Interaction and Binding Modes of bis-Ruthenium(II) Complex to Synthetic DNAs

[μ-(linker)L2(dipyrido[3,2-a:2′,3′-c]phenazine)2(phenanthroline)2Ru(II)2]2+ with linker: 1,3-bis-(4-pyridyl)-propane, L: PF6 (bis-Ru-bpp) was synthesized and their binding properties to a various polynucleotides were investigated by spectroscopy, including normal absorption, circular dichroism(CD), linear dichroism(LD), and luminescence techniques in this study. On binding to polynucleotides, the bis-Ru-bpp complex with poly[d(A-T)2], and poly[d(I-C)2] exhibited a negative LDr signal whose intensity was as large as that in the DNA absorption region, followed by a complicated LDr signal in the metal-to-ligand charge transfer region. Also, the emission intensity and equilibrium constant of the bis-Ru-bpp complex with poly[d(A-T)2], and poly[d(I-C)2] were enhanced. It was reported that both of dppz ligand of the bis-Ru-bpp complex intercalated between DNA base-pairs when bound to native, mixed sequence DNA. Observed spectral properties resemble to those observed for poly[d(A-T)2] and poly[d(I-C)2], led us to be concluded that both dppz ligands intercalate between alternated AT and IC bases-pairs In contrast when bis-Ru-bpp complex was bound to poly[d(G-C)2], the magnitude of the LDr in the dppz absorption region, as well as the emission intensity, was half in comparison to that of bound to poly[d(A-T)2], and poly[d(I-C)2]. Therefore the spectral properties of the bis-Ru-bpp-poly[d(G-C)2] complex suggested deviation from bis-intercalation model in the poly[d(G-C)2] case. These results can be explained by a model whereby one of the dppz ligands is intercalated while the other is exposed to solvent or may exist near to phosphate. Also it is indicative that the amine group of guanine in the minor groove provides the steric hindrance for incoming intercalation binder and it also takes an important role in a difference in binding of bis-Ru-bpp bound to poly[d(A-T)2] and poly[d(I-C)2].