title: The two modes of binding of Ru(phen)(2)dppz(2+) to DNA: thermodynamic evidence and kinetic studies.
abstract: 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)x10(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).
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy. tarita@dcci.unipi.it
authors.forename: Tarita
authors.initials: T
authors.lastname: Biver
authors.forename: Claudia
authors.initials: C
authors.lastname: Cavazza
authors.forename: Fernando
authors.initials: F
authors.lastname: Secco
authors.forename: Marcella
authors.initials: M
authors.lastname: Venturini
mesh_terms: D000818:Animals; D002417:Cattle; D004247:DNA / Q000737:chemistry*; D007364:Intercalating Agents / Q000138:chemical synthesis / Q000737:chemistry; D007700:Kinetics; D008956:Models, Chemical; D009942:Organometallic Compounds / Q000138:chemical synthesis / Q000737:chemistry*; D010618:Phenanthrolines; D012428:Ruthenium / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D007364:Intercalating Agents; D009942:Organometallic Compounds; D010618:Phenanthrolines; C466600:Ru(phen)(2)dipyrido(3,2-a-2',3'-c)phenazine; D012428:Ruthenium; D004247:DNA; C427203:calf thymus DNA