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A large size-selective DNA nanopore with sensing applications

Author

Listed:
  • Rasmus P. Thomsen

    (Aarhus University)

  • Mette Galsgaard Malle

    (University of Copenhagen
    University of Copenhagen)

  • Anders Hauge Okholm

    (Aarhus University
    Arla Innovation Centre)

  • Swati Krishnan

    (Technische Universität München)

  • Søren S.-R. Bohr

    (University of Copenhagen
    University of Copenhagen)

  • Rasmus Schøler Sørensen

    (Aarhus University)

  • Oliver Ries

    (University of Southern Denmark)

  • Stefan Vogel

    (University of Southern Denmark)

  • Friedrich C. Simmel

    (Technische Universität München)

  • Nikos S. Hatzakis

    (University of Copenhagen
    University of Copenhagen)

  • Jørgen Kjems

    (Aarhus University
    Aarhus University)

Abstract

Transmembrane nanostructures like ion channels and transporters perform key biological functions by controlling flow of molecules across lipid bilayers. Much work has gone into engineering artificial nanopores and applications in selective gating of molecules, label-free detection/sensing of biomolecules and DNA sequencing have shown promise. Here, we use DNA origami to create a synthetic 9 nm wide DNA nanopore, controlled by programmable, lipidated flaps and equipped with a size-selective gating system for the translocation of macromolecules. Successful assembly and insertion of the nanopore into lipid bilayers are validated by transmission electron microscopy (TEM), while selective translocation of cargo and the pore mechanosensitivity are studied using optical methods, including single-molecule, total internal reflection fluorescence (TIRF) microscopy. Size-specific cargo translocation and oligonucleotide-triggered opening of the pore are demonstrated showing that the DNA nanopore can function as a real-time detection system for external signals, offering potential for a variety of highly parallelized sensing applications.

Suggested Citation

  • Rasmus P. Thomsen & Mette Galsgaard Malle & Anders Hauge Okholm & Swati Krishnan & Søren S.-R. Bohr & Rasmus Schøler Sørensen & Oliver Ries & Stefan Vogel & Friedrich C. Simmel & Nikos S. Hatzakis & J, 2019. "A large size-selective DNA nanopore with sensing applications," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13284-1
    DOI: 10.1038/s41467-019-13284-1
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    Cited by:

    1. Xiaoming Liu & Fengyu Liu & Hemani Chhabra & Christopher Maffeo & Zhuo Chen & Qiang Huang & Aleksei Aksimentiev & Tatsuo Arai, 2024. "A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Smrithi Krishnan R & Kalyanashis Jana & Amina H. Shaji & Karthika S. Nair & Anjali Devi Das & Devika Vikraman & Harsha Bajaj & Ulrich Kleinekathöfer & Kozhinjampara R. Mahendran, 2022. "Assembly of transmembrane pores from mirror-image peptides," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Solveig G. Schmidt & Mette Galsgaard Malle & Anne Kathrine Nielsen & Søren S.-R. Bohr & Ciara F. Pugh & Jeppe C. Nielsen & Ida H. Poulsen & Kasper D. Rand & Nikos S. Hatzakis & Claus J. Loland, 2022. "The dopamine transporter antiports potassium to increase the uptake of dopamine," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Swarup Dey & Adam Dorey & Leeza Abraham & Yongzheng Xing & Irene Zhang & Fei Zhang & Stefan Howorka & Hao Yan, 2022. "A reversibly gated protein-transporting membrane channel made of DNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Zhao Zhang & Zhaomeng Feng & Xiaowei Zhao & Dominique Jean & Zhiheng Yu & Edwin R. Chapman, 2023. "Functionalization and higher-order organization of liposomes with DNA nanostructures," Nature Communications, Nature, vol. 14(1), pages 1-9, December.

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