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Boosting functionality of synthetic DNA circuits with tailored deactivation

Author

Listed:
  • Kevin Montagne

    (University of Tokyo)

  • Guillaume Gines

    (LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo)

  • Teruo Fujii

    (LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo)

  • Yannick Rondelez

    (LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo
    Gulliver UMR7083 CNRS, ESPCI Paris, PSL Research University)

Abstract

Molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. The function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. Here we introduce a mechanism to tune the nonlinearities associated with individual nodes of a synthetic network. This mechanism is based on programming deactivation laws using dedicated saturable pathways. We demonstrate this approach through the conversion of a single-node homoeostatic network into a bistable and reversible switch. Furthermore, we prove its generality by adding new functions to the library of reported man-made molecular devices: a system with three addressable bits of memory, and the first DNA-encoded excitable circuit. Specific saturable deactivation pathways thus greatly enrich the functional capability of a given circuit topology.

Suggested Citation

  • Kevin Montagne & Guillaume Gines & Teruo Fujii & Yannick Rondelez, 2016. "Boosting functionality of synthetic DNA circuits with tailored deactivation," Nature Communications, Nature, vol. 7(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13474
    DOI: 10.1038/ncomms13474
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    Cited by:

    1. Hyowon Jang & Jayeon Song & Sunjoo Kim & Jung-Hyun Byun & Kyoung G. Lee & Kwang-Hyun Park & Euijeon Woo & Eun-Kyung Lim & Juyeon Jung & Taejoon Kang, 2023. "ANCA: artificial nucleic acid circuit with argonaute protein for one-step isothermal detection of antibiotic-resistant bacteria," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Adrian Zambrano & Giorgio Fracasso & Mengfei Gao & Martina Ugrinic & Dishi Wang & Dietmar Appelhans & Andrew deMello & T-Y. Dora Tang, 2022. "Programmable synthetic cell networks regulated by tuneable reaction rates," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Fabian Schnitter & Benedikt Rieß & Christian Jandl & Job Boekhoven, 2022. "Memory, switches, and an OR-port through bistability in chemically fueled crystals," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    4. Jianbang Wang & Zhenzhen Li & Itamar Willner, 2022. "Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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