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 s equence 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 dist ances, along with torsion angles for sugar rings and additional data derive d from canonical A-and B-DNA, have been used for structure refinement by re strained molecular dynamics (rMD). Six rMD simulations have been carried ou t starting from both regular A-and B-DNA forms. The pairwise rms deviations calculated for each refined structure are < 1 Angstrom, indicating converg ence to essentially the same geometry. The accuracy of the rMD structures h as been assessed by complete relaxation matrix backcalculation. The average sixth-root residual index (R-x = 0.052 +/- 0.003) indicated that a good fi t between experimental and calculated NOESY spectra has been achieved. Deta iled analysis revealed a right-handed DNA conformation for the duplex in wh ich both the T17 nucleotide opposite the abasic site and the lactone ring a re 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 oligonu cleotide with the identical sequence containing the stable tetrahydrofuran abasic site analogue that we reported previously.