View source for 8rw2


==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>
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== 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 8rw2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Vianney YM]]
[[Category: Weisz K]]