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Modulating transformation of DNA origami nanoarray via sequence design

Author

Listed:
  • Dongfang Wang

    (University of Science and Technology of China
    University of Science and Technology of China)

  • Fiona Cole

    (Ludwig-Maximilians-Universität München)

  • Martina Pfeiffer

    (Ludwig-Maximilians-Universität München)

  • Mengting Cao

    (University of Science and Technology of China
    University of Science and Technology of China)

  • Tim Schröder

    (Ludwig-Maximilians-Universität München)

  • Philip Tinnefeld

    (Ludwig-Maximilians-Universität München)

  • Yonggang Ke

    (Emory University and Georgia Institute of Technology)

Abstract

The four-way DNA junction is the most prevalent structural motif in DNA nanotechnology. Recently, a reconfigurable DNA nanoarray (domino array) was created with this basic motif to realize intricate, stepwise transformation by the information relay between neighboring four-way junction units. Here, we generate a DNA domino array with same sequences at every junction, and use it as a platform to study how the design of DNA bases at junctions influences the kinetics and thermodynamics of transformation of four-way junctions in reconfigurable DNA nanoarrays. By regulating the energy difference and thus the conversion between the two configurations of four-way junctions, we show the transformation of DNA nanoarray can be modulated in a designable manner. The coordinated transformation of four-way junctions in the DNA domino array enables a detailed investigation on array transformation by using Atomic Force Microscopy (AFM) imaging and single-molecule Förster resonance energy transfer (FRET) microscopy.

Suggested Citation

  • Dongfang Wang & Fiona Cole & Martina Pfeiffer & Mengting Cao & Tim Schröder & Philip Tinnefeld & Yonggang Ke, 2025. "Modulating transformation of DNA origami nanoarray via sequence design," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61421-w
    DOI: 10.1038/s41467-025-61421-w
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