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Titolo:
Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs
Autore:
Wittberger, D; Berens, C; Hammann, C; Westhof, E; Schroeder, R;
Indirizzi:
Univ Vienna, Inst Microbiol & Genet, Vienna Bioctr, A-1030 Vienna, AustriaUniv Vienna Vienna Austria A-1030 Vienna Bioctr, A-1030 Vienna, Austria Univ Dundee, Dept Biochem, CRC, Nucl Acid Struct Res Grp, Dundee DD1 4HN, Scotland Univ Dundee Dundee Scotland DD1 4HN ct Res Grp, Dundee DD1 4HN, Scotland CNRS, Inst Biol Mol & Cellulaire, F-67084 Strasbourg, France CNRS Strasbourg France F-67084 & Cellulaire, F-67084 Strasbourg, France
Titolo Testata:
JOURNAL OF MOLECULAR BIOLOGY
fascicolo: 2, volume: 300, anno: 2000,
pagine: 339 - 352
SICI:
0022-2836(20000707)300:2<339:EOUPAA>2.0.ZU;2-V
Fonte:
ISI
Lingua:
ENG
Soggetto:
HEPATITIS-DELTA-VIRUS; YEAST TRANSFER-RNAPHE; GROUP-I INTRON; HAMMERHEAD RIBOZYME CLEAVAGE; PHENYLALANINE TRANSFER-RNA; DIVALENT METAL-IONS; TERTIARY STRUCTURE; SELF-CLEAVAGE; EFFICIENT CLEAVAGE; CRYSTAL-STRUCTURE;
Keywords:
RNA structure; chemical probing; metal ions; ribozyme; tRNA; hammerhead; HDV; Tetrahymena intron;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
84
Recensione:
Indirizzi per estratti:
Indirizzo: Schroeder, R Univ Vienna, Inst Microbiol & Genet, Vienna Bioctr, Dr Bohrgasse 9, A-1030Vienna, Austria Univ Vienna Dr Bohrgasse 9 Vienna Austria A-1030 na, Austria
Citazione:
D. Wittberger et al., "Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs", J MOL BIOL, 300(2), 2000, pp. 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 MgCl2. Uranyl photocleavage correlateswell 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, andonly 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. (C) 2000 Academic Press.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 01/04/20 alle ore 18:04:25