Solution Structure of a Metallointercalator Bound Site Specifically to DNA

The solution structure of the complex of the metallointercalator Δ-α-[Rh[( R,R )-Me 2 trien]phi] 3+ (( R,R )-Me 2 trien = 2 R,9 R -diamino-4,7-diazadecane; phi = 9,10-phenanthrenequinone diimine) bound to d(GAGTGCACTC) 2 at 4 °C has been determined using 1 H NMR spectroscopy coupled with restrained molecular dynamics calculations. Δ-α-[Rh[( R,R )-Me 2 trien]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 D 2 O and H 2 O 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 Å. 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 Me 2 trien ligand in the major groove. C 2 symmetry is maintained with no kinking or bending of the DNA double helix. The binding site is deformed from canonical B-DNA and appears to be pulled slightly out of the major groove into a conformation which maximizes favorable interactions with the complex. The axial amines of the metallointercalator are positioned to hydrogen bond to the N7 and O6 of the G 5 (G 15 ) bases. Van der Waals contacts between the axial methyl groups of Δ-α-[Rh[( R,R )-Me 2 trien]phi] 3+ and the methyl groups of T 4 (T 14 ) are apparent, with conformational changes in the binding site creating a binding pocket across the major groove face of the T 4 nucleotide. The intercalated 5‘-GC-3‘ step experiences a positive slide and significant overwinding (helical twist = 53°) which allows the guanine bases to stack exclusively on the phi ligand. The site selectivity and small size of this DNA-binding molecule also permit an examination of how intercalation is propagated through the DNA helix. While the intercalated step is overwound, adjacent steps are unwound, with maximal unwinding (helical twist = 22°) occurring at the 5‘-G 3 T 4 -3‘ and 5‘-A 7 C 8 -3‘ steps which define both the edge of the 5‘-TGCA-3‘ binding site and the edge of the conformational changes associated with binding. The flanking trimers are relatively unperturbed from canonical B-DNA, with the duplex experiencing a net unwinding of 39 ± 4°.