Wittberger, D. ; Berens, C. ; Hammann, Christian ; Westhof, E. ; Schroeder, R. (2000)
Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs.
In: Journal of molecular biology, 300 (2)
Artikel, Bibliographie
Kurzbeschreibung (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.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2000 |
| Autor(en): | Wittberger, D. ; Berens, C. ; Hammann, Christian ; Westhof, E. ; Schroeder, R. |
| Art des Eintrags: | Bibliographie |
| Titel: | Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs. |
| Sprache: | Englisch |
| Publikationsjahr: | 2000 |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | Journal of molecular biology |
| Jahrgang/Volume einer Zeitschrift: | 300 |
| (Heft-)Nummer: | 2 |
| Kurzbeschreibung (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. |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie ?? fb10_mikrobiologie ?? 10 Fachbereich Biologie > Regulatorische RNAs und Ribozyme |
| Hinterlegungsdatum: | 29 Jul 2010 12:13 |
| Letzte Änderung: | 05 Mär 2013 09:34 |
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