes (ethidium bromide or thiazole orange), results were obtained for all complexes studied which were consistent with relative affinities and stereoselectivities observed with other techniques, including NMR, affinity chromatography and equilibrium dialysis. It is believed that the difference in binding mode between the minor groove-binding Ru(II) complexes and the intercalating fluorescent dyes they are displacing may contribute to these discrepancies.
Spillane
Caitriona B
CB
School of Pharmacy and Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia.
Smith
Jayden A
JA
Morgan
Joy L
JL
Keene
F Richard
FR
D001665:Binding Sites; D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry; D008722:Methods; D017975:Ruthenium Compounds / Q000737:chemistry
D005456:Fluorescent Dyes; D007364:Intercalating Agents; D017975:Ruthenium Compounds; D004247:DNA