A H-1 NMR study of the binding of Δ-[Ru(phen)(2)DPQ](2+) to the hexanucleotide d(GTCGAC)(2). Evidence for intercalation from the minor groove

There has been considerable interest in the DNA binding properties of inert transition metal complexes that are capable of binding to DNA by intercalation. These complexes can be used to help establish the principles of nucleic acid recognition, probe the tertiary structure of nucleic acids, and examine electron transfer mediated by DNA. The determination of the DNA binding geometry is a very important aspect in the study of the interactions of metallointercalators with nucleic acids. While it has been unambiguously demonstrated that metallointercalators based on the 9,10-phenanthrenequinone diimine (phi) ligand intercalate from the major groove, the DNA binding location of Ru(II) polypyridyls is not yet firmly established. On the basis of NMR evidence, Dupureur and Barton have shown that Delta-[Ru(phen)2DPPZ]2+ (DPPZ ) dipyridophenazine) intercalates from the major groove. However, on the basis of a similarity of the DNA binding geometry of Delta-[Ru(phen)2DPPZ]2+ with actinomycin D, Lincoln et al. have proposed that the metal complex may intercalate from the minor groove. In this paper, we report a NMR study of the binding of Delta-[Ru(phen)2DPQ]2+ (DPQ=dipyrido[2,2-d:2',3'-f]quinoxaline), an analogue of Delta-[Ru-(phen)2DPPZ]2+, to the hexanucleotide d(GTCGAC)2. Evidence is presented which demonstrates that this particular metal complex intercalates from the DNA minor groove.