Minor groove intercalation of Δ-[Ru(Me2phen)2dppz]2+ to the hexanucleotide d(GTCGAC)2

The metal complex Δ-[Ru(Me₂phen)₂dppz]²⁺ (Me₂phen = 2,9-dimethyl-1,10-phenanthroline; dppz = dipyrido[3,2-a:2′,3′-c]phenazine) has been synthesised and its binding to the hexanucleotide d(GTCGAC)₂ studied by ¹H NMR spectroscopy. The crystal structure of rac-[Ru(Me₂phen)₂dppz](PF₆)₂·2H₂O has been determined. Addition of Δ-[Ru(Me₂phen)₂dppz]²⁺ to d(GTCGAC)₂ induced significant broadening of the Me₂phen and dppz resonances and large upfield shifts of the dppz resonances, consistent with the metal complex binding through intercalation of the dppz ligand. Also indicative of intercalation are the observed upfield shifts of the T₂ and G₄ imino protons and the 17 °C increase in the melting temperature of the hexanucleotide upon addition of the metal complex. NOE cross-peaks from the Me₂phen protons were only observed to hexanucleotide minor groove H1′ and H4′/H5′/H5″ protons in NOESY spectra of the hexanucleotide with added metal complex. In addition, NOEs were also observed between the H13/14 protons of the dppz ligand and the hexanucleotide major groove T₂methyl and sugar H2′/H2″ protons. From the combined NMR data it is concluded that the dppz-based ruthenium(II) complex Δ-[Ru(Me₂phen)₂dppz]²⁺ intercalates from the minor groove of the hexanucleotide mini-duplex d(GTCGAC)₂