Solution structure of a metallointercalator bound site specifically to DNA

The solution structure of the complex of the metallointercalator Delta-alpha-[Rh[(R,R)-Me(2)trien]phi](3+) ((R,R)Me(2)trien = 2R,9R-diamino-4,7-diazadecane; phi = 9,10-phenanthrenequinone diimine) bound to d(GAGTG-CACTC)(2) at 4 degrees C has been determined using H-1 NMR spectroscopy coupled with restrained molecular dynamics calculations. Delta-alpha-[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 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 Angstrom. 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 Delta-alpha-[Rh[(R,R)-Me2trien] 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 lace of the T-4 nucleotide. The intercalated 5'-GC-3' step experiences a positive slide and significant overwinding (helical twist = 53 degrees) 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 degrees) 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 degrees.