6qjs: Difference between revisions
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The | ==Crystal structure of a DNA dodecamer containing a tetramethylpiperidinoxyl (nitroxide) spin label== | ||
<StructureSection load='6qjs' size='340' side='right'caption='[[6qjs]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6qjs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QJS FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S6M:[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-[1-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)-1,2,3-triazol-4-yl]oxolan-2-yl]methyl+dihydrogen+phosphate'>S6M</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=6qjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qjs OCA], [https://pdbe.org/6qjs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qjs RCSB], [https://www.ebi.ac.uk/pdbsum/6qjs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qjs ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2' position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2'-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation. | |||
2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.,Hardwick JS, Haugland MM, El-Sagheer AH, Ptchelkine D, Beierlein FR, Lane AN, Brown T, Lovett JE, Anderson EA Nucleic Acids Res. 2020 Apr 6;48(6):2830-2840. doi: 10.1093/nar/gkaa086. PMID:32052020<ref>PMID:32052020</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Anderson | <div class="pdbe-citations 6qjs" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Hardwick | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Ptchelkine | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Anderson EE]] | |||
[[Category: Brown T]] | |||
[[Category: Hardwick JS]] | |||
[[Category: Haugland MM]] | |||
[[Category: Ptchelkine D]] | |||
Latest revision as of 15:02, 24 January 2024
Crystal structure of a DNA dodecamer containing a tetramethylpiperidinoxyl (nitroxide) spin labelCrystal structure of a DNA dodecamer containing a tetramethylpiperidinoxyl (nitroxide) spin label
Structural highlights
Publication Abstract from PubMedThe determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of such distances for a conformational ensemble remains a significant challenge. Using several techniques, we show that electron paramagnetic resonance (EPR) spectroscopy of oligonucleotides spin-labelled with triazole-appended nitroxides at the 2' position offers a robust and minimally perturbing tool for obtaining such measurements. For two nitroxides, we present results from EPR spectroscopy, X-ray crystal structures of B-form spin-labelled DNA duplexes, molecular dynamics simulations and nuclear magnetic resonance spectroscopy. These four methods are mutually supportive, and pinpoint the locations of the spin labels on the duplexes. In doing so, this work establishes 2'-alkynyl nitroxide spin-labelling as a minimally perturbing method for probing DNA conformation. 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.,Hardwick JS, Haugland MM, El-Sagheer AH, Ptchelkine D, Beierlein FR, Lane AN, Brown T, Lovett JE, Anderson EA Nucleic Acids Res. 2020 Apr 6;48(6):2830-2840. doi: 10.1093/nar/gkaa086. PMID:32052020[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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