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Regulatory RNA Design Through Evolutionary Computation and Strand Displacement

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Computational Methods in Synthetic Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1244))

Abstract

The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators, in particular, have been used to activate or repress gene expression. However, to accelerate and scale up the design process, synthetic biologists require computer-assisted design tools, without which riboregulator engineering will remain a case-by-case design process requiring expert attention. Recently, the design of RNA circuits by evolutionary computation and adapting strand displacement techniques from nanotechnology has proven to be suited to the automated generation of DNA sequences implementing regulatory RNA systems in bacteria. Herein, we present our method to carry out such evolutionary design and how to use it to create various types of riboregulators, allowing the systematic de novo design of genetic control systems in synthetic biology.

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Acknowledgements

Work supported by the FP7-ICT-043338 (BACTOCOM) grant (to A.J.). We thank Anna Młynarczyk for critical reading of the manuscript. W.R. is supported by a DGA graduate fellowship, T.E.L by an AXA research fund Ph.D. fellowship, and G.R. by an EMBO long-term fellowship co-funded by Marie Curie actions (ALTF-1177-2011).

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    Authors and Affiliations

    1. Institute of Systems and Synthetic Biology (iSSB-CNRS), Université d’Evry val d’Essonne, Genopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030, Evry Cedex, France

      William Rostain, Thomas E. Landrain, Guillermo Rodrigo & Alfonso Jaramillo

    2. School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK

      Alfonso Jaramillo

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    1. William Rostain
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    2. Thomas E. Landrain
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    3. Guillermo Rodrigo
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    4. Alfonso Jaramillo
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    Corresponding authors

    Correspondence to Guillermo Rodrigo or Alfonso Jaramillo .

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    Editors and Affiliations

    1. School of Life Science and Technology, Harbin Institute of Technology, Harbin, China

      Mario Andrea Marchisio

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    Rostain, W., Landrain, T.E., Rodrigo, G., Jaramillo, A. (2015). Regulatory RNA Design Through Evolutionary Computation and Strand Displacement. In: Marchisio, M. (eds) Computational Methods in Synthetic Biology. Methods in Molecular Biology, vol 1244. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1878-2_4

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    • DOI: https://doi.org/10.1007/978-1-4939-1878-2_4

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    • Publisher Name: Humana Press, New York, NY

    • Print ISBN: 978-1-4939-1877-5

    • Online ISBN: 978-1-4939-1878-2

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