IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-32526-3.html
   My bibliography  Save this article

A nanopore interface for higher bandwidth DNA computing

Author

Listed:
  • Karen Zhang

    (University of Washington)

  • Yuan-Jyue Chen

    (Microsoft Research)

  • Delaney Wilde

    (University of Washington)

  • Kathryn Doroschak

    (University of Washington)

  • Karin Strauss

    (Microsoft Research)

  • Luis Ceze

    (University of Washington)

  • Georg Seelig

    (University of Washington
    University of Washington
    University of Washington)

  • Jeff Nivala

    (University of Washington
    University of Washington)

Abstract

DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device). These results increase DSD output bandwidth by an order of magnitude over what is currently feasible with fluorescence spectroscopy.

Suggested Citation

  • Karen Zhang & Yuan-Jyue Chen & Delaney Wilde & Kathryn Doroschak & Karin Strauss & Luis Ceze & Georg Seelig & Jeff Nivala, 2022. "A nanopore interface for higher bandwidth DNA computing," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32526-3
    DOI: 10.1038/s41467-022-32526-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-32526-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-32526-3?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. Li-Qun Gu & Orit Braha & Sean Conlan & Stephen Cheley & Hagan Bayley, 1999. "Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter," Nature, Nature, vol. 398(6729), pages 686-690, April.
    2. Lulu Qian & Erik Winfree & Jehoshua Bruck, 2011. "Neural network computation with DNA strand displacement cascades," Nature, Nature, vol. 475(7356), pages 368-372, July.
    3. Kevin M. Cherry & Lulu Qian, 2018. "Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks," Nature, Nature, vol. 559(7714), pages 370-376, July.
    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. Linlin Yang & Qian Tang & Mingzhi Zhang & Yuan Tian & Xiaoxing Chen & Rui Xu & Qian Ma & Pei Guo & Chao Zhang & Da Han, 2024. "A spatially localized DNA linear classifier for cancer diagnosis," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Kanakov, Oleg & Chen, Shangbin & Zaikin, Alexey, 2024. "Learning by selective plasmid loss for intracellular synthetic classifiers," Chaos, Solitons & Fractals, Elsevier, vol. 179(C).
    3. Ahmed A. Agiza & Kady Oakley & Jacob K. Rosenstein & Brenda M. Rubenstein & Eunsuk Kim & Marc Riedel & Sherief Reda, 2023. "Digital circuits and neural networks based on acid-base chemistry implemented by robotic fluid handling," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    4. Avik Samanta & Maximilian Hörner & Wei Liu & Wilfried Weber & Andreas Walther, 2022. "Signal-processing and adaptive prototissue formation in metabolic DNA protocells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Ilona Kulikovskikh & Sergej Prokhorov & Tomislav Lipić & Tarzan Legović & Tomislav Šmuc, 2019. "BioGD: Bio-inspired robust gradient descent," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-19, July.
    6. Russell Bates & Oleg Blyuss & Ahmed Alsaedi & Alexey Zaikin, 2015. "Effect of Noise in Intelligent Cellular Decision Making," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-16, May.
    7. Tai-Yin Chiu & Hui-Ju K Chiang & Ruei-Yang Huang & Jie-Hong R Jiang & François Fages, 2015. "Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications," PLOS ONE, Public Library of Science, vol. 10(9), pages 1-27, September.
    8. Gabriel de Freitas Viscondi & Solange N. Alves-Souza, 2021. "Solar Irradiance Prediction with Machine Learning Algorithms: A Brazilian Case Study on Photovoltaic Electricity Generation," Energies, MDPI, vol. 14(18), pages 1-15, September.
    9. Pingping Fan & Shanyu Zhang & Yuqin Wang & Tian Li & Hanhan Zhang & Panke Zhang & Shuo Huang, 2024. "Nanopore analysis of salvianolic acids in herbal medicines," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    10. Jabadurai Jayapaul & Sanna Komulainen & Vladimir V. Zhivonitko & Jiří Mareš & Chandan Giri & Kari Rissanen & Perttu Lantto & Ville-Veikko Telkki & Leif Schröder, 2022. "Hyper-CEST NMR of metal organic polyhedral cages reveals hidden diastereomers with diverse guest exchange kinetics," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    11. Ferdinand Greiss & Nicolas Lardon & Leonie Schütz & Yoav Barak & Shirley S. Daube & Elmar Weinhold & Vincent Noireaux & Roy Bar-Ziv, 2024. "A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    12. Betz, Ulrich A.K. & Arora, Loukik & Assal, Reem A. & Azevedo, Hatylas & Baldwin, Jeremy & Becker, Michael S. & Bostock, Stefan & Cheng, Vinton & Egle, Tobias & Ferrari, Nicola & Schneider-Futschik, El, 2023. "Game changers in science and technology - now and beyond," Technological Forecasting and Social Change, Elsevier, vol. 193(C).
    13. Hong Kang & Yuexuan Yang & Bryan Wei, 2024. "Synthetic molecular switches driven by DNA-modifying enzymes," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    14. 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.
    15. Colangeli, Matteo & Rugiano, Francesco & Pasero, Eros, 2014. "Pattern recognition at different scales: A statistical perspective," Chaos, Solitons & Fractals, Elsevier, vol. 64(C), pages 48-66.
    16. Luna Rizik & Loai Danial & Mouna Habib & Ron Weiss & Ramez Daniel, 2022. "Synthetic neuromorphic computing in living cells," Nature Communications, Nature, vol. 13(1), pages 1-17, 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:13:y:2022:i:1:d:10.1038_s41467-022-32526-3. 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.