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Leak-Resistant Design of DNA Strand Displacement Systems

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Bio-inspired Information and Communication Technologies (BICT 2020)

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Abstract

Although a number of dynamically-controlled nanostructures and programmable DNA Strand Displacement (DSD) systems have been designed using DNA strand displacement, predictability and scalability of these DNA-based systems remain limited due to leakages introduced by spuriously triggered displacement events. We present a systematic design method for implementing leak-resistant DNA strand displacement systems in which each legitimate displacement event requires signal species to bind cooperatively at the two designated toehold binding sites in the protected fuel complexes, and thus inhibits spurious displacement events. To demonstrate the potential of the leak-resistant design approach for the construction of arbitrary complex digital circuits and systems with analog behaviors, we present domain-level designs and displacement pathways of the basic building blocks of the DNA strand displacement cascades, e.g. OR, AND gates, and an elementary bimolecular reaction.

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Notes

  1. 1.

    The antiparallel DX molecule provides a rigid structure  [21], where its two helices are tightly held together (helical axes separated by \(\approx \)4.0 nm) by two crossovers. Note that, since we use only two ends of the helices to sequester the signal and create two toehold sticky ends, the second crossover is replaced by a half-crossover  [20].

  2. 2.

    The stability of the base-pairs flanking a bulge loop within the DNA duplex depends on the types of flanking bases and other structural aspects  [13]. The destabilizing effect can be mitigated by using stronger G-C pairs on each side of the bulge loop.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Aalto University, 00076, Aalto, Finland

    Vinay Gautam

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  1. Vinay Gautam
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Correspondence to Vinay Gautam .

Editor information

Editors and Affiliations

  1. University of Electronic Science and Technology, Chengdu, China

    Yifan Chen

  2. Osaka University, Osaka, Japan

    Tadashi Nakano

  3. Tongji University, Shanghai, China

    Lin Lin

  4. Resch School of Engineering, University of Wisconsiin-Green Bay, Green Bay, WI, USA

    Mohammad Upal Mahfuz

  5. School of Engineering, Cranfield University, Cranfield, UK

    Weisi Guo

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© 2020 ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering

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Gautam, V. (2020). Leak-Resistant Design of DNA Strand Displacement Systems. In: Chen, Y., Nakano, T., Lin, L., Mahfuz, M., Guo, W. (eds) Bio-inspired Information and Communication Technologies. BICT 2020. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol 329. Springer, Cham. https://doi.org/10.1007/978-3-030-57115-3_7

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  • DOI: https://doi.org/10.1007/978-3-030-57115-3_7

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-57114-6

  • Online ISBN: 978-3-030-57115-3

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