1vro
From Proteopedia
(New page: 200px<br /><applet load="1vro" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vro, resolution 1.10Å" /> '''Selenium-Assisted Nu...) |
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| - | [[Image:1vro.gif|left|200px]]<br /><applet load="1vro" size=" | + | [[Image:1vro.gif|left|200px]]<br /><applet load="1vro" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1vro, resolution 1.10Å" /> | caption="1vro, resolution 1.10Å" /> | ||
'''Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure'''<br /> | '''Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The combination of synchrotron radiation and a variety of atoms or ions | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1VRO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with SPM and MG as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 1VRO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SPM:'>SPM</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1N6S. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VRO OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Pattanayek, R.]] | [[Category: Pattanayek, R.]] | ||
[[Category: Wawrzak, Z.]] | [[Category: Wawrzak, Z.]] | ||
| - | [[Category: Wilds, C | + | [[Category: Wilds, C J.]] |
[[Category: MG]] | [[Category: MG]] | ||
[[Category: SPM]] | [[Category: SPM]] | ||
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[[Category: synchrotron]] | [[Category: synchrotron]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:37:57 2008'' |
Revision as of 13:38, 21 February 2008
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Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure
Overview
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.
About this Structure
1VRO is a Protein complex structure of sequences from [1] with and as ligands. This structure supersedes the now removed PDB entry 1N6S. Full crystallographic information is available from OCA.
Reference
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
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