8rw2: Difference between revisions
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New page: '''Unreleased structure''' The entry 8rw2 is ON HOLD Authors: Vianney, Y.M., Weisz, K. Description: Structure of a chair-type antiparallel quadruplex-duplex hybrid at pH 6 [[Category: ... |
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==Structure of a chair-type antiparallel quadruplex-duplex hybrid at pH 6== | |||
<StructureSection load='8rw2' size='340' side='right'caption='[[8rw2]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8rw2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RW2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8RW2 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=A1H3G:2-DEOXYADENOSINE-5-MONOPHOSPHATE+(protonated+at+N1)'>A1H3G</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=8rw2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rw2 OCA], [https://pdbe.org/8rw2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8rw2 RCSB], [https://www.ebi.ac.uk/pdbsum/8rw2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8rw2 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs. NMR-derived high-resolution structures reveal that an adenine protonation is prerequisite for the formation of a non-canonical base quartet, capping the outer G-tetrad at the quadruplex-duplex interface and stabilizing the antiparallel chair conformation in an acidic environment. Being directly associated with interactions at the quadruplex-duplex interface, this unique pH-dependent topological transition is fully reversible. Coupled with a conformation-sensitive optical readout demonstrated as a proof of concept using the fluorescent dye thiazole orange, the present quadruplex-duplex hybrid architecture represents a potentially valuable pH-sensing system responsive in a physiological pH range of 7+/-1. | |||
A pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid.,Vianney YM, Jana J, Weisz K Chemistry. 2024 May 23;30(29):e202400722. doi: 10.1002/chem.202400722. Epub 2024 , Apr 9. PMID:38497675<ref>PMID:38497675</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Vianney | <div class="pdbe-citations 8rw2" style="background-color:#fffaf0;"></div> | ||
[[Category: Weisz | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Vianney YM]] | |||
[[Category: Weisz K]] | |||
Latest revision as of 05:59, 5 June 2024
Structure of a chair-type antiparallel quadruplex-duplex hybrid at pH 6
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