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Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases

Author

Listed:
  • Yusuke Takezawa

    (The University of Tokyo)

  • Keita Mori

    (The University of Tokyo)

  • Wei-En Huang

    (The University of Tokyo)

  • Kotaro Nishiyama

    (The University of Tokyo)

  • Tong Xing

    (The University of Tokyo)

  • Takahiro Nakama

    (The University of Tokyo)

  • Mitsuhiko Shionoya

    (The University of Tokyo)

Abstract

Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH–A base pair and a metal-mediated UOH–GdIII–UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH–A and UOH–GdIII–UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.

Suggested Citation

  • Yusuke Takezawa & Keita Mori & Wei-En Huang & Kotaro Nishiyama & Tong Xing & Takahiro Nakama & Mitsuhiko Shionoya, 2023. "Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40353-3
    DOI: 10.1038/s41467-023-40353-3
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    References listed on IDEAS

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    1. Bernard Yurke & Andrew J. Turberfield & Allen P. Mills & Friedrich C. Simmel & Jennifer L. Neumann, 2000. "A DNA-fuelled molecular machine made of DNA," Nature, Nature, vol. 406(6796), pages 605-608, August.
    2. Qiu-Long Zhang & Liang-Liang Wang & Yan Liu & Jiao Lin & Liang Xu, 2021. "A kinetically controlled platform for ligand-oligonucleotide transduction," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    3. Simona Ranallo & Daniela Sorrentino & Francesco Ricci, 2019. "Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    4. Minghui Liu & Jinglin Fu & Christian Hejesen & Yuhe Yang & Neal W. Woodbury & Kurt Gothelf & Yan Liu & Hao Yan, 2013. "A DNA tweezer-actuated enzyme nanoreactor," Nature Communications, Nature, vol. 4(1), pages 1-5, October.
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