The influence of GC/AT composition on intercalating and semi-intercalating binding of ethidium bromide to DNA

Abstract

The binding parameters of ethidium bromide (EtBr) with DNA of various GC/AT ratios were determined using absorption and fluorescence spectroscopy. Our experimental data clearly demonstrate the co-existence of fluorescing and non-fluorescing types of "strong" binding at low concentration of EtBr. The fluorescent complex corresponds to the ordinary intercalative model. The non-fluorescent complex is referred to semi-intercalative binding of EtBr. The binding constant (K) and the number of base pairs corresponding to a binding site (n) of the fluorescent (Kf and nf) and non-fluorescent (Knf, nnf) types of interactions were determined. The average size of binding site (n) is equal to 1.5 bp (absorption spectroscopy), and nf ca. 2 bp (fluorescence spectroscopy). It was shown that nnf is dependent on GC-content and total n is independent of it. © 2012 Sociedade Brasileira de Química.