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CRISPR-induced DNA reorganization for multiplexed nucleic acid detection

Author

Listed:
  • Margot Karlikow

    (University of Toronto)

  • Evan Amalfitano

    (University of Toronto)

  • Xiaolong Yang

    (University of Toronto)

  • Jennifer Doucet

    (University of Toronto)

  • Abigail Chapman

    (University of British Columbia)

  • Peivand Sadat Mousavi

    (University of Toronto)

  • Paige Homme

    (University of Toronto)

  • Polina Sutyrina

    (University of Toronto)

  • Winston Chan

    (University of Toronto)

  • Sofia Lemak

    (University of Toronto)

  • Alexander F. Yakunin

    (University of Toronto
    Bangor University)

  • Adam G. Dolezal

    (University of Illinois at Urbana–Champaign)

  • Shana Kelley

    (University of Toronto
    University of Toronto
    University of Toronto
    Northwestern University)

  • Leonard J. Foster

    (University of British Columbia)

  • Brock A. Harpur

    (Purdue University)

  • Keith Pardee

    (University of Toronto
    University of Toronto)

Abstract

Nucleic acid sensing powered by the sequence recognition of CRIPSR technologies has enabled major advancement toward rapid, accurate and deployable diagnostics. While exciting, there are still many challenges facing their practical implementation, such as the widespread need for a PAM sequence in the targeted nucleic acid, labile RNA inputs, and limited multiplexing. Here we report FACT (Functionalized Amplification CRISPR Tracing), a CRISPR-based nucleic acid barcoding technology compatible with Cas12a and Cas13a, enabling diagnostic outputs based on cis- and trans-cleavage from any sequence. Furthermore, we link the activation of CRISPR-Cas12a to the expression of proteins through a Reprogrammable PAIRing system (RePAIR). We then combine FACT and RePAIR to create FACTOR (FACT on RePAIR), a CRISPR-based diagnostic, that we use to detect infectious disease in an agricultural use case: honey bee viral infection. With high specificity and accuracy, we demonstrate the potential of FACTOR to be applied to the sensing of any nucleic acid of interest.

Suggested Citation

  • Margot Karlikow & Evan Amalfitano & Xiaolong Yang & Jennifer Doucet & Abigail Chapman & Peivand Sadat Mousavi & Paige Homme & Polina Sutyrina & Winston Chan & Sofia Lemak & Alexander F. Yakunin & Adam, 2023. "CRISPR-induced DNA reorganization for multiplexed nucleic acid detection," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36874-6
    DOI: 10.1038/s41467-023-36874-6
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    References listed on IDEAS

    as
    1. Evan Amalfitano & Margot Karlikow & Masoud Norouzi & Katariina Jaenes & Seray Cicek & Fahim Masum & Peivand Sadat Mousavi & Yuxiu Guo & Laura Tang & Andrew Sydor & Duo Ma & Joel D. Pearson & Daniel Tr, 2021. "A glucose meter interface for point-of-care gene circuit-based diagnostics," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    2. 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.
    3. Yongmoon Jeon & You Hee Choi & Yunsu Jang & Jihyeon Yu & Jiyoung Goo & Gyejun Lee & You Kyeong Jeong & Seung Hwan Lee & In-San Kim & Jin-Soo Kim & Cherlhyun Jeong & Sanghwa Lee & Sangsu Bae, 2018. "Direct observation of DNA target searching and cleavage by CRISPR-Cas12a," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    4. Gallai, Nicola & Salles, Jean-Michel & Settele, Josef & Vaissière, Bernard E., 2009. "Economic valuation of the vulnerability of world agriculture confronted with pollinator decline," Ecological Economics, Elsevier, vol. 68(3), pages 810-821, January.
    5. Daphne Collias & Chase L. Beisel, 2021. "CRISPR technologies and the search for the PAM-free nuclease," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    6. Benjamin P. Kleinstiver & Michelle S. Prew & Shengdar Q. Tsai & Ved V. Topkar & Nhu T. Nguyen & Zongli Zheng & Andrew P. W. Gonzales & Zhuyun Li & Randall T. Peterson & Jing-Ruey Joanna Yeh & Martin J, 2015. "Engineered CRISPR-Cas9 nucleases with altered PAM specificities," Nature, Nature, vol. 523(7561), pages 481-485, July.
    7. Ines Fonfara & Hagen Richter & Majda Bratovič & Anaïs Le Rhun & Emmanuelle Charpentier, 2016. "The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA," Nature, Nature, vol. 532(7600), pages 517-521, April.
    8. Gallai, Nicola & Salles, Jean-Michel & Settele, Josef & Vaissière, Bernard E., 2009. "Economic valuation of the vulnerability of world agriculture confronted with pollinator decline," Ecological Economics, Elsevier, vol. 68(3), pages 810-821, January.
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    Cited by:

    1. Jeong Moon & Changchun Liu, 2023. "Asymmetric CRISPR enabling cascade signal amplification for nucleic acid detection by competitive crRNA," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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