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Kim H, Jang H, Song J, Lee SM, Lee S, Kwon HJ, Kim S, Kang T, Park HG. A CRISPR/Cas12 trans-cleavage reporter enabling label-free colorimetric detection of SARS-CoV-2 and its variants. Biosens Bioelectron 2024; 251:116102. [PMID: 38350240 DOI: 10.1016/j.bios.2024.116102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/17/2024] [Accepted: 02/03/2024] [Indexed: 02/15/2024]
Abstract
We present a label-free colorimetric CRISPR/Cas-based method enabling affordable molecular diagnostics for SARS-CoV-2. This technique utilizes 3,3'-diethylthiadicarbocyanine iodide (DISC2(5)) which exhibits a distinct color transition from purple to blue when it forms dimers by inserting into the duplex of the thymidine adenine (TA) repeat sequence. Loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA) was used to amplify target samples, which were subsequently subjected to the CRISPR/Cas12a system. The target amplicons would activate Cas12a to degrade nearby TA repeat sequences, preserving DISC2(5) in its free form to display purple as opposed to blue in the absence of the target. Based on this design approach, SARS-CoV-2 RNA was colorimetrically detected very sensitively down to 2 copies/μL, and delta and omicron variants of SARS-CoV-2 were also successfully identified. The practical diagnostic utility of this method was further validated by reliably identifying 179 clinical samples including 20 variant samples with 100% clinical sensitivity and specificity. This technique has the potential to become a promising CRISPR-based colorimetric platform for molecular diagnostics of a wide range of target pathogens.
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sang Mo Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, KRIBB, 181 Ipsin-gil, Jeongeup, Jeollabuk-do, 56212, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju, Gyeongsangnam-do, 52727, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Wang R, Liu Y, Chen S, Bai L, Guo K, Pang Y, Qian F, Li Y, Ding L, Wang Y. utPCR: A Strategy for the Highly Specific and Absolutely Quantitative Detection of Single Molecules within Only Minutes. Biosensors 2023; 13:910. [PMID: 37887103 PMCID: PMC10605045 DOI: 10.3390/bios13100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Bloodstream infection is a major health problem worldwide, with extremely high mortality. Detecting infection in the early stage is challenging due to the extremely low concentration of bacteria in the blood. Digital PCR provides unparalleled sensitivity and can achieve absolute quantification, but it is time-consuming. Moreover, the presence of unavoidable background signals in negative controls poses a significant challenge for single-molecule detection. Here, we propose a novel strategy called "Ultrafast flexible thin tube-based droplet digital PCR (utPCR)" that can shorten the digital PCR process from 2 h to only 5 min, with primer annealing/extension time reduced from minutes to only 5 s. Importantly, the ultrafast PCR eliminates nonspecific amplification and thus enables single-molecule detection. The utPCR enabled the sensitive detection and digital quantification of E. coli O157 in the high background of a 106-fold excess of E. coli K12 cells. Moreover, this method also displayed the potential to detect rare pathogens in blood samples, and the limit of detection (LOD) could be as low as 10 CFU per mL of blood without false positive results. Considered ultrafast (<5 min) and highly sensitive (single-molecule detection), the utPCR holds excellent prospects in the next generation of molecular diagnosis.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Ying Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
| | - Shuaiwei Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
| | - Linlin Bai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
| | - Kaiming Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
| | - Yanan Pang
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
| | - Yongfang Li
- School of Food Science and Engineering, Foshan University, Foshan 528231, China
| | - Li Ding
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Human Phenome Institute, Pudong Hospital, Fudan University, Shanghai 200438, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
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Zhang X, Yang Y, Cao J, Qi Z, Li G. Point-of-care CRISPR/Cas biosensing technology: A promising tool for preventing the possible COVID-19 resurgence caused by contaminated cold-chain food and packaging. Food Front 2022; 4:FFT2176. [PMID: 36712576 PMCID: PMC9874772 DOI: 10.1002/fft2.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/1912] [Revised: 12/12/1912] [Accepted: 12/12/1912] [Indexed: 02/01/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused great public health concern and has been a global threat due to its high transmissibility and morbidity. Although the SARS-CoV-2 transmission mainly relies on the person-to-person route through the respiratory droplets, the possible transmission through the contaminated cold-chain food and packaging to humans has raised widespread concerns. This review discussed the possibility of SARS-CoV-2 transmission via the contaminated cold-chain food and packaging by tracing the occurrence, the survival of SARS-CoV-2 in the contaminated cold-chain food and packaging, as well as the transmission and outbreaks related to the contaminated cold-chain food and packaging. Rapid, accurate, and reliable diagnostics of SARS-CoV-2 is of great importance for preventing and controlling the COVID-19 resurgence. Therefore, we summarized the recent advances on the emerging clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system-based biosensing technology that is promising and powerful for preventing the possible COVID-19 resurgence caused by the contaminated cold-chain food and packaging during the COVID-19 pandemic, including CRISPR/Cas system-based biosensors and their integration with portable devices (e.g., smartphone, lateral flow assays, microfluidic chips, and nanopores). Impressively, this review not only provided an insight on the possibility of SARS-CoV-2 transmission through the food supply chain, but also proposed the future opportunities and challenges on the development of CRISPR/Cas system-based detection methods for the diagnosis of SARS-CoV-2.
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Affiliation(s)
- Xianlong Zhang
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Yan Yang
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Juanjuan Cao
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Zihe Qi
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Guoliang Li
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
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Zhang Z, Zhao S, Jiang L, Wu J, Zhao W, Guo X, Peng N, Hu F. A sample-to-answer DNA detection microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR. Analyst 2022; 147:4876-4887. [DOI: 10.1039/d2an00908k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a microfluidic system integrating sample pretreatment and smartphone-readable gradient plasmonic photothermal continuous-flow PCR, paving the way for low-cost and rapid implementation of PCR diagnostics.
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Affiliation(s)
- Zengming Zhang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Shuhao Zhao
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Lei Jiang
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Junjun Wu
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Wenhan Zhao
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Xiaoniu Guo
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Niancai Peng
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
| | - Fei Hu
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University No. 99, Yanxiang Road, Xi'an, 710054, P. R. China
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