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RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing

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Riboregulator Design and Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2518))

Abstract

Riboswitches are an attractive target for the directed design of RNA-based regulators by in silico prediction. These noncoding RNA elements consist of an aptamer platform for the highly selective ligand recognition and an expression platform which controls gene activity typically at the level of transcription or translation. In previous work, we could successfully apply RNA folding prediction to implement a new riboswitch mechanism regulating processing of a tRNA by RNase P. In this contribution, we present detailed information about our pipeline consisting of in silico design combined with the biochemical analysis for the verification of the implemented mechanism. Furthermore, we discuss the applicability of the presented biochemical in vivo and in vitro methods for the characterization of other artificial riboswitches.

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Acknowledgments

We thank Dr. Stefan Hammer for his ongoing support although he left academia. Furthermore, we thank Dr. Manuela Geiß for fruitful discussion on all mathematical aspects especially of the applied scoring. Special thanks to Dr. Christina Weinberg for valuable discussions about the experimental setup and Felix Kühnl for fruitful discussions about the project in general.

This work was supported by the Deutsche Forschungsgemeinschaft (grant numbers MO 634/9-2 and STA 850/15-2).

Author information

Authors and Affiliations

  1. Institute for Biochemistry, Leipzig University, Leipzig, Germany

    Anna Ender & Mario Mörl

  2. Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany

    Peter F. Stadler & Sven Findeiß

  3. Max Planck Institute for Mathematics in the Science, Leipzig, Germany

    Peter F. Stadler

  4. Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

    Peter F. Stadler

  5. Santa Fe Institute, Santa Fe, NM, USA

    Peter F. Stadler

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  1. Anna Ender
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  2. Peter F. Stadler
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  3. Mario Mörl
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  4. Sven Findeiß
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Corresponding author

Correspondence to Sven Findeiß .

Editor information

Editors and Affiliations

  1. Biosciences Department, Rice University, Houston, TX, USA

    James Chappell

  2. Department of Biology, California State University, Northridge, Northridge, CA, USA

    Melissa K. Takahashi

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Ender, A., Stadler, P.F., Mörl, M., Findeiß, S. (2022). RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. In: Chappell, J., Takahashi, M.K. (eds) Riboregulator Design and Analysis. Methods in Molecular Biology, vol 2518. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2421-0_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2421-0_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2420-3

  • Online ISBN: 978-1-0716-2421-0

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