1VRO

Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure

Replaces:  1N6S

Summary for 1VRO

• Entry DOI: 10.2210/pdb1vro/pdb
• Descriptor: 5'-D(*CP*(GMS)P*CP*GP*CP*G)-3', SPERMINE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: left-handed z-dna, phosphoroselenoate, multiwavelength anomalous dispersion (mad), covalent modification of oligonucleotides, oligonucleotide analogue, phasing strategy, synchrotron, dna
• Total number of polymer chains: 2
• Total formula weight: 3972.98

Authors

Wilds, C.J.,Pattanayek, R.,Pan, C.,Wawrzak, Z.,Egli, M. (deposition date: 2005-04-14, release date: 2005-04-19, Last modification date: 2023-12-27)

Primary citation

Wilds, C.J.,Pattanayek, R.,Pan, C.,Wawrzak, Z.,Egli, M.
Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure
J.Am.Chem.Soc., 124:14910-14916, 2002

PubMed Abstract: 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.

PubMed: 12475332
DOI: 10.1021/ja021058b

Experimental method

X-RAY DIFFRACTION (1.1 Å)