Effect of the bridge structure on the binding mode of the binuclear ruthenium complex to native DNA

Ruthenium(II) polypyridyl dimer containing large planar aromatic bridging ligands [μ-(tpphz)(phen)₄Ru₂]⁴⁺ (phen = 1,10-phenanthroline, tpphz = tetrapyrido[3,2-a:2′,3′-c:3″, 2″-h:2‴, 3‴-j]phenazine, bis-Ru-tpphz) were synthesized and characterized by elemental analysis, and ¹H nuclear magnetic spectroscopy. The binding mode of the synthesized bis-Ru-tpphz to DNA was compared with those of the bis-Ru-bip, and bis-Ru-tatpp complexes. The structures of the connecting bridge of bis-Ru complexes were different. The absorption and reduced linear dichroism spectrum showed that the planar linker moiety of the bis-Ru-tatpp complex is inserted between the DNA base-pairs despite the steric hindrance originating from its large ruthenium ligand part, whereas the bis-Ru-bip complex has flexible linker binds at the groove of the DNA. The binding mode of the bis-Ru-tpphz complex, which has fused shorter bridge ligands than the bis-Ru-tatpp complex, was in contrast with the other two complexes. The bis-Ru-tpphz complex binds either at the groove of the DNA or to the negatively charged phosphate group; intercalative binding was prevented by either short bridge structure or steric hindrances from the phenanthroline ligand. In conclusion, the structure of the bridge of the bis-Ru(II) complex plays an important role in determining the binding mode of these compounds to DNA. To have the mode of insertion, the bridge ligand structure must be fused and have a sufficiently long distance.