214d
From Proteopedia
OCA (Talk | contribs)
(New page: 200px<br /><applet load="214d" size="350" color="white" frame="true" align="right" spinBox="true" caption="214d" /> '''THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTA...)
Next diff →
Revision as of 15:47, 29 January 2008
|
THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT
Overview
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.
About this Structure
214D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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., Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP, Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:8950487
Page seeded by OCA on Tue Jan 29 17:47:21 2008
