5lig: Difference between revisions

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'''Unreleased structure'''


The entry 5lig is ON HOLD
==G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2==
<StructureSection load='5lig' size='340' side='right'caption='[[5lig]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5lig]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LIG 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=6XM:8,12-BIS(2-MORPHOLINOETHYL)-8H-BENZO[IJ]XANTHENO[1,9,8-CDEF][2,7]NAPHTHYRIDIN-12-IUMHEXAFLUOROPHOSPHATE'>6XM</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=5lig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lig OCA], [https://pdbe.org/5lig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lig RCSB], [https://www.ebi.ac.uk/pdbsum/5lig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lig ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through pi-pi stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.


Authors: Kotar, A., Wang, B., Shivalingam, A., Gonzalez-Garcia, J., Vilar, R., Plavec, J.
NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.,Kotar A, Wang B, Shivalingam A, Gonzalez-Garcia J, Vilar R, Plavec J Angew Chem Int Ed Engl. 2016 Aug 31. doi: 10.1002/anie.201606877. PMID:27577037<ref>PMID:27577037</ref>


Description: G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Shivalingam, A]]
<div class="pdbe-citations 5lig" style="background-color:#fffaf0;"></div>
[[Category: Gonzalez-Garcia, J]]
== References ==
[[Category: Vilar, R]]
<references/>
[[Category: Wang, B]]
__TOC__
[[Category: Plavec, J]]
</StructureSection>
[[Category: Kotar, A]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Gonzalez-Garcia J]]
[[Category: Kotar A]]
[[Category: Plavec J]]
[[Category: Shivalingam A]]
[[Category: Vilar R]]
[[Category: Wang B]]
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