IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-61421-w.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-61421-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-61421-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Fiona Cole & Martina Pfeiffer & Dongfang Wang & Tim Schröder & Yonggang Ke & Philip Tinnefeld, 2024. "Controlled mechanochemical coupling of anti-junctions in DNA origami arrays," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Luvena L. Ong & Nikita Hanikel & Omar K. Yaghi & Casey Grun & Maximilian T. Strauss & Patrick Bron & Josephine Lai-Kee-Him & Florian Schueder & Bei Wang & Pengfei Wang & Jocelyn Y. Kishi & Cameron Myh, 2017. "Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components," Nature, Nature, vol. 552(7683), pages 72-77, December.
    3. Grigory Tikhomirov & Philip Petersen & Lulu Qian, 2017. "Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns," Nature, Nature, vol. 552(7683), pages 67-71, December.
    4. Klaus F. Wagenbauer & Christian Sigl & Hendrik Dietz, 2017. "Gigadalton-scale shape-programmable DNA assemblies," Nature, Nature, vol. 552(7683), pages 78-83, December.
    5. Yonggang Ke & Travis Meyer & William M. Shih & Gaetan Bellot, 2016. "Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator," Nature Communications, Nature, vol. 7(1), pages 1-8, April.
    6. Erik Winfree & Furong Liu & Lisa A. Wenzler & Nadrian C. Seeman, 1998. "Design and self-assembly of two-dimensional DNA crystals," Nature, Nature, vol. 394(6693), pages 539-544, August.
    7. Bryan Wei & Mingjie Dai & Peng Yin, 2012. "Complex shapes self-assembled from single-stranded DNA tiles," Nature, Nature, vol. 485(7400), pages 623-626, May.
    8. Shawn M. Douglas & Hendrik Dietz & Tim Liedl & Björn Högberg & Franziska Graf & William M. Shih, 2009. "Self-assembly of DNA into nanoscale three-dimensional shapes," Nature, Nature, vol. 459(7245), pages 414-418, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yahong Chen & Chaoyong Yang & Zhi Zhu & Wei Sun, 2022. "Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Johann M. Weck & Amelie Heuer-Jungemann, 2025. "Fully addressable designer superstructures assembled from one single modular DNA origami," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    3. Eva Bertosin & Christopher M. Maffeo & Thomas Drexler & Maximilian N. Honemann & Aleksei Aksimentiev & Hendrik Dietz, 2021. "A nanoscale reciprocating rotary mechanism with coordinated mobility control," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    4. Wen Wang & Abdulmelik Mohammed & Rong Chen & Antti Elonen & Silian Chen & Mengfan Tian & Junhao Yang & Ye Xiang & Pekka Orponen & Bryan Wei, 2025. "Automated design of scaffold-free DNA wireframe nanostructures," Nature Communications, Nature, vol. 16(1), pages 1-7, December.
    5. Sungwook Woo & Sinem K. Saka & Feng Xuan & Peng Yin, 2024. "Molecular robotic agents that survey molecular landscapes for information retrieval," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Vishal Maingi & Zhao Zhang & Chris Thachuk & Namita Sarraf & Edwin R. Chapman & Paul W. K. Rothemund, 2023. "Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Da-Jung Cho, 2025. "Formalization of Side-Aware DNA Origami Words and Their Rewriting System, and Equivalent Classes," Mathematics, MDPI, vol. 13(6), pages 1-26, March.
    8. Jessica A. Kretzmann & Anna Liedl & Alba Monferrer & Volodymyr Mykhailiuk & Samuel Beerkens & Hendrik Dietz, 2023. "Gene-encoding DNA origami for mammalian cell expression," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    9. Molly F. Parsons & Matthew F. Allan & Shanshan Li & Tyson R. Shepherd & Sakul Ratanalert & Kaiming Zhang & Krista M. Pullen & Wah Chiu & Silvi Rouskin & Mark Bathe, 2023. "3D RNA-scaffolded wireframe origami," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    10. Kumar S. Ray & Mandrita Mondal, 2016. "Logical Inference by DNA Strand Algebra," New Mathematics and Natural Computation (NMNC), World Scientific Publishing Co. Pte. Ltd., vol. 12(01), pages 29-44, March.
    11. Wenqing Xu & Guanheng Huang & Zhan Yang & Ziqi Deng & Chen Zhou & Jian-An Li & Ming-De Li & Tao Hu & Ben Zhong Tang & David Lee Phillips, 2024. "Nucleic-acid-base photofunctional cocrystal for information security and antimicrobial applications," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    12. Daniela Sorrentino & Simona Ranallo & Francesco Ricci & Elisa Franco, 2024. "Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    13. Martina F. Ober & Anna Baptist & Lea Wassermann & Amelie Heuer-Jungemann & Bert Nickel, 2022. "In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    14. Zhen Wang & Qing-Pu Zhang & Fei Guo & Hui Ma & Zi-Hui Liang & Chang-Hai Yi & Chun Zhang & Chuan-Feng Chen, 2024. "Self-similar chiral organic molecular cages," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    15. Omar A. Saleh & Sam Wilken & Todd M. Squires & Tim Liedl, 2023. "Vacuole dynamics and popping-based motility in liquid droplets of DNA," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    16. Francis Schuknecht & Karol Kołątaj & Michael Steinberger & Tim Liedl & Theobald Lohmueller, 2023. "Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    17. Agnese I. Curatolo & Ofer Kimchi & Carl P. Goodrich & Ryan K. Krueger & Michael P. Brenner, 2023. "A computational toolbox for the assembly yield of complex and heterogeneous structures," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    18. Chi Chen & Xingfei Wei & Molly F. Parsons & Jiajia Guo & James L. Banal & Yinong Zhao & Madelyn N. Scott & Gabriela S. Schlau-Cohen & Rigoberto Hernandez & Mark Bathe, 2022. "Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    19. Xiang Tian & Xiyu Liu & Hongyan Zhang & Minghe Sun & Yuzhen Zhao, 2020. "A DNA algorithm for the job shop scheduling problem based on the Adleman-Lipton model," PLOS ONE, Public Library of Science, vol. 15(12), pages 1-21, December.
    20. Huacheng Li & Xin Xu & Rongcheng Guan & Artur Movsesyan & Zhenni Lu & Qiliang Xu & Ziyun Jiang & Yurong Yang & Majid Khan & Jin Wen & Hongwei Wu & Santiago Moya & Gil Markovich & Huatian Hu & Zhiming , 2024. "Collective chiroptical activity through the interplay of excitonic and charge-transfer effects in localized plasmonic fields," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61421-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.