The solution structure of a DNA duplex containing a single 1-(2-O,3-C-ethylene-β-D-arabinofuranosyl)thymidine nucleoside

The structure of a DNA duplex containing one 1-(2-O,3-C-ethylene-beta-D-arabinofuranosyl)-thymidine nucleoside (TS) modification was investigated by use of two-dimensional H-1 NMR spectroscopy at 750 MHz. The structure of the d(CCGCT(5)AGCG):d(CGCTAGCGG) duplex (CT(5)AG) containing one of this 2'-O,3'-C-linked bicycloarabino conformational restricted modification has been determined. We obtained inter-proton distance bounds from NOESY spectra by including a complete relaxation matrix analysis. These distance bounds were used as restraints in molecular dynamics (rMD) calculations. We also analyzed the fine structure of the cross peaks in a selective DQF-COSY spectra to determine the sugar conformations of the nucleotides. Forty final structures were generated for CT(5)AG from A-form and B-form dsDNA starting structures. The root-mean-square deviation (RMSD) of the coordinates for the forty structures of the complex was 0.92 Angstrom. The structures were observed to be markedly irregular compared to canonical B-DNA, especially in terms of large variations in propeller twist anti buckle. Also, lack of stacking of two bases near the modification site is observed. The sugar conformations of all the unmodified nucleotides are close to pure C2'-endo conformation. The structural feature of CT5AG was discussed in relation to the thermal stability and resistance towards exonucleolytic degradation.