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)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).
Biver
Tarita
T
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy. tarita@dcci.unipi.it
Cavazza
Claudia
C
Secco
Fernando
F
Venturini
Marcella
M
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
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