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The ruthenium complex [Ru(phen)(2)(dppz)](2+) (where phen is phenanthroline and dppzdipyridophenazine is known as a 'light switch' complex because its luminescence in solution is significantly enhanced in the presence of DNA. This property is poised to serve in diagnostic and therapeutic applications, but its binding mode with DNA needs to be elucidated further. Here, we describe the crystal structures of the Λ enantiomer bound to two oligonucleotide duplexes. The dppz ligand intercalates symmetrically and perpendicularly from the minor groove of the d(CCGGTACCGG)(2) duplex at the central TA/TA step, but not at the central AT/AT step of d(CCGGATCCGG)(2). In both structures, however, a second ruthenium complex links the duplexes through the combination of a shallower angled intercalation into the C(1)C(2)/G(9)G(10) step at the end of the duplex, and semi-intercalation into the G(3)G(4) step of an adjacent duplex. The TA/TA specificity of the perpendicular intercalation arises from the packing of phenanthroline ligands against the adenosine residue.

Crystal structures of Λ-[Ru(phen)2dppz]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes