7w9n: Difference between revisions

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== Structural highlights ==

<table><tr><td colspan='2'>Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W9N FirstGlance]. <br>

<table><tr><td colspan='2'>[[7w9n]] 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=7W9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W9N FirstGlance]. <br>

</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=7w9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w9n OCA], [https://pdbe.org/7w9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w9n RCSB], [https://www.ebi.ac.uk/pdbsum/7w9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w9n ProSAT]</span></td></tr>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=97U:(2~{S})-2-[[(3~{R})-5-chloranyl-3-methyl-8-oxidanyl-1-oxidanylidene-3,4-dihydroisochromen-7-yl]carbonylamino]-3-phenyl-propanoic+acid'>97U</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=7w9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w9n OCA], [https://pdbe.org/7w9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w9n RCSB], [https://www.ebi.ac.uk/pdbsum/7w9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w9n ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg(2+) and Na(+) ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through pi-pi stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.

Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer.,Xu G, Zhao J, Yu H, Wang C, Huang Y, Zhao Q, Zhou X, Li C, Liu M J Am Chem Soc. 2022 May 4;144(17):7731-7740. doi: 10.1021/jacs.2c00478. Epub 2022 , Apr 20. PMID:35442665<ref>PMID:35442665</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Synthetic construct]]

[[Category: Li CG]]

[[Category: Xu GH]]

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@@ Line 3: / Line 3: @@
 <StructureSection load='7w9n' size='340' side='right'caption='[[7w9n]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W9N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7w9n]] 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=7W9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W9N FirstGlance]. <br>
-</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=7w9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w9n OCA], [https://pdbe.org/7w9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w9n RCSB], [https://www.ebi.ac.uk/pdbsum/7w9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w9n ProSAT]</span></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=97U:(2~{S})-2-[[(3~{R})-5-chloranyl-3-methyl-8-oxidanyl-1-oxidanylidene-3,4-dihydroisochromen-7-yl]carbonylamino]-3-phenyl-propanoic+acid'>97U</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=7w9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w9n OCA], [https://pdbe.org/7w9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w9n RCSB], [https://www.ebi.ac.uk/pdbsum/7w9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w9n ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A (OTA) and B (OTB), showing prominent recognition specificity and affinity among hundreds of aptamers for small molecules. Why OBA36 has &gt;100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg(2+) and Na(+) ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through pi-pi stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications.
+Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer.,Xu G, Zhao J, Yu H, Wang C, Huang Y, Zhao Q, Zhou X, Li C, Liu M J Am Chem Soc. 2022 May 4;144(17):7731-7740. doi: 10.1021/jacs.2c00478. Epub 2022 , Apr 20. PMID:35442665<ref>PMID:35442665</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7w9n" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
+[[Category: Synthetic construct]]
 [[Category: Li CG]]
 [[Category: Xu GH]]