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Dynamic Management of Codon Compression for Saturation Mutagenesis

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Synthetic Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1772))

Abstract

Saturation mutagenesis is conveniently located between the two extremes of protein engineering, namely random mutagenesis, and rational design. It involves mutating a confined number of target residues to other amino acids, and hence requires knowledge regarding the sites for mutagenesis, but not their final identity. There are many different strategies for performing and designing such experiments, ranging from simple single degenerate codons to codon collections that code for distinct sets of amino acids. Here, we provide detailed information on the Dynamic Management for Codon Compression (DYNAMCC) approaches that allow us to precisely define the desired amino acid composition to be introduced to a specific target site. DYNAMCC allows us to set usage thresholds and to eliminate undesirable stop and wild-type codons, thus allowing us to control library size and subsequently downstream screening efforts. The DYNAMCC algorithms are free of charge and are implemented in a website for easy access and usage: www.dynamcc.com.

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Acknowledgments

We thank James Winkler, Marcelo Bassalo, and Wayne Patrick for insightful comments on the manuscript. This work was funded by the U.S. Department of Energy Grant No. DE-SC008812.

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Authors and Affiliations

  1. Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA

    Gur Pines & Ryan T. Gill

  2. Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA

    Gur Pines & Ryan T. Gill

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  1. Gur Pines
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  2. Ryan T. Gill
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Correspondence to Gur Pines .

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Editors and Affiliations

  1. Agilent Technologies, Inc, La Jolla, California, USA

    Jeffrey Carl Braman

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Pines, G., Gill, R.T. (2018). Dynamic Management of Codon Compression for Saturation Mutagenesis. In: Braman, J. (eds) Synthetic Biology. Methods in Molecular Biology, vol 1772. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7795-6_9

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  • DOI: https://doi.org/10.1007/978-1-4939-7795-6_9

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