Ru(bpy)2(L)]Cl2: luminescent metal complexes that bind DNA base mismatches

Here we report the synthesis of luminescent ruthenium complexes that bind DNA base pair mismatches. Ru(bpy)2(tpqp)]Cl2 (tpqp = 7,8,13,14-tetrahydro-6-phenylquino8,7-k]1,8]phenanthroline), Ru(bpy)2(pqp)]Cl2 (pqp = 6-phenylquino8,7-k]1,8]phenanthroline), and Ru(bpy)2(tactp)]Cl2 tactp = 4,5,9,18-tetraazachryseno9,10-b]triphenylene] have been synthesized, and their spectroscopic properties in the absence and presence of DNA have been examined. While Ru(bpy)2(pqp)]2+ shows no detectable luminescence, Ru(bpy)2(tpqp)]2+ is luminescent in the absence and presence of DNA with an excited-state lifetime of 10 ns and a quantum yield of 0.002. Although no increase in emission intensity is associated with binding to mismatch-containing DNA, luminescence quenching experiments and measurements of steady-state fluorescence polarization provide evidence for preferential binding to oligonucleotides containing a CC mismatch. Furthermore, by marking the site of binding through singlet oxygen sensitized damage, the complex has been shown to target a CC mismatch site directly with a specific binding affinity, Kb = 4 x 10(6) M(-1). Ru(bpy)2(tactp)]2+, an analogue of Ru(bpy)2(dppz)]2+ containing a bulky intercalating ligand, is luminescent in aqueous solution at micromolar concentrations and exhibits a 12-fold enhancement in luminescence in the presence of DNA. The complex, however, tends to aggregate in aqueous solution; we find a dimerization constant of 9.8 x 10(5) M(-1). Again, by singlet oxygen sensitization it is apparent that Ru(bpy)2(tactp)]2+ binds preferentially to a CC mismatch; using a DNase I footprinting assay, a binding constant to a CC mismatch of 8 x 10(5) M(-1) is found. Hence results with these novel luminescent complexes support the concept of using a structurally demanding ligand to obtain selectivity in targeting single base mismatches in DNA. The challenge is coupling the differential binding we can obtain to differential luminescence.