SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A NITROXIDE SPIN-LABELED PLATINUM D(GPG) INTRASTRAND CROSS-LINK REFINED WITH NMR-DERIVED LONG-RANGE ELECTRON-PROTON DISTANCE RESTRAINTS

Modification of an undecamer deoxyribonucleotide, d(CTCTCGGTCTC), with the paramagnetic cisplatin analogue cis-[Pt(NH3)(4AT)ClI] afforded tw o orientational isomers of the platinated DNA containing a site-specif ic intrastrand d(GpG) cross-link. The DNA strand containing the 3' ori entational isomer was annealed to its complement, and the resulting du plex was investigated by NMR spectroscopy. The structure was determine d from conventional NOE studies of the reduced, diamagnetic undecamer and 99 long-range (10-20 Angstrom) electron-proton restraints from the paramagnetic duplex. The platinum-modified duplex is substantially be nt toward the major groove. Refinements of the structure with either c onventional interproton restraints or a combination of the electron-pr oton and interproton restraints afforded the same local but different global structures. Both refinements resulted in duplexes that deviated from canonical B-form DNA with widened minor grooves. Addition of the long-range electron-proton restraints allowed for refinement of a dup lex structure in excellent agreement with the diamagnetic NMR data (R- factor = 6.08) but exhibiting different positioning of the duplex ends . In particular, the long-range distance restraints afforded a refined duplex with marked similarity (RMSD for all backbone atoms = 1.98 Ang strom) to the tertiary structure of a cisplatin-modified dodecamer dup lex solved by X-ray crystallography (J. Am. Chem. Soc. 1996, 118, 1230 9-21321). The described approach, combining long-range electron-proton and short-range interproton distance restraints in DNA structure refi nement, has improved our understanding of the delocalized nature of pl atinum-induced distortions in duplex DNA and may facilitate high-resol ution structural studies of other distorted oligonucleotide duplexes.