1k8l

<StructureSection load='1k8l' size='340' side='right'caption='[[1k8l]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>

</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2S:CYTIDINE-5-DITHIOPHOSPHORATE'>C2S</scene>, <scene name='pdbligand=G2S:GUANOSINE-5-DITHIOPHOSPHORATE'>G2S</scene>, <scene name='pdbligand=T2S:THYMIDINE-5-DITHIOPHOSPHORATE'>T2S</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1k8j|1k8j]], [[1k8n|1k8n]]</div></td></tr>

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== 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.

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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<div class="pdbe-citations 1k8l" style="background-color:#fffaf0;"></div>

== References ==

<references/>

[[Category: Bassett, S E]]

[[Category: Fennewald, S M]]

[[Category: Gorenstein, D G]]

[[Category: Herzog, N]]

[[Category: King, D J]]

[[Category: Luxon, B A]]

[[Category: Venkitachalam, S]]

[[Category: Volk, D E]]

[[Category: Yang, X]]

[[Category: Xby6]]