Record Details

Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network

CGSpace

View Archive Info
 
 
Field Value
 
Title Rapid visual CRISPR assay: A naked-eye colorimetric detection method for nucleic acids based on CRISPR/Cas12a and a convolutional neural network
 
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.
 
Subject crispr
diagnosis
 
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.
 
Date 2022-01-21
2021-12-27T16:41:02Z
2021-12-27T16:41:02Z
 
Type Journal Article
 
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
 
Language en
 
Rights Other
Open Access
 
Format 383-396
 
Publisher American Chemical Society (ACS)
 
Source ACS Synthetic Biology