7zyx: Difference between revisions

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'''Unreleased structure'''


The entry 7zyx is ON HOLD  until Paper Publication
==Dimeric i-motif from 2'Farabinocytidine-modified TC5==
<StructureSection load='7zyx' size='340' side='right'caption='[[7zyx]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7zyx]] is a 2 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=7ZYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZYX FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</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=7zyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zyx OCA], [https://pdbe.org/7zyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zyx RCSB], [https://www.ebi.ac.uk/pdbsum/7zyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zyx ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC(5) normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC(5) to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.


Authors: Garavis, M., El Khoury, R., Damha, M.J., Gonzalez, C.
i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F...H and O...H hydrogen bonds.,El-Khoury R, Macaluso V, Hennecker C, Mittermaier AK, Orozco M, Gonzalez C, Garavis M, Damha MJ Commun Chem. 2023 Feb 16;6(1):31. doi: 10.1038/s42004-023-00831-7. PMID:36797370<ref>PMID:36797370</ref>


Description: Dimeric i-motif from 2''Farabinocytidine-modified TC5
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: El Khoury, R]]
<div class="pdbe-citations 7zyx" style="background-color:#fffaf0;"></div>
[[Category: Garavis, M]]
== References ==
[[Category: Damha, M.J]]
<references/>
[[Category: Gonzalez, C]]
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Damha MJ]]
[[Category: El Khoury R]]
[[Category: Garavis M]]
[[Category: Gonzalez C]]
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