The spectroscopic titrations, circular dichroism (CD), electric linear dichroism (LD), emission measurements, and photoactivated reactions have been used to study the interactions of the enantiomers of [Ru(bpy)(2)phi]Cl-2 and [Ru(phen)(2)phi]Cl-2 (bpy 2,2’-bipyridine, phen 1,10-phenanthroline and phi = 9,10-phenanthrenequinone diimine) with different compositions and conformations of polynucleotides. The investigated polynucleotides are calf thymus DNA, B-poly[d(G-C)](2), B- and Z-poly[d(G-m(5)C)](2), B-poly[d(A-T)](2), and B-[poly(dA).poly(dT)]. These complexes are bound to polynucleotides with the binding constants larger than 10(4) M(-1). From the CD and LD spectra, the phi ligands of both enantiomers are concluded to be intercalated between the base pairs of polynucleotides. According to the LD spectra, the opposite enantiomers orient the ancillary two ligands (bpy or phen) in different directions, indicating the presence of chiral discriminations by DNA. Z-poly[d(G-m(5)C)](2) is found to be transformed into the B-form upon intercalative binding with chiral complexes. There are no emission and photoactivated cleavage activities between enantiomers and polynucleotides.