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Computational Design of Reaction-Diffusion Patterns Using DNA-Based Chemical Reaction Networks

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DNA Computing and Molecular Programming (DNA 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8727))

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Abstract

DNA self-assembly is a powerful technology for controlling matter at the nanometre to micron scale, with potential applications in high-precision organisation and positioning of molecular components. However, the ability to program DNA-only self-organisation beyond the microscopic scale is currently lacking. In this paper we propose a computational method for programming spatial organisation of DNA at the centimetre scale, by means of DNA strand displacement reaction diffusion systems. We use this method to analyse the spatiotemporal dynamics of an autocatalytic system, a predator-prey oscillator and a two-species consensus network. We find that both autocatalytic and oscillating systems can support travelling waves across centimetre distances, and that consensus in a spatial context results in the spontaneous formation of distinct spatial domains, in which one species is completely eliminated. Together, our results suggest that programmed spatial self-organisation of DNA, through a reaction diffusion mechanism, is achievable with current DNA strand displacement technology.

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Author information

Authors and Affiliations

  1. Microsoft Research, Cambridge, CB1 2FB, UK

    Neil Dalchau & Andrew Phillips

  2. University of Washington, WA, USA

    Georg Seelig

Authors
  1. Neil Dalchau
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  2. Georg Seelig
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  3. Andrew Phillips
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Editor information

Editors and Affiliations

  1. Graduate School of Engineering, Department of Bioengineering and Robotics, Tohoku University, 6-6-01 Aoba-yama, 980-8579, Sendai, Japan

    Satoshi Murata

  2. Graduate School of Informatics and Engineering, Department of Communication Engineering and Informatics, University of Electro-Communications, 1-5-1 Chofugaoka, 182-8585, Chofu, Tokyo, Japan

    Satoshi Kobayashi

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Dalchau, N., Seelig, G., Phillips, A. (2014). Computational Design of Reaction-Diffusion Patterns Using DNA-Based Chemical Reaction Networks. In: Murata, S., Kobayashi, S. (eds) DNA Computing and Molecular Programming. DNA 2014. Lecture Notes in Computer Science, vol 8727. Springer, Cham. https://doi.org/10.1007/978-3-319-11295-4_6

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  • DOI: https://doi.org/10.1007/978-3-319-11295-4_6

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11294-7

  • Online ISBN: 978-3-319-11295-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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