Summary
Chemical probing of RNA structure has become one of the most popular approaches to map the conformation of RNA molecules of various sizes under well-defined experimental conditions. The method monitors the sensitivity of each nucleotide to various chemicals, which reflects its hydrogen-bonding environment within the RNA molecule. The goal of this chapter is to provide the reader with an experimental guide to mapping the secondary structure of RNA thermosensors in vitro with the most suitable chemical probes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Narberhaus, F., Waldminghaus, T. and Chowdhury, S. (2006). RNA thermometers. FEMS Microbiol. Rev. 30, 3–16.
Morita, M. T., Tanaka, Y., Kodama, T. S., Kyogoku, Y., Yanagi, H. and Yura, T. (1999). Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev. 13, 655–665.
Johansson, J., Mandin, P., Renzoni, A., Chiaruttini, C., Springer, M. and Cossart, P. (2002). An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 110, 551–561.
Hoe, N. P. and Goguen, J. D. (1993). Temperature sensing in Yersinia pestis: translation of the LcrF activator protein is thermally regulated. J. Bacteriol. 175, 7901–7909.
Yamanaka, K., Mitta, M. and Inouye, M. (1999). Mutation analysis of the 5′ untranslated region of the cold shock cspA mRNA of Escherichia coli. J. Bacteriol. 181, 6284–6291.
Altuvia, S., Kornitzer, D., Teff, D. and Oppenheim, A. B. (1989). Alternative mRNA structures of the cIII gene of bacteriophage lambda determine the rate of its translation initiation. J. Mol. Biol. 210, 265–280.
Mayford, M. and Weisblum, B. (1989). Conformational alterations in the ermC transcript in vivo during induction. EMBO J. 8, 4307–4314.
Benito, Y., Kolb, F. A., Romby, P., Lina, G., Etienne, J. and Vandenesch, F. (2000). Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression. RNA 6, 668–679.
Balzer, M. and Wagner, R. (1998). A chemical modification method for the structural analysis of RNA and RNA–protein complexes within living cells. Anal. Biochem. 256, 240–242.
Lindell, M., Romby, P. and Wagner, E. G. (2002). Lead(II) as a probe for investigating RNA structure in vivo. RNA 8, 534–541.
Michel, F. and Costa, M. (1998). in RNA Structure and Function, eds. Simons, R. W. and Grunberg-Manago, M. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 175–202.
Eddy, S. R. (2002). A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3, 18.
Xu, X., Ji, Y. and Stormo, G. D. (2007). RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics 23, 1883–1891.
van Batenburg, F. H., Gultyaev, A. P. and Pleij, C. W. (1995). An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theor. Biol. 174, 269–280.
Acknowledgments
We thank Ciaran Condon for critical reading of the manuscript. This work was supported by the CNRS (UPR9073), the University of Paris Diderot-Paris VII, and the ANR (ANR-05-BLAN-0159-01).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Chiaruttini, C., Allem, F., Springer, M. (2009). Structural Probing of RNA Thermosensors . In: Serganov, A. (eds) Riboswitches. Methods in Molecular Biology, vol 540. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-558-9_17
Download citation
DOI: https://doi.org/10.1007/978-1-59745-558-9_17
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-934115-88-6
Online ISBN: 978-1-59745-558-9
eBook Packages: Springer Protocols