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Microfluidic space coding for multiplexed nucleic acid detection via CRISPR-Cas12a and recombinase polymerase amplification

Author

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  • Zhichen Xu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Dongjuan Chen

    (Huazhong University of Science and Technology)

  • Tao Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jiayu Yan

    (Chinese Academy of Sciences
    China University of Geosciences)

  • Jiang Zhu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Ting He

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Rui Hu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Ying Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yunhuang Yang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Maili Liu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

Abstract

Fast, inexpensive, and multiplexed detection of multiple nucleic acids is of great importance to human health, yet it still represents a significant challenge. Herein, we propose a nucleic acid testing platform, named MiCaR, which couples a microfluidic device with CRISPR-Cas12a and multiplex recombinase polymerase amplification. With only one fluorescence probe, MiCaR can simultaneously test up to 30 nucleic acid targets through microfluidic space coding. The detection limit achieves 0.26 attomole, and the multiplexed assay takes only 40 min. We demonstrate the utility of MiCaR by efficiently detecting the nine HPV subtypes targeted by the 9-valent HPV vaccine, showing a sensitivity of 97.8% and specificity of 98.1% in the testing of 100 patient samples at risk for HPV infection. Additionally, we also show the generalizability of our approach by successfully testing eight of the most clinically relevant respiratory viruses. We anticipate this effective, undecorated and versatile platform to be widely used in multiplexed nucleic acid detection.

Suggested Citation

  • Zhichen Xu & Dongjuan Chen & Tao Li & Jiayu Yan & Jiang Zhu & Ting He & Rui Hu & Ying Li & Yunhuang Yang & Maili Liu, 2022. "Microfluidic space coding for multiplexed nucleic acid detection via CRISPR-Cas12a and recombinase polymerase amplification," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34086-y
    DOI: 10.1038/s41467-022-34086-y
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    References listed on IDEAS

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    1. Cheri M. Ackerman & Cameron Myhrvold & Sri Gowtham Thakku & Catherine A. Freije & Hayden C. Metsky & David K. Yang & Simon H. Ye & Chloe K. Boehm & Tinna-Sólveig F. Kosoko-Thoroddsen & Jared Kehe & Ti, 2020. "Massively multiplexed nucleic acid detection with Cas13," Nature, Nature, vol. 582(7811), pages 277-282, June.
    2. Gilberto A. Santiago & Jesús Vázquez & Sean Courtney & Katia Y. Matías & Lauren E. Andersen & Candimar Colón & Angela E. Butler & Rebecca Roulo & John Bowzard & Julie M. Villanueva & Jorge L. Muñoz-Jo, 2018. "Performance of the Trioplex real-time RT-PCR assay for detection of Zika, dengue, and chikungunya viruses," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    3. Xiong Ding & Kun Yin & Ziyue Li & Rajesh V. Lalla & Enrique Ballesteros & Maroun M. Sfeir & Changchun Liu, 2020. "Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
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    Cited by:

    1. Yichuan Chen & Xinping Wang & Junqi Zhang & Qingyuan Jiang & Bin Qiao & Baoxia He & Wenhao Yin & Jie Qiao & Yi Liu, 2024. "Split crRNA with CRISPR-Cas12a enabling highly sensitive and multiplexed detection of RNA and DNA," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Yunxiang Wang & Hong Chen & Kai Lin & Yongjun Han & Zhixia Gu & Hongjuan Wei & Kai Mu & Dongfeng Wang & Liyan Liu & Ronghua Jin & Rui Song & Zhen Rong & Shengqi Wang, 2024. "Ultrasensitive single-step CRISPR detection of monkeypox virus in minutes with a vest-pocket diagnostic device," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Chang Yeol Lee & Hyunho Kim & Ismail Degani & Hanna Lee & Angel Sandoval & Yoonho Nam & Madeleine Pascavis & Hyun Gyu Park & Thomas Randall & Amy Ly & Cesar M. Castro & Hakho Lee, 2024. "Empowering the on-site detection of nucleic acids by integrating CRISPR and digital signal processing," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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