Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network
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...
| Autores principales: | , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
American Chemical Society
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/117245 |
| _version_ | 1855526360651399168 |
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| author | 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. |
| author_browse | Fu, L. Fu, Y. Han Jianlin Hemmink, Johanneke D. Huang, X. Li, X. Liu, X. Ma, Y. Nie, X. Pan, W. Ruan, J. Steinaa, Lucilla Tang, Y. Tao, D. Xie, S. Xu, B. Zhang, Y. Zhao, C. Zhao, S. |
| author_facet | 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. |
| author_sort | Xie, S. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace117245 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | American Chemical Society |
| publisherStr | American Chemical Society |
| record_format | dspace |
| spelling | CGSpace1172452025-10-26T13:01:28Z Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network 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. crispr diagnosis 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. 2022-01-21 2021-12-27T16:41:02Z 2021-12-27T16:41:02Z Journal Article https://hdl.handle.net/10568/117245 en Open Access American Chemical Society 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. |
| spellingShingle | crispr diagnosis 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. Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network |
| title | Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network |
| title_full | Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network |
| title_fullStr | Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network |
| title_full_unstemmed | Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network |
| title_short | Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network |
| title_sort | rapid visual crispr assay a naked eye colorimetric detection method for nucleic acids based on crispr cas12a and a convolutional neural network |
| topic | crispr diagnosis |
| url | https://hdl.handle.net/10568/117245 |
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