The relationship between the structures of periphery ligands and the DNA binding mode of [Ru(II)(1,10-phenanthroline)(L1L2)dipyrido[3,2-a:2',3'-c]phenazine](n+) (L1=Cl or pyridine and L2=pyridine, n=1,2).

The binding modes of the [Ru(II)(1,10-phenanthroline)(L(1)L(2)) dipyrido[3,2-a:2',3'-c]phenazine](2+) {[Ru(phen)(py) Cl dppz](+) (L(1)=Cl, L(2)=pyridine) and ([Ru(phen)(py)(2)dppz](2+) (L(1)=L(2)=pyridine)} to native DNA is compared to that of the [Ru(II)(1,10-phenanthroline)(2)dipyrido[3,2-a:2',3'-c]phenazine](2+) complex ([Ru(phen)(2)dppz](2+)) by various spectroscopic and hydrodynamic methods including electric absorption, linear dichroism (LD), fluorescence spectroscopy, and viscometric titration. All measured properties, including red-shift and hypochromism in the dppz absorption band, nearly perpendicular molecular plane of the dppz ligand with respect to the local DNA helix axis, prohibition of the ethidium binding, the light switch effect and binding stoichiometry, increase in the viscosity upon binding to DNA, increase in the melting temperature are in agreement with classical intercalation of dppz ligand of the [Ru(phen)(2)dppz](2+) complex, in which both phenanthroline ligand anchored to the DNA phosphate groups by electrostatic interaction. [Ru(phen)(py)(2) dppz](2+) and [Ru(phen)(py) Cl dppz](+) complexes had one of the phenanthroline ligand replaced by either two pyridine ligands or one pyridine plus a chlorine ion. They exhibited similar protection from water molecules, interaction with DNA bases, and occupying site that is common with ethidium. The dppz ligand of these two Ru(II) complex were greatly tilted relative to the DNA helix axis, suggesting that the dppz ligand resides inside the DNA and is not perpendicular relative to the DNA helix axis. These observation suggest that anchoring the [Ru(phen)(2)dppz](2+)complex by both phenanthroline is essential for the dppz ligand to be classically intercalated between DNA base-pairs.