2′-deoxyribonolactone lesion in DNA:: Refined solution structure determined by nuclear magnetic resonance and molecular modeling

The solution conformation of the DNA duplex d(C(1)G(2)C(3)A(4)C(5)L(6)C(7)A(8)C(8)G(10)C(11)).d(G(12)C(13)G(14)T(15)G(16)T(17)G(18)T(19)G(20)C(21)G(22)) containing the 2'-deoxyribonolactone lesion (L-6) in the middle of the sequence has been investigated by NMR spectroscopy and restrained molecular dynamics calculations. Interproton distances have been obtained by complete relaxation matrix analysis of the NOESY cross-peak intensities. These distances, along with torsion angles for sugar rings and additional data derived from canonical A-and B-DNA, have been used for structure refinement by restrained molecular dynamics (rMD). Six rMD simulations have been carried out starting from both regular A-and B-DNA forms. The pairwise rms deviations calculated for each refined structure are < 1 Angstrom, indicating convergence to essentially the same geometry. The accuracy of the rMD structures has been assessed by complete relaxation matrix backcalculation. The average sixth-root residual index (R-x = 0.052 +/- 0.003) indicated that a good fit between experimental and calculated NOESY spectra has been achieved. Detailed analysis revealed a right-handed DNA conformation for the duplex in which both the T17 nucleotide opposite the abasic site and the lactone ring are located inside the helix. No kinking is observed for this molecule, even at the abasic site step. This structure is compared to that of the oligonucleotide with the identical sequence containing the stable tetrahydrofuran abasic site analogue that we reported previously.