Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B-DNA Oligonucleotide

Herein we report the separation of the three stereoisomers of the DNA light-switch compound [{Ru-(bpy)(2)}(2)(tpphz)](4+) (tpphz = tetrapyrido [3,2-a:2',3'-c:3 '',2 ''-h:2"',3"'-j]phenazine)by column chromatography and the characterization of each stereoisomer by X-ray crystallography. The interaction of these compounds with a DNA octanucleotide d(GCATATCG)center dot d(CGATATGC) has been studied using NMR techniques. Selective deuteration of the bipyridyl rings was needed to provide sufficient spectral resolution to characterize structures. NMR-derived structures for these complexes show a threading intercalation binding mode with slow and chirality-dependent rates. This represents the first solution structure of an intercalated bis-ruthenium ligand. Intriguingly, we find that the binding site selectivity is dependent on the nature of the stereoisomer employed, with A Ru-II centers showing a better intercalation fit.