[Ru(bpy)_2(L)]Cl_2: Luminescent Metal Complexes That Bind DNA Base Mismatches

Abstract

Here we report the synthesis of luminescent ruthenium complexes that bind DNA base pair mismatches. [Ru(bpy)_2(tpqp)]Cl_2 (tpqp = 7,8,13,14-tetrahydro-6-phenylquino[8,7-k][1,8]phenanthroline), [Ru(bpy)_2(pqp)]Cl_2 (pqp = 6-phenylquino[8,7-k][1,8]phenanthroline), and [Ru(bpy)_2(tactp)]Cl_2 [tactp = 4,5,9,18-tetraazachryseno[9,10-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, K_b = 4 × 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 × 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 × 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.