Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N⁴-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics

The d(C-G-T-A-C-εC-C-A-T-G-C)-d(G-C-A-T-G-A-G-T-A-C-G) oligodeoxynucleotide duplex containing the 3,N⁴-etheno-2'-deoxycytidine adduct positioned opposite 2'-deoxyadenosine in the center of the helix has been analyzed by proton NMR spectroscopy and restrained molecular dynamics. The spectroscopic data establish a right-handed duplex, with sugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti conformation around the glycosidic torsion angle and, with the exception of εC-dA. Watson-Crick hydrogen bond alignment for all base pairs. Molecular dynamics simulations, restrained by the full relaxation 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 exocyclic adduct and its partner dA are incorporated into the helix without producing a noticeable kink. The εC-dA alignment adopts a staggered conformation with each residue displaced toward the 5'-terminus and intercalated between bases on the opposite strand, without increase of inter- phosphate distances. The partial intercalation of the εC(anti)-dA(anti) alignment allows stacking between the aromatic rings of εC and dA and with base pairs adjacent to the lesion, suggesting an important role played by hydrophobic forces in the stabilization of the solution structure.