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DNA dynamics and computation based on toehold-free strand displacement

Author

Listed:
  • Hong Kang

    (Tsinghua University)

  • Tong Lin

    (Tsinghua University
    The Hong Kong University of Science and Technology, Clear Water Bay)

  • Xiaojin Xu

    (The Hong Kong University of Science and Technology, Clear Water Bay)

  • Qing-Shan Jia

    (Tsinghua University)

  • Richard Lakerveld

    (The Hong Kong University of Science and Technology, Clear Water Bay)

  • Bryan Wei

    (Tsinghua University)

Abstract

We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.

Suggested Citation

  • Hong Kang & Tong Lin & Xiaojin Xu & Qing-Shan Jia & Richard Lakerveld & Bryan Wei, 2021. "DNA dynamics and computation based on toehold-free strand displacement," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25270-7
    DOI: 10.1038/s41467-021-25270-7
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    Cited by:

    1. Hong Kang & Yuexuan Yang & Bryan Wei, 2024. "Synthetic molecular switches driven by DNA-modifying enzymes," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Katya Ahmad & Abid Javed & Conor Lanphere & Peter V. Coveney & Elena V. Orlova & Stefan Howorka, 2023. "Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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