Wittberger D, Berens C, Hammann C, Westhof E, Schroeder R
Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs Article de journal
Dans: J Mol Biol, vol. 300, no. 2, p. 339-352, 2000, ISBN: 10873469, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Pairing Base Sequence Ethylnitrosourea/metabolism Hepatitis Delta Virus/genetics Hydrogen Peroxide/metabolism Introns/genetics Ions/metabolism Iron/metabolism Lead/metabolism Magnesium Chloride/pharmacology Models, Asp/chemistry/genetics/metabolism RNA, Catalytic/chemistry/genetics/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation *Photolysis/drug effects Pliability RNA/*chemistry/genetics/*metabolism RNA, Non-U.S. Gov't Tetrahymena/genetics Uranyl Nitrate/*metabolism Yeasts/genetics, Phe/chemistry/genetics/metabolism RNA, Protozoan/chemistry/genetics/metabolism RNA, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Solvents Support
@article{,
title = {Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs},
author = {D Wittberger and C Berens and C Hammann and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10873469},
isbn = {10873469},
year = {2000},
date = {2000-01-01},
journal = {J Mol Biol},
volume = {300},
number = {2},
pages = {339-352},
abstract = {In order to evaluate uranyl photocleavage as a tool to identify and characterize structural and dynamic properties in RNA, we compared uranyl cleavage sites in five RNA molecules with known X-ray structures, namely the hammerhead and hepatitis delta virus ribozymes, the P4-P6 domain of the Tetrahymena group I intron, as well as tRNA(Phe) and tRNA(Asp) from yeast. Uranyl photocleavage was observed at specific positions in all molecules investigated. In order to characterize the sites, photocleavage was performed in the absence and in increasing amounts of MgCl(2). Uranyl photocleavage correlates well with sites of low calculated accessibility, suggesting that uranyl ions bind in tight RNA pockets formed by close approach of phosphate groups. RNA foldings require ion binding, usually magnesium ions. Thus, upon the adoption of the native structure, uranyl ions can no longer bind well except in flexible and open to the solvent regions that can undergo induced-fit without disrupting the native fold. Uranyl photocleavage was compared to N-ethyl-N-nitrosourea and lead-induced cleavages in the context of the three-dimensional X-ray structures. Overall, the regions protected from ENU attack are sites of uranyl cleavage, indicating sites of low accessibility which can form ion binding sites. On the contrary, lead cleavages occur at flexible and accessible sites and correlate with the unspecific cleavages prevalent in dynamic and open regions. Applied in a magnesium-dependent manner, and only in combination with other backbone probing agents such as N-ethyl-N-nitrosourea, lead and Fenton cleavage, uranyl probing has the potential to reveal high-affinity metal ion environments, as well as regions involved in conformational transitions.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Pairing Base Sequence Ethylnitrosourea/metabolism Hepatitis Delta Virus/genetics Hydrogen Peroxide/metabolism Introns/genetics Ions/metabolism Iron/metabolism Lead/metabolism Magnesium Chloride/pharmacology Models, Asp/chemistry/genetics/metabolism RNA, Catalytic/chemistry/genetics/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation *Photolysis/drug effects Pliability RNA/*chemistry/genetics/*metabolism RNA, Non-U.S. Gov't Tetrahymena/genetics Uranyl Nitrate/*metabolism Yeasts/genetics, Phe/chemistry/genetics/metabolism RNA, Protozoan/chemistry/genetics/metabolism RNA, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Solvents Support},
pubstate = {published},
tppubtype = {article}
}