Abstract
The solution structure of the complex of the metallointercalator Δ-α-[Rh[(R,R)-Me2trien]phi]3+ ((R,R)-Me2trien = 2R,9R-diamino-4,7-diazadecane; phi = 9,10-phenanthrenequinone diimine) bound to d(GAGTGCACTC)2 at 4 °C has been determined using 1H NMR spectroscopy coupled with restrained molecular dynamics calculations. Δ-α-[Rh[(R,R)-Me2trien]phi]3+ binds specifically to its designed site, 5‘-TGCA−3‘, with slow exchange kinetics. Using interproton distance restraints (including 70 intermolecular restraints) derived from NOESY spectra in both D2O and H2O and torsional restraints derived from ECOSY data, 20 disparate starting structures converged to a set of final structures with an average RMSD (between structures) of 1.0 A. As shown previously, binding occurs by deep intercalation of the phi ligand at the central 5‘-GC-3‘ step of the decamer, positioning the ancillary Me2trien ligand in the major groove. C2 symmetry is maintained with no kinking or bending of the DNA double helix. The binding site is deforme...
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