5lig: Difference between revisions
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==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]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5lig]] is a 1 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LIG FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5lig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lig OCA], [http://pdbe.org/5lig PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lig RCSB], [http://www.ebi.ac.uk/pdbsum/5lig PDBsum], [http://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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5lig" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Gonzalez-Garcia, J]] | |||
[[Category: Kotar, A]] | |||
[[Category: Plavec, J]] | |||
[[Category: Shivalingam, A]] | [[Category: Shivalingam, A]] | ||
[[Category: Vilar, R]] | [[Category: Vilar, R]] | ||
[[Category: Wang, B]] | [[Category: Wang, B]] | ||
[[Category: | [[Category: C-myc promoter]] | ||
[[Category: | [[Category: Daota-m2]] | ||
[[Category: Dna]] | |||
[[Category: G-quadruplex]] | |||
[[Category: Ligand]] | |||
