The two modes of binding of Ru(phen)2dppz2+ to DNA: Thermodynamic evidence and kinetic studies

The binding of Ru(phen)2dppz2+ (dppz = dipyrido[3,2-a:2′,3′-c]phenazine) to DNA was investigated at pH 7.0 and 25 °C using stopped-flow and spectrophotometric methods. Equilibrium measurements show that two modes of binding, whose characteristics depend on the polymer to dye ratio (CP/CD), are operative. The binding mode occurring for values of CP/CD higher than 3 exhibits positive cooperativity, which is confirmed by kinetic experiments. The reaction parameters are K = 2 × 103 M−1, ω = 550, n = 1, kr = (1.9 ± 0.5) × 107 M−1 s−1 and kd = (9.5 ± 2.5) × 103 s−1 at I = 0.012 M. The results are discussed in terms of prevailing surface interaction with DNA grooves accompanied by partial intercalation of the dppz residue. The other binding mode becomes operative for CP/CD < 3 and the equilibria analysis shows this is an ordinary intercalation mode (K = 1.3 × 106 M−1, n = 1.5 at I = 0.012 M and K = 2 × 105 M−1, n = 1.2 at I = 0.21 M). Similar behaviour is displayed by double-stranded poly(A).