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Implementing Arbitrary CRNs Using Strand Displacing Polymerase

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DNA Computing and Molecular Programming (DNA 2019)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11648))

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Abstract

The regulation of cellular and molecular processes typically involves complex biochemical networks. Synthetic nucleic acid reaction networks (both enzyme-based and enzyme-free) can be systematically designed to approximate sophisticated biochemical processes. However, most of the prior experimental protocols for reaction networks relied on either strand-displacement hybridization or restriction and exonuclease enzymatic reactions. These resulting synthetic systems usually suffer from either slow rates or leaky reactions. In this work, we propose an alternative architecture to implement arbitrary reaction networks, that is based entirely on strand-displacing polymerase reactions with non-overlapping I/O sequences. We first design a simple protocol that approximates arbitrary unimolecular and bimolecular reactions using polymerase strand displacement reactions. Then we use these fundamental reaction systems as modules to show three large-scale applications of our architecture, including an autocatalytic amplifier, a molecular-scale consensus protocol, and a dynamic oscillatory system.

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Acknowledgements

This work was supported by National Science Foundation Grants CCF-1813805 and CCF-1617791. The authors thank Keerti Anand for useful theoretical discussions on ODEs and chemical kinetics. The most up-to-date simulation scripts are available online as a GitHub repository at https://bit.ly/2X3axAh.

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Authors and Affiliations

  1. Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27701, USA

    Shalin Shah, Xin Song & John Reif

  2. Department of Computer Science, Duke University, Durham, NC, 27701, USA

    Tianqi Song, Ming Yang & John Reif

  3. Department of Biomedical Engineering, Duke University, Durham, NC, 27701, USA

    Xin Song

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  1. Shalin Shah
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  2. Tianqi Song
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  3. Xin Song
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  4. Ming Yang
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  5. John Reif
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Corresponding author

Correspondence to Shalin Shah .

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Editors and Affiliations

  1. California Institute of Technology, Pasadena, CA, USA

    Chris Thachuk

  2. Arizona State University, Tempe, AZ, USA

    Yan Liu

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Shah, S., Song, T., Song, X., Yang, M., Reif, J. (2019). Implementing Arbitrary CRNs Using Strand Displacing Polymerase. In: Thachuk, C., Liu, Y. (eds) DNA Computing and Molecular Programming. DNA 2019. Lecture Notes in Computer Science(), vol 11648. Springer, Cham. https://doi.org/10.1007/978-3-030-26807-7_2

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  • DOI: https://doi.org/10.1007/978-3-030-26807-7_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-26806-0

  • Online ISBN: 978-3-030-26807-7

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