Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling

The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Δ-cis-α- and Δ-cis-β-[Ru(RR-picchxnMe₂) (bidentate)]²⁺, where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2′,3′-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe₂ is N,N′-dimethyl-N,N′-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Δ-cis-α,-[Ru(RR-picchxnMe₂)(phen)]²⁺ complex indicate fast exchange kinetics on the chemical shift time scale and a "partial intercalation" mode of binding. This complex binds to [d(CGCGATCGCG)]₂ and [d(ATATCGATAT)]₂ at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Δ-cis-β-[Ru(RR-picchxnMe₂)(phen)]²⁺ complex with [d(CGCGATCGCG)]₂ showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Δ-cis-α-[Ru(RR-picchxnMe₂)-(dpq)]²⁺ with [d(CGCGATCGCG)]₂ showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Δ-cis-α- and Δ-cis-β-[Ru-(RR-picchxnMe₂)(phi)]²⁺ showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)]₂ (measured as ΔT_m) increases in the order phen < dpq and DNA affinity in the order phen < dpq < phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.