SOLUTION STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE DUPLEX CONTAINING THE EXOCYCLIC LESION 3,N-4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE 2'-DEOXYADENOSINE, DETERMINED BY NMR-SPECTROSCOPY AND RESTRAINED MOLECULAR-DYNAMICS

The d(C-G-T-A-C-epsilon C-C-A-T-G-C). d(G-C-A-T-G-A-G-T-A-C-G) oligode oxynucleotide duplex containing the 3,N-4-etheno-2'-deoxycytidine addu ct positioned opposite 2'-deoxyadenosine in the center of the helix ha s been analyzed by proton NMR spectroscopy and restrained molecular dy namics, The spectroscopic data establish a right-handed duplex, with s ugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti conformation around the glycosidic torsion angle and, with the excepti on of epsilon C . dA, Watson-Crick hydrogen bond alignment for all bas e pairs. Molecular dynamics simulations, restrained by the full relaxa tion matrix approach, produced a three-dimensional model with an NMR R -factor of 7%. The duplex structure shows no significant perturbation of the sugar-phosphate backbone, which remains in B-form. The exocycli c adduct and its partner dA are incorporated into the helix without pr oducing a noticeable kink. The epsilon C . dA alignment adopts a stagg ered conformation with each residue displaced toward the 5'-terminus a nd intercalated between bases on the opposite strand, without increase of inter-phosphate distances. The partial intercalation of the epsilo n C(anti). dA(anti) alignment allows stacking between the aromatic rin gs of epsilon C and dA and with base pairs adjacent to the lesion, sug gesting an important role played by hydrophobic forces in the stabiliz ation of the solution structure.