View source for 214d


==THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT==
<StructureSection load='214d' size='340' side='right'caption='[[214d]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[214d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=214D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=214D FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=T41:1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE+5-MONOPHOSPHATE'>T41</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=214d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=214d OCA], [https://pdbe.org/214d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=214d RCSB], [https://www.ebi.ac.uk/pdbsum/214d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=214d ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
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.

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<ref>PMID:8950487</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 214d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Gotfredsen CH]]
[[Category: Jacobsen JP]]
[[Category: Spielmann HP]]
[[Category: Wengel J]]