Structure of a DNA duplex containing a single 2′-O-methyl-β-D-araT: Combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement

Two-dimensional ¹H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5′-CGCATATAGCC-3′): d(5′-GGCTAXATGCG-3′), where X is 1-(2-O-methyl-β-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 Å. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2′-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH₃O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position.