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In-Line Probing Analysis of Riboswitches

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Part of the Methods In Molecular Biology™ book series (MIMB,volume 419)

Summary

Riboswitches are intricate, metabolite-binding RNA structures found in the non-coding regions of mRNA. Allosteric changes in the riboswitch that are induced by metabolite binding are harnessed to control the genes of a variety of essential metabolic pathways in eubacteria and in some eukaryotes. In this chapter, we describe an RNA structure analysis technique called “in-line probing.” This assay makes use of the natural instability of RNA to elucidate secondary structure characteristics and ligand-binding capabilities of riboswitches in an entirely protein-free manner. Although this method has most frequently been used to examine riboswitches, the structures of any RNAs can be examined using this technique.

Key Words

  • Allosteric
  • aptamer
  • phosphoester transfer
  • RNA structure
  • spontaneous RNA cleavage

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Regulski, E.E., Breaker, R.R. (2008). In-Line Probing Analysis of Riboswitches. In: Wilusz, J. (eds) Post-Transcriptional Gene Regulation. Methods In Molecular Biology™, vol 419. Humana Press. https://doi.org/10.1007/978-1-59745-033-1_4

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  • DOI: https://doi.org/10.1007/978-1-59745-033-1_4

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-783-9

  • Online ISBN: 978-1-59745-033-1

  • eBook Packages: Springer Protocols