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Computational Methods for the Design of Recombinase Logic Circuits with Adaptable Circuit Specifications

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Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2553))

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Abstract

Synthetic biology aims at engineering new biological systems and functions that can be used to provide new technological solutions to worldwide challenges. Detection and processing of multiple signals are crucial for many synthetic biology applications. A variety of logic circuits operating in living cells have been implemented. One particular class of logic circuits uses site-specific recombinases mediating specific DNA inversion or excision. Recombinase logic offers many interesting features, including single-layer architectures, memory, low metabolic footprint, and portability in many species. Here, we present two automated design strategies for both Boolean and history-dependent recombinase-based logic circuits. One approach is based on the distribution of computation within multicellular consortia, and the other is a single-cell design. Both are complementary and adapted for non-expert users via a web design interface, called CALIN and RECOMBINATOR, for multicellular and single-cell design strategies, respectively. In this book chapter, we are guiding the reader step by step through recombinase logic circuit design, from selecting the design strategy fitting to their final system of interest to obtaining the final design using one of our design web interfaces.

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Author information

Authors and Affiliations

  1. Centre de Biologie Structurale (CBS), Univ. Montpellier, INSERM U1054, CNRS UMR5048, Montpellier, France

    Ana Zúñiga & Jérôme Bonnet

  2. Department of Biology, University of Washington, Seattle, WA, USA

    Sarah Guiziou

Authors
  1. Ana Zúñiga
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  2. Jérôme Bonnet
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  3. Sarah Guiziou
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Editors and Affiliations

  1. Bioinformatics Institute, Agency for Science, Technology & Research, Singapore, Singapore

    Kumar Selvarajoo

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Zúñiga, A., Bonnet, J., Guiziou, S. (2023). Computational Methods for the Design of Recombinase Logic Circuits with Adaptable Circuit Specifications. In: Selvarajoo, K. (eds) Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. Methods in Molecular Biology, vol 2553. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2617-7_8

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  • DOI: https://doi.org/10.1007/978-1-0716-2617-7_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2616-0

  • Online ISBN: 978-1-0716-2617-7

  • eBook Packages: Springer Protocols

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