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Monitoring Global Structural Changes and Specific Metal-Ion-Binding Sites in RNA by In-line Probing and Tb(III) Cleavage

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RNA Folding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1086))

Abstract

In this chapter we describe the use of two methods, in-line probing as well as terbium(III) cleavage. Both methods can be applied to RNAs of any size, structure, and function. Aside from revealing directly metal ion-binding sites these techniques also provide structural information for longer RNA sequences that are out of range to be analyzed with other techniques such as NMR. The cleavage pattern derived from in-line probing experiments reflects local and overall conformational changes in RNA upon the addition of metal ions, metal complexes, or other ligands. On the other side, terbium(III) cleavage experiments are applied to locate specific metal ion-binding sites in RNA molecules.

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Acknowledgements

Financial support by the European Research Council (ERC Starting Grant to RKOS), the Swiss National Science Foundation, the Swiss State Secretariat for Education, Research, and Innovation (COST Action CM1105), and the University of Zurich is gratefully acknowledged.

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Authors and Affiliations

  1. Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland

    Pallavi K. Choudhary, Sofia Gallo & Roland K. O. Sigel

Authors
  1. Pallavi K. Choudhary
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  2. Sofia Gallo
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  3. Roland K. O. Sigel
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Editor information

Editors and Affiliations

  1. Dept. of Biochemistry & Cell Biology, University of Vienna Max F. Perutz Laboratories, Vienna, Austria

    Christina Waldsich

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Choudhary, P.K., Gallo, S., Sigel, R.K.O. (2014). Monitoring Global Structural Changes and Specific Metal-Ion-Binding Sites in RNA by In-line Probing and Tb(III) Cleavage. In: Waldsich, C. (eds) RNA Folding. Methods in Molecular Biology, vol 1086. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-667-2_8

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  • DOI: https://doi.org/10.1007/978-1-62703-667-2_8

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-666-5

  • Online ISBN: 978-1-62703-667-2

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