214D

THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT

Summary for 214D

• Entry DOI: 10.2210/pdb214d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*GP*CP*C)-3'), DNA (5'-D(*GP*GP*CP*TP*AP*(T41)P*AP*TP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: dna, double helix
• Total number of polymer chains: 2
• Total formula weight: 6737.43

Authors

Gotfredsen, C.H.,Spielmann, H.P.,Wengel, J.,Jacobsen, J.P. (deposition date: 1995-07-07, release date: 1995-10-15, Last modification date: 2024-05-22)

Primary citation

Gotfredsen, C.H.,Spielmann, H.P.,Wengel, J.,Jacobsen, J.P.
Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.
Bioconjug.Chem., 7:680-688, 1996

PubMed Abstract: 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-beta-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 A. 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.

PubMed: 8950487
DOI: 10.1021/bc960061f

Experimental method

SOLUTION NMR