1k8n: Difference between revisions

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{{Seed}}
[[Image:1k8n.png|left|200px]]


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==NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24==
The line below this paragraph, containing "STRUCTURE_1k8n", creates the "Structure Box" on the page.
<StructureSection load='1k8n' size='340' side='right'caption='[[1k8n]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
{{STRUCTURE_1k8n|  PDB=1k8n  |  SCENE=  }}
<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.


===NMR STRUCTURE OF THE XBY2 DNA DUPLEX, AN ANALOG OF CK14 CONTAINING PHOSPHORODITHIOATE GROUPS AT C22 AND C24===
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>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_12642125}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1k8n" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 12642125 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_12642125}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K8N OCA].
[[Category: Bassett SE]]
 
[[Category: Fennewald SM]]
==Reference==
[[Category: Gorenstein DG]]
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://www.ncbi.nlm.nih.gov/pubmed/12642125 12642125]
[[Category: Herzog N]]
[[Category: Bassett, S E.]]
[[Category: King DJ]]
[[Category: Fennewald, S M.]]
[[Category: Luxon BA]]
[[Category: Gorenstein, D G.]]
[[Category: Venkitachalam S]]
[[Category: Herzog, N.]]
[[Category: Volk DE]]
[[Category: King, D J.]]
[[Category: Yang X]]
[[Category: Luxon, B A.]]
[[Category: Venkitachalam, S.]]
[[Category: Volk, D E.]]
[[Category: Yang, X.]]
[[Category: Ck1]]
[[Category: Ck14]]
[[Category: Nf-kb]]
[[Category: Phosphorodithioate]]
[[Category: Thiophosphate]]
[[Category: Xby2]]
[[Category: Xby6]]
 
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