214d: Difference between revisions
From Proteopedia
Jump to navigationJump to search
m Protected "214d" [edit=sysop:move=sysop] |
No edit summary |
||
| Line 1: | Line 1: | ||
[[ | ==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]], [[NMR_Ensembles_of_Models | 40 NMR models]]' 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=214D FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=214d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=214d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=214d RCSB], [http://www.ebi.ac.uk/pdbsum/214d PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
</StructureSection> | |||
[[Category: Gotfredsen, C H.]] | [[Category: Gotfredsen, C H.]] | ||
[[Category: Jacobsen, J P.]] | [[Category: Jacobsen, J P.]] | ||
