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A one-pot CRISPR/Cas13a-based contamination-free biosensor for low-cost and rapid nucleic acid diagnostics


Available online 13 January 2022, 113994

Biosensors and Bioelectronics rights and content


A one-pot CRISPR/Cas13a-based visual biosensor for the rapid and low-cost nucleic acid detection is proposed.

With a newly developed tube-in-tube vessel used in the biosensor, aerosol cross contamination could be completely avoided.

The sensor can not only detect pathogen nucleic acids less than 30min without any special equipment, but also be used in conjunction with an automated miniaturized instrument to perform the contamination-free detection of multiple nucleic acid samples without any manual operation.

The newly developed biosensor detection results were consistent with the results of traditional fluorescence quantitative PCR detection, and the detection sensitivity reached 3 copy/uL.


The pandemic due to the outbreak of 2019 coronavirus disease (COVID-19) caused by novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has raised significant public health concerns. Rapid, affordable, and accurate diagnostic testing not only paves the way for the effective treatment of diseases, but also plays a crucial role in preventing the spreading of infectious diseases. Herein, a one-pot CRISPR/Cas13a-based visual biosensor was proposed and developed for the rapid and low-cost nucleic acid detection. By combining Cas13a cleavage and Recombinase Polymerase Amplification (RPA) in a one-pot reaction in a disposable tube-in-tube vessel, amplicon contamination could be completely avoided. The RPA reaction is carried out in the inner tube containing two hydrophobic holes at the bottom. After the completion of amplification reaction, the reaction solution enters the outer tube containing pre-stored Cas13a reagent under the action of centrifugation or shaking. Inner and outer tubes are combined to form an independent reaction pot to complete the nucleic acid detection without opening the lid. This newly developed nucleic acid detection method not only meets the need of rapid nucleic acid detection at home without the need for any specialized equipment, but also fulfils the requirement of rapid on-site nucleic acid detection with the aid of small automated instruments. In this study, CRISPR/Cas13a and CRISPR/Cas12a were used to verify the reliability of the developed one-pot nucleic acid detection method. The performance of the system was verified by detecting the DNA virus, i.e., African swine fever virus (ASFV) and the RNA virus, i.e., SARS-Cov-2. The results indicate that the proposed method possesses a limit of detection of 3 copy/μL. The negative and positive test results are consistent with the results of real-time fluorescence quantitative polymerase chain reaction (PCR), but the time required is shorter and the cost is lower. Thus, this study makes this method available in resource-limited areas for the purpose of large-scale screening and in case of epidemic outbreak.



One-pot reaction

Nucleic acid diagnostics

Contamination-free detection

Low-cost detection

View Abstract

© 2022 Elsevier B.V. All rights reserved.

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