Dinuclear ruthenium(II) complexes as probes for DNA bulge sites

The binding of the dinuclear ruthenium(II) complexes ΔΔ-[{Ru(Me2bpy)2}2(μ-bpm)]4+ and ΔΔ-[{Ru(bpy)2}(μ-bpm){Ru(Me2bpy)2}]4+ {bpy = 2,2′-bipyridine; Me2bpy = 4,4′-dimethyl-2,2′-bipyridine; bpm = 2,2′-bipyrimidine} to a tridecanucleotide containing a single adenine bulge has been studied by 1H NMR spectroscopy. The addition of either complex to d(CCGAGAATTCCGG)2 induced significant chemical shift changes for the base and sugar resonances of the residues at the bulge site (G3A4G5/C11C10). In NOESY spectra of the tridecanucleotide bound with either ruthenium species, NOEs were observed from the H1′ and H4′ protons of the nucleotide residues at the bulge site to the Me2bpy and bpm protons of the metal complex. These results indicate that the dinuclear ruthenium species selectively bind at the adenine bulge site in the minor groove. A simple model was constructed for the binding of the non-symmetrical ΔΔ-[{Ru(bpy)2}(μ-bpm){Ru(Me2bpy)2}]4+ complex, which shows that the minor groove has significantly widened to allow the relatively bulky complex to bind. As the metal complexes specifically bind at an adenine bulge site in a segment of DNA with an affinity considerably greater than that for standard duplex DNA, the results presented here suggest that non-intercalating dinuclear complexes may be excellent diagnostic agents for DNA bulged sequences.