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Autonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks

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  • Jie Deng

    (University of Mainz
    Dana-Farber Cancer Institute, Harvard Medical School)

  • Andreas Walther

    (University of Mainz
    University of Freiburg)

Abstract

Concatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. Here, to provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds. This allows to achieve hierarchical non-equilibrium systems by concurrent ATP-powered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. We introduce indirect and direct activation of DNT self-assemblies, and orthogonal molecular recognition allows ATP-fueled self-sorting of transient multicomponent DNTs. Coupling ATP dissipation to DNA nanostructures via programmable DSD is a generic concept which should be widely applicable to organize other DNA nanostructures, and enable the design of automatons and life-like systems of higher structural complexity.

Suggested Citation

  • Jie Deng & Andreas Walther, 2021. "Autonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25450-5
    DOI: 10.1038/s41467-021-25450-5
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    Cited by:

    1. Xianhua Lang & Yingjie Huang & Lirong He & Yixi Wang & Udayabhaskararao Thumu & Zonglin Chu & Wilhelm T. S. Huck & Hui Zhao, 2023. "Mechanosensitive non-equilibrium supramolecular polymerization in closed chemical systems," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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