DNA binding geometries of ruthenium(II) complexes with 1,10-phenanthroline and 2,2′-bipyridine ligands studied with linear dichroism spectroscopy.: Borderline cases of intercalation

The DNA binding geometries for a series of enantiomerically purr substitution-inert ruthenium(II) complexes, containing 1,10-phenanthroline (phen) and 2,2'-bipyridine (bpy) as ligands, have been studied with linear dichroism (LD) spectroscopy, Based on flow LD and emission anisotropy (EA) spectra of the complexes in the presence of calf thymus DNA, their absorption spectra in the visible region have been resolved into three component spectra that are polarized nearly perpendicular to each other. Spectral similarities between the D-3 symmetric [Ru(phen)(3)](2+) and C-2 symmetric [Ru(phen)(2)dppz](2+) (dppz dipyrido[3,2-a :2',3'-c]phenazine), in which dppz is known to be intercalated between the DNA basepairs, indicates a symmetry breaking in the former chromophore, bringing up the long debated question whether one of the three phen ligands of [Ru-(phen)(3)](2+) may be intercalated. Indeed, the complete analysis of the flow LD spectra for [Ru(L)(2)Y](2+) complexes (L bpy or phen) reveals similar angular binding geometries whether Y = dppz or phen. When Y = phen, for both the Delta- and Lambda-enantiomers this ligand is thus found oriented nearly perpendicular to the DNA helix axis as if intercalated and, similar to the orientation of dppz in dppz complexes, with a small but distinct clockwise rotation around the pseudo-dyad axis when viewed toward the minor groove ("positive roll"). A markedly less ordered binding observed when passing from [Ru(bpy)(2)phen](2+) to [Ru(bpy)(3)](2+) supports a stacking interaction of the phen ligand with the nucleobases. However, in contrast to the lengthening of DNA observed with [Ru(phen)(2)dppz](2+) and classical intercalators, the absence of lengthening with [Ru-(phen)(3)](2+) indicates that although a phen may have stacking interaction with the nucleobases, it does not enter a fully opened intercalation pocket. Two alternative binding modes are discussed: semi-intercalation (only edge of the intercalation pocket opened) and quasi-intercalation (indenture of a basepair allowing stacking of adjacent bases with the intruding phen ligand). Fair agreement is found between the proposed binding geometry of [Ru(phen)(3)](2+) and previously reported 2D-NMR NOE data.