SUNY at Albany
June 19-23, 2001
Strong and Weak Interaction of Ethidium Bromide with ds-DNA
Ethidium Bromide (EtBr) is the classic example of a ligand that binds to double-stranded DNA (ds-DNA) by intercalation. However a comparison of theory and experiments revealed at least three types of complexes of EtBr with ds-DNA .. We present experimental results from absorbency and fluorescence intensity spectroscopic methods, which prove multimodal binding of EtBr with ds-DNA. Analyses of the Scatchard isotherms points to the existence of two "strong" interactions of the ligand with ds-DNA at low dye concentration (1 ligand to six b.p.), one of which is resistant to ionic strength (m. We assume that here the molecules are apparently bound more to the minor groove of DNA, a kind of hemi-intercalative binding. Examination of the binding isotherms of EtBr to ds-DNA over a wide concentration range including high dye concentration, at which saturation of the biopolymer with ligand occurred, revealed one more type of interaction, binding constant of which is two orders smaller than that of "strong" interactions. We plotted the dependence of the ligand concentration (cq) corresponding to each type of binding sites on the total concentration of EtBr and obtained that the greater the ratio of Ki/r i (Ki-is the binding constant, ri is the number of b.p. corresponding to a given binding site) the smaller the concentration at which saturation of the corresponding site.
Armen T.Karapetian**, Zaruhi R.Boyagyan, Grigor A.Manukian, Ara P.Antonian(1),
Yerevan State University of Architecture and Construction, Yerevan 375009, Armenia