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

The binding of Ru(phen)(2)dppz(2+) (dppz = dipyrido[3,2-a:2',3'-c]phenazine) to DNA was investigated at pH 7.0 and 25 degrees C using stopped-flow and spectrophotometric methods. Equilibrium measurements show that two modes of binding, whose characteristics depend on the polymer to dye ratio (C-P/C-D), are operative. The binding mode occurring for values Of C-P/C-D higher than 3 exhibits positive cooperativity, which is confirmed by kinetic experiments. The reaction parameters are K = 2 x 10(3) M-1, omega = 550, n = 1, k(r) = (1.9 +/- 0.5) x 10(7) M-1 s(-1) and k(d) = (9.5 +/- 2.5) x 10(3) 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 C-P/C-D < 3 and the equilibria analysis shows this is an ordinary intercalation mode (K = 1.3 x 10(6) M-1, n = 1.5 at I = 0.012 M and K = 2 x 10(5) M-1. n = 1.2 at I = 0.21 M). Similar behaviour is displayed by double-stranded poly(A). (c) 2006 Elsevier Inc. All rights reserved.