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 two orientational isomers of the platinated DNA containing a site-specific intrastrand d(GpG) cross-link. The DNA strand containing the 3' orientational isomer was annealed to its complement, and the resulting duplex was investigated by NMR spectroscopy. The structure was determined 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 bent toward the major groove. Refinements of the structure with either conventional interproton restraints or a combination of the electron-proton 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 duplex 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 Angstrom) to the tertiary structure of a cisplatin-modified dodecamer duplex solved by X-ray crystallography (J. Am. Chem. Soc. 1996, 118, 12309-21321). The described approach, combining long-range electron-proton and short-range interproton distance restraints in DNA structure refinement, has improved our understanding of the delocalized nature of platinum-induced distortions in duplex DNA and may facilitate high-resolution structural studies of other distorted oligonucleotide duplexes.