Differentiating quadruplexes: binding preferences of a luminescent dinuclear ruthenium(II) complex with four-stranded DNA structures

The interaction of luminescent dinuclear ruthenium(II) complexes containing the bridging ligand tetrapyrido[3,2-a:2',3'-c:3 '',2 ''-h:2 '',3 ''-j]phenazine with several intramolecular and intermolecular quadruplex DNA structures has been explored. It was found that these interactions produced distinctly different luminescence signatures. Binding curves constructed from these optical changes reveal that binding affinities for the quadruplex structures vary by over two orders of magnitude. The differences in quadruplex binding affinity and optical signature are rationalized through a consideration of the structural features of the quadruplexes. In particular we conclude large blue shifted emission enhancements are only observed on binding to quadruplexes containing lateral loops that are at least three base pairs long.