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

Abstract

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.