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[[Image:1k8n.png|left|200px]]
==NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24==
<StructureSection load='1k8n' size='340' side='right' caption='[[1k8n]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1k8n]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K8N FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2S:CYTIDINE-5-DITHIOPHOSPHORATE'>C2S</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k8j|1k8j]], [[1k8l|1k8l]]</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k8n RCSB], [http://www.ebi.ac.uk/pdbsum/1k8n PDBsum]</span></td></tr>
<table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.


{{STRUCTURE_1k8n|  PDB=1k8n  |  SCENE=  }}
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB.,Volk DE, Yang X, Fennewald SM, King DJ, Bassett SE, Venkitachalam S, Herzog N, Luxon BA, Gorenstein DG Bioorg Chem. 2002 Dec;30(6):396-419. PMID:12642125<ref>PMID:12642125</ref>


===NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_12642125}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[1k8n]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8N OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:012642125</ref><references group="xtra"/>
[[Category: Bassett, S E.]]
[[Category: Bassett, S E.]]
[[Category: Fennewald, S M.]]
[[Category: Fennewald, S M.]]
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