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==Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure== | |||
<StructureSection load='1vro' size='340' side='right'caption='[[1vro]], [[Resolution|resolution]] 1.10Å' scene=''> | |||
| | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1vro]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1n6s 1n6s]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VRO 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]] 1.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMS:2-DEOXYGUANOSINE-5-MONOSELENOPHOSPHATE'>GMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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=1vro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vro OCA], [https://pdbe.org/1vro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vro RCSB], [https://www.ebi.ac.uk/pdbsum/1vro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vro ProSAT]</span></td></tr> | |||
</table> | |||
''' | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | |||
== | |||
The combination of synchrotron radiation and a variety of atoms or ions (either covalently attached to the biomolecule prior to crystallization or soaked into crystals) that serve as anomalous scatterers constitutes a powerful tool in the X-ray crystallographer's repertoire of structure determination techniques. Phosphoroselenoates in which one of the nonbridging phosphate oxygens in the backbone is replaced by selenium offer a simplified means for introducing an anomalous scatterer into oligonucleotides by conventional solid-phase synthesis. Unlike other methods that are used to derivatize DNA or RNA by covalent attachment of a heavy atom (i.e., bromine at the C5 position of pyrimidines), tedious synthesis of specialized nucleosides is not required. Introduction of selenium is readily accomplished in solid-phase oligonucleotide synthesis by replacing the standard oxidation agent with a solution of potassium selenocyanide. This results in a diastereomeric mixture of phosphoroselenoates that can be separated by strong anion-exchange HPLC. As a test case, all 10 DNA hexamers of the sequence CGCGCG containing a single phosphoroselenoate linkage (PSe) were prepared. Crystals were grown for a subset of them, and the structure of [d(C(PSe)GCGCG)](2) was determined by the multiwavelength anomalous dispersion technique and refined to 1.1 A resolution. | The combination of synchrotron radiation and a variety of atoms or ions (either covalently attached to the biomolecule prior to crystallization or soaked into crystals) that serve as anomalous scatterers constitutes a powerful tool in the X-ray crystallographer's repertoire of structure determination techniques. Phosphoroselenoates in which one of the nonbridging phosphate oxygens in the backbone is replaced by selenium offer a simplified means for introducing an anomalous scatterer into oligonucleotides by conventional solid-phase synthesis. Unlike other methods that are used to derivatize DNA or RNA by covalent attachment of a heavy atom (i.e., bromine at the C5 position of pyrimidines), tedious synthesis of specialized nucleosides is not required. Introduction of selenium is readily accomplished in solid-phase oligonucleotide synthesis by replacing the standard oxidation agent with a solution of potassium selenocyanide. This results in a diastereomeric mixture of phosphoroselenoates that can be separated by strong anion-exchange HPLC. As a test case, all 10 DNA hexamers of the sequence CGCGCG containing a single phosphoroselenoate linkage (PSe) were prepared. Crystals were grown for a subset of them, and the structure of [d(C(PSe)GCGCG)](2) was determined by the multiwavelength anomalous dispersion technique and refined to 1.1 A resolution. | ||
Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure.,Wilds CJ, Pattanayek R, Pan C, Wawrzak Z, Egli M J Am Chem Soc. 2002 Dec 18;124(50):14910-6. PMID:12475332<ref>PMID:12475332</ref> | |||
Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure., Wilds CJ, Pattanayek R, Pan C, Wawrzak Z, Egli M | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1vro" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Egli M]] | |||
[[Category: Pan C]] | |||
[[Category: Pattanayek R]] | |||
[[Category: Wawrzak Z]] | |||
[[Category: Wilds CJ]] | |||
Latest revision as of 00:05, 28 December 2023
Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure
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