Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network
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Title |
Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network
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Creator |
Xie, S.
Tao, D. Fu, Y. Xu, B. Tang, Y. Steinaa, Lucilla Hemmink, Johanneke D. Pan, W. Huang, X. Nie, X. Zhao, C. Ruan, J. Zhang, Y. Han, Jianlin Fu, L. Ma, Y. Li, X. Liu, X. Zhao, S. |
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Subject |
crispr
diagnosis |
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Description |
This article is made available via the ACS COVID-19 subset (https://pubs.acs.org/page/vi/chemistry_coronavirus_research) for unrestricted RESEARCH re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization declaration of COVID-19 as a global pandemic. Rapid diagnosis based on naked-eye colorimetric detection remains challenging, but it could build new capacities for molecular point-of-care testing (POCT). In this study, we evaluated the performance of 16 types of single-stranded DNA-fluorophore-quencher (ssDNA-FQ) reporters for use with clusters of regularly spaced short palindrome repeats (CRISPR)/Cas12a-based visual colorimetric assays. Among them, nine ssDNA-FQ reporters were found to be suitable for direct visual colorimetric detection, with especially very strong performance using ROX-labeled reporters. We optimized the reaction concentrations of these ssDNA-FQ reporters for a naked-eye read-out of assay results (no transducing component required for visualization). In particular, we developed a convolutional neural network algorithm to standardize and automate the analytical colorimetric assessment of images and integrated this into the MagicEye mobile phone software. A field-deployable assay platform named RApid VIsual CRISPR (RAVI-CRISPR) based on a ROX-labeled reporter with isothermal amplification and CRISPR/Cas12a targeting was established. We deployed RAVI-CRISPR in a single tube toward an instrument-less colorimetric POCT format that required only a portable rechargeable hand warmer for incubation. The RAVI-CRISPR was successfully used for the high-sensitivity detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and African swine fever virus (ASFV). Our study demonstrates this RAVI-CRISPR/MagicEye system to be suitable for distinguishing different pathogenic nucleic acid targets with high specificity and sensitivity as the simplest-to-date platform for rapid pen- or bed-side testing. |
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Date |
2022-01-21
2021-12-27T16:41:02Z 2021-12-27T16:41:02Z |
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Type |
Journal Article
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Identifier |
Xie, S., Tao, D., Fu, Y., Xu, B., Tang, Y., Steinaa, L., Hemmink, J.D., Pan, W., Huang, X., Nie, X., Zhao, C., Ruan, J., Zhang, Y., Han, J., Fu, L., Ma, Y., Li, X., Liu, X. and Zhao, S. 2022. Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network. ACS Synthetic Biology 11(1): 383–396.
2161-5063 https://hdl.handle.net/10568/117245 https://doi.org/10.1021/acssynbio.1c00474 |
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Language |
en
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Rights |
Other
Open Access |
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Format |
383-396
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Publisher |
American Chemical Society (ACS)
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Source |
ACS Synthetic Biology
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