X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes

The new complexes [Ru(TAP)(2)(11-CN-dppz)](2+), [Ru(TAP)(2)(11-Br-dppz)](2+)and [Ru(TAP)(2)(11,12-diCN-dppz)](2+) are reported. The addition of nitrile substituents to the dppz ligand of the DNA photo-oxidising complex [Ru(TAP)(2)(dppz)](2+) promote pi-stacking interactions and ordered binding to DNA, as shown by X-ray crystallography. The structure of Lambda-[Ru(TAP)(2)(11-CN-dppz)](2+) with the DNA duplex d(TCGGCGCCGA)(2) shows, for the first time with this class of complex, a closed intercalation cavity with an AT base pair at the terminus. The structure obtained is compared to that formed with the 11-Br and 11,12-dinitrile derivatives, highlighting the stabilization of syn guanine by this enantiomer when the terminal base pair is GC. In contrast the AT base pair has the normal Watson-Crick orientation, highlighting the difference in charge distribution between the two purine bases and the complementarity of the dppz-purine interaction. The asymmetry of the cavity highlights the importance of the purine-dppz-purine stacking interaction.