1H NMR studies of tris(phenanthroline) metal complexes bound to oligonucleotides: characterization of binding modes.

The binding of Ru(phen)3(2+), Rh(phen)3(3+), and Co(phen)3(3+) to the oligonucleotides d(GTGCAC)2 and 5'-pd(CGCGCG)2 has been examined by 1H NMR spectroscopy as a function of temperature, concentration, and chirality of the metal complex. The duplex oligonucleotides act as chiral shift reagents for the metal complexes; phenanthroline protons associated with each enantiomer are resolved upon binding to the oligomer. The spectral titrations, consistent with photophysical studies, indicate that the complexes bind to the oligomer through two modes: one assigned as intercalation favoring the delta-isomer, and the other assigned as the surface-bound interaction favoring the lambda-isomer. The ligand protons are perturbed in a manner that implies sensitivity of particular protons to binding mode; specifically, the H4,7 protons appear to be altered most for the lambda-enantiomer while the H5,6 protons are perturbed more for the delta-enantiomer. The NMR chemical shift variations appear particularly sensitive to this surface-bound interaction, which, on the basis of a comparison of binding and photophysical parameters for Ru(phen)3(2+), appears more prominant in binding to oligonucleotides than that to polynucleotides. With respect to oligonucleotide proton shifts, the adenine H2 proton, positioned in the minor groove of the helix, shows the largest upfield shifts with metal binding, and more dramatically with lambda-isomers. The major groove thymine methyl protons (TMe) shift downfield to a lesser extent, and more so for delta-isomers. The different binding modes also differ with respect to their dynamics of association; the longitudinal relaxation rates of delta- and lambda-4,7 phenanthroline protons of Rh(phen)3(3+) are 0.88 and 1.14 s, respectively, in the presence of d(GTGCAC)2.(ABSTRACT TRUNCATED AT 250 WORDS)