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New page: left|200px<br /><applet load="1k8n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k8n" /> '''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANA...
 
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[[Image:1k8n.gif|left|200px]]<br /><applet load="1k8n" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1k8n" />
'''NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24'''<br />


==Overview==
==NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24==
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.
<StructureSection load='1k8n' size='340' side='right'caption='[[1k8n]]' 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 [https://proteopedia.org/fgij/fg.htm?mol=1K8N 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=C2S:CYTIDINE-5-DITHIOPHOSPHORATE'>C2S</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=1k8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k8n OCA], [https://pdbe.org/1k8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k8n RCSB], [https://www.ebi.ac.uk/pdbsum/1k8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k8n ProSAT]</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.


==About this Structure==
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>
1K8N is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K8N OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12642125 12642125]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1k8n" style="background-color:#fffaf0;"></div>
[[Category: Bassett, S.E.]]
== References ==
[[Category: Fennewald, S.M.]]
<references/>
[[Category: Gorenstein, D.G.]]
__TOC__
[[Category: Herzog, N.]]
</StructureSection>
[[Category: King, D.J.]]
[[Category: Large Structures]]
[[Category: Luxon, B.A.]]
[[Category: Bassett SE]]
[[Category: Venkitachalam, S.]]
[[Category: Fennewald SM]]
[[Category: Volk, D.E.]]
[[Category: Gorenstein DG]]
[[Category: Yang, X.]]
[[Category: Herzog N]]
[[Category: ck1]]
[[Category: King DJ]]
[[Category: ck14]]
[[Category: Luxon BA]]
[[Category: nf-kb]]
[[Category: Venkitachalam S]]
[[Category: phosphorodithioate]]
[[Category: Volk DE]]
[[Category: thiophosphate]]
[[Category: Yang X]]
[[Category: xby2]]
[[Category: xby6]]
 
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