Dinuclear ruthenium(II) complexes with flexible bridges as non-duplex DNA binding agents

The stereoisomers of a series of dinuclear ruthenium(II) complexes [{Ru(phen)₂}₂(µ-BL)]⁴⁺ (phen = 1,10-phenanthroline) with flexible bridging ligands (BL) bb2 {1,2-bis[4(4′-methyl-2,2′-bipyridyl)]ethane}, bb5 {1,5-bis[4(4′-methyl-2,2′-bipyridyl)]pentane}, bb7 {1,7-bis[4(4′-methyl-2,2′-bipyridyl)]heptane}, and bb10 {1,10-bis[4(4′-methyl-2,2′-bipyridyl)]decane} have been synthesised. Their binding to a control dodecanucleotide, d(CCGGAATTCCGG)₂, and a tridecanucleotide, d(CCGAGAATTCCGG)₂, which contains a single adenine bulge have been studied using fluorescence displacement assays involving intercalating and groove-binding dyes, equilibrium dialysis and binding affinity chromatography. The fluorescence intercalator displacement (FID) assay indicated that ΛΛ-[{Ru(phen)₂}₂(µ-bb7)]⁴⁺ had the greatest binding affinity with all the oligonucleotides, whereas an analogous fluorescence technique using a minor-groove binding dye, equilibrium dialysis and affinity binding chromatography showed that ΔΔ-[{Ru(phen)₂}₂(µ-bb7)]⁴⁺ had the strongest binding. An ¹H NMR study of the binding of the ΔΔ-enantiomer of [{Ru(phen)₂}₂(µ-bb7)]⁴⁺ to d(CCGAGAATTCCGG)₂ confirmed the selectivity of the metal complex for the bulge site and provided the basis for an energy-minimised binding model of the dinuclear ruthenium complex with the single adenine bulge containing trinucleotide. The binding model demonstrated the ability of the flexibly-linked complex to follow the curvature of the DNA minor groove.