1
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Hu J, Yu Y, Pan X, Yue Han, She X, Liu X, Zhang Q, Gai H, Zong C. Highly sensitive and specific detection of human papillomavirus type 16 using CRISPR/Cas12a assay coupled with an enhanced single nanoparticle dark-field microscopy imaging technique. Talanta 2024; 278:126449. [PMID: 38908140 DOI: 10.1016/j.talanta.2024.126449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
Human papillomavirus (HPV) is a prevalent sexually transmitted pathogen associated with cervical cancer. Detecting high-risk HPV (hr-HPV) infections is crucial for cervical cancer prevention, particularly in resource-limited settings. Here, we present a highly sensitive and specific sensor for HPV-16 detection based on CRISPR/Cas12a coupled with enhanced single nanoparticle dark-field microscopy (DFM) imaging techniques. Ag-Au satellites were assembled through the hybridization of AgNPs-based spherical nucleic acid (Ag-SNA) and AuNPs-based spherical nucleic acid (Au-SNA), and their disassembly upon target-mediated cleavage by the Cas12a protein was monitored using DFM for HPV-16 quantification. To enhance the cleavage efficiency and detection sensitivity, the composition of the ssDNA sequences on Ag-SNA and Au-SNA was optimized. Additionally, we explored using the SynSed technique (synergistic sedimentation of Brownian motion suppression and dehydration transfer) as an alternative particle transfer method in DFM imaging to traditional electrostatic deposition. This addresses the issue of inconsistent deposition efficiency of Ag-Au satellites and their disassembly due to their size and charge differences. The sensor achieved a remarkable limit of detection (LOD) of 10 fM, lowered by 9-fold compared to traditional electrostatic deposition methods. Clinical testing in DNA extractions from 10 human cervical swabs demonstrated significant response differences between the positive and negative samples. Our sensor offers a promising solution for sensitive and specific HPV-16 detection, with implications for cancer screening and management.
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Affiliation(s)
- Jiajia Hu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Yang Yu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Xiaoyan Pan
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Yue Han
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Xinyi She
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Xiaojun Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Qingquan Zhang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Hongwei Gai
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Chenghua Zong
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China.
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2
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Sun H, Zhang X, Ma H, Zhang L, Zhang Y, Sun R, Zheng H, Wang H, Guo J, Liu Y, Wang Y, Qi Y. A programmable sensitive platform for pathogen detection based on CRISPR/Cas12a -hybridization chain reaction-poly T-Cu. Anal Chim Acta 2024; 1317:342888. [PMID: 39030018 DOI: 10.1016/j.aca.2024.342888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/18/2024] [Accepted: 06/17/2024] [Indexed: 07/21/2024]
Abstract
Rapid and sensitive detection of pathogenic bacteria is crucial for disease prevention and control. The CRISPR/Cas12a system with the DNA cleavage capability holds promise in pathogenic bacteria diagnosis. However, the sensitivity of CRISPR-based assays remains a challenge. Herein, we report a versatile and sensitive pathogen sensing platform (HTCas12a) based on the CRISPR/Cas12a system, hybridization chain reaction (HCR) and Poly T-copper fluorescence nanoprobe. The sensitivity is improved by HCR and the Poly-T-Cu reporter probe reduces the overall experiment cost to less than one dollar per sample. Our results demonstrate the specific recognition of target nucleic acid fragments from other pathogens. Furthermore, a good linear correlation between fluorescence intensity and target quantities were achieved with detection limits of 23.36 fM for Target DNA and 4.17 CFU/mL for S.aureus, respectively. The HTCas12a system offers a universal platform for pathogen detection in various fields, including environmental monitoring, clinical diagnosis, and food safety.
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Affiliation(s)
- Haolin Sun
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Xiaoyu Zhang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Hainan Ma
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Lina Zhang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yang Zhang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Ruimeng Sun
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Haoran Zheng
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Han Wang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Jiayu Guo
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yanqi Liu
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yurou Wang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yanfei Qi
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China.
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3
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Zhuang L, Gong J, Zhang P, Zhang D, Zhao Y, Yang J, Liu G, Zhang Y, Shen Q. Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications. DISCOVER NANO 2024; 19:124. [PMID: 39105889 DOI: 10.1186/s11671-024-04075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Guofang Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China.
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4
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Yao Z, He K, Wang H, Feng S, Ding X, Xu Y, Wang Q, Xu X, Wu Q, Wang L. Tuning the Dynamic Reaction Balance of CRISPR/Cas12a and RPA in One Pot: A Key to Switch Nucleic Acid Quantification. ACS Sens 2024; 9:3511-3519. [PMID: 38651662 DOI: 10.1021/acssensors.3c02485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Excavating nucleic acid quantitative capabilities by combining clustered regularly interspaced short palindromic repeats (CRISPR) and isothermal amplification in one pot is of common interest. However, the mutual interference between CRISPR cleavage and isothermal amplification is the primary obstacle to quantitative detection. Though several works have demonstrated enhanced detection sensitivity by reducing the inhibition of CRISPR on amplification in one pot, few paid attention to the amplification process and even dynamic reaction processes between the two. Herein, we find that DNA quantification can be realized by regulating either recombinase polymerase amplification (RPA) efficiency or CRISPR/Cas12a cleaving efficiency (namely, tuning the dynamic reaction balance) in one pot. The sensitive quantification is realized by utilizing dual PAM-free crRNAs for CRISPR/Cas12a recognition. The varied RPA primer concentration with stabilized CRISPR systems significantly affects the amplification efficiency and quantitative performances. Alternatively, quantitative detection can also be achieved by stabilizing the amplification process while regulating the CRISPR/Cas12a concentration. The quantitative capability is proved by detecting DNA targets from Lactobacillus acetotolerans and SARS-CoV-2. The quantitative performance toward real samples is comparable to quantitative real-time PCR for detecting L. acetotolerans spiked in fermented food samples and SARS-CoV-2 clinical samples. We expect that the presented method will be a powerful tool for quantifying other nucleic acid targets.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hongmei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Suyin Feng
- Department of Neurosurgery, Affiliated Hospital of Jiangnan University, Wuxi 214062, China
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Xiaoqing Ding
- Department of Laboratory Medicine, Affiliated Hospital of Jiangnan University, Wuxi 214062, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
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5
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Pan CY, Kijamnajsuk P, Chen JJ. Portable loop-mediated isothermal amplification device with spectrometric detection for rapid pathogen identification. Anal Biochem 2024; 694:115615. [PMID: 39002745 DOI: 10.1016/j.ab.2024.115615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
With the rise in extreme weather due to global warming, coupled with globalization facilitating the spread of infectious diseases, there's a pressing need for portable testing platforms offering simplicity, low cost, and remote transmission, particularly beneficial in resource-limited and non-urban areas. We have developed a portable device using loop-mediated isothermal amplification (LAMP) with spectrometric detection to identify Salmonella Typhimurium DNA. The device utilizes the LinkIt 7697 microcontroller and a microspectrometer to capture and transmit spectral signals in real-time, allowing for improved monitoring and analysis of the reaction progress. We built a hand-held box containing a microspectrometer, thermoelectric cooler, ultraviolet LED, disposable reaction tube, and homemade thermal module, all powered by rechargeable batteries. Additionally, we conducted thorough experiments to ensure temperature accuracy within 1 °C under thermal control, developed a heating module with a LinkIt 7697 IoT development board to heat the DNA mixture to the reaction temperature within 3 min, and integrated foam insulation and a 3D-printed frame to enhance the device's thermal stability. We successfully demonstrated the amplification of Salmonella Typhimurium DNA with an impressive sensitivity of 2.83 × 10-4 ng/μL. A remote webpage interface allows for monitoring the temperature and fluorescence during the LAMP process, improving usability. This portable LAMP device with real-time detection offers a cost-effective solution for detecting Salmonella Typhimurium in food products. Its unique design and capabilities make it a promising tool for ensuring food safety.
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Affiliation(s)
- Chun Yu Pan
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
| | - Puchong Kijamnajsuk
- Department of Physics, Kasetsart University, 50 Ngamwongwan Rd, Lat Yao, Chatuchak, Bangkok, 10900, Thailand.
| | - Jyh Jian Chen
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
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6
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Qiu M, Yuan Z, Li N, Yang X, Zhang X, Jiang Y, Zhao Q, Man C. Self-assembled bifunctional nanoflower-enabled CRISPR/Cas biosensing platform for dual-readout detection of Salmonella enterica. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134323. [PMID: 38640680 DOI: 10.1016/j.jhazmat.2024.134323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
Sensitive detection and point-of-care test of bacterial pathogens is of great significance in safeguarding the public health worldwide. Inspired by the characteristics of horseradish peroxidase (HRP), we synthesized a hybrid nanoflower with peroxidase-like activity via a three-component self-assembled strategy. Interestingly, the prepared nanozyme not only could act as an alternative to HRP for colorimetric biosensing, but also function as a unique signal probe that could be recognized by a pregnancy test strip. By combining the bifunctional properties of hybrid nanoflower, isothermal amplification of LAMP, and the specific recognition and non-specific cleavage properties of CRISPR/Cas12a system, the dual-readout CRISPR/Cas12a biosensor was developed for sensitive and rapid detection of Salmonella enterica. Moreover, this platform in the detection of Salmonella enterica had limits of detection of 1 cfu/mL (colorimetric assay) in the linear range of 101-108 cfu/mL and 102 cfu/mL (lateral flow assay) in the linear range of 102-108 cfu/mL, respectively. Furthermore, the developed biosensor exhibited good recoveries in the spiked samples (lake water and milk) with varying concentrations of Salmonella enterica. This work provides new insights for the design of multifunctional nanozyme and the development of innovative dual-readout CRISPR/Cas system-based biosensing platform for the detection of pathogens.
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Affiliation(s)
- Manyan Qiu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhiyu Yuan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Nan Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xianlong Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
| | - Qianyu Zhao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
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7
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Kou J, Li Y, Zhao Z, Qiao J, Zhang Q, Han X, Cheng X, Man S, Ma L. Simultaneous Dual-Gene Test of Methicillin-Resistant Staphylococcus Aureus using an Argonaute-Centered Portable and Visual Biosensor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311764. [PMID: 38506607 DOI: 10.1002/smll.202311764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Indexed: 03/21/2024]
Abstract
The development of novel method for drug-resistant bacteria detection is imperative. A simultaneous dual-gene Test of methicillin-resistant Staphylococcus aureus (MRSA) is developed using an Argonaute-centered portable biosensor (STAR). This is the first report concerning Argonaute-based pathogenic bacteria detection. Simply, the species-specific mecA and nuc gene are isothermally amplified using loop-mediated isothermal amplification (LAMP) technique, followed by Argonaute-based detection enabled by its programmable, guided, sequence-specific recognition and cleavage. With the strategy, the targeted nucleic acid signals gene are dexterously converted into fluorescent signals. STAR is capable of detecting the nuc gene and mecA gene simultaneously in a single reaction. The limit of detection is 10 CFU/mL with a dynamic range from 10 to 107 CFU/mL. The sample-to-result time is <65 min. This method is successfully adapted to detect clinical samples, contaminated foods, and MRSA-infected animals. This work broadens the reach of Argonaute-based biosensing and presents a novel bacterial point-of-need (PON) detection platform.
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Affiliation(s)
- Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, 300250, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
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8
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Han X, Lu M, Zhang Y, Liu X, Zhang Q, Bai X, Man S, Zhao L, Ma L. A Thermostable Cas12b-Powered Bioassay Coupled with Loop-Mediated Isothermal Amplification in a Customized "One-Pot" Vessel for Visual, Rapid, Sensitive, and On-Site Detection of Genetically Modified Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11195-11204. [PMID: 38564697 DOI: 10.1021/acs.jafc.4c01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genetically modified crops (GMCs) have been discussed due to unknown safety, and thus, it is imperative to develop an effective detection technology. CRISPR/Cas is deemed a burgeoning technology for nucleic acid detection. Herein, we developed a novel detection method for the first time, which combined thermostable Cas12b with loop-mediated isothermal amplification (LAMP), to detect genetically modified (GM) soybeans in a customized one-pot vessel. In our method, LAMP-specific primers were used to amplify the cauliflower mosaic virus 35S promoter (CaMV35S) of the GM soybean samples. The corresponding amplicons activated the trans-cleavage activity of Cas12b, which resulted in the change of fluorescence intensity. The proposed bioassay was capable of detecting synthetic plasmid DNA samples down to 10 copies/μL, and as few as 0.05% transgenic contents could be detected in less than 40 min. This work presented an original detection method for GMCs, which performed rapid, on-site, and deployable detection.
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Affiliation(s)
- Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yaru Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xinru Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Qiang Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
- Branch of Tianjin Third Central Hospital, Tianjin 300457, China
| | - Xue Bai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing, Ministry of Agriculture, Beijing 100193, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Liangjuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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9
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Zhou C, Zhao Y, Guo B, Yang M, Xu Q, Lei C, Wang H. Establishment of a Simple, Sensitive, and Specific Salmonella Detection Method Based on Recombinase-Aided Amplification Combined with dsDNA-Specific Nucleases. Foods 2024; 13:1380. [PMID: 38731750 PMCID: PMC11083397 DOI: 10.3390/foods13091380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Salmonella is a common foodborne pathogen that can cause food poisoning, posing a serious threat to human health. Therefore, quickly, sensitively, and accurately detecting Salmonella is crucial to ensuring food safety. For the Salmonella hilA gene, we designed Recombinase-aided amplification (RAA) primers and dsDNA-specific nuclease (DNase) probes. The ideal primer and probe combination was found when conditions were optimized. Under UV light, a visual Salmonella detection technique (RAA-dsDNase) was developed. Additionally, the RAA-dsDNase was modified to further reduce pollution hazards and simplify operations. One-pot RAA-dsDNase-UV or one-pot RAA-dsDNase-LFD was developed as a Salmonella detection method, using UV or a lateral flow dipstick (LFD) for result observation. Among them, one-pot RAA-dsDNase and one-pot RAA-dsDNase-LFD had detection times of 50 min and 60 min, respectively, for detecting Salmonella genomic DNA. One-pot RAA-dsDNase-UV had a detection limit of 101 copies/μL and 101 CFU/mL, while one-pot RAA-dsDNase-LFD had a sensitivity of 102 copies/μL and 102 CFU/mL. One-pot RAA-dsDNase-UV and one-pot RAA-dsDNase-LFD assays may identify 17 specific Salmonella serovars witho ut causing a cross-reaction with the remaining 8 bacteria, which include E. coli. Furthermore, Salmonella in tissue and milk samples has been reliably detected using both approaches. Overall, the detection method developed in this study can quickly, sensitively, and accurately detect Salmonella, and it is expected to become an important detection tool for the prevention and control of Salmonella in the future.
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Affiliation(s)
- Changyu Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Yu Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Boyan Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Ming Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Qiang Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610017, China; (C.Z.); (Y.Z.); (B.G.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
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10
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Wang Y, Du P, Shao Y, Wang W, Liu Y, Ma Y, Hu P, Cao J, Wang X, Abd El-Aty AM. An Innovative and Efficient Fluorescent Detection Technique for Salmonella in Animal-Derived Foods Using the CRISPR/Cas12a-HCR System Combined with PCR/RAA. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8831-8839. [PMID: 38575365 DOI: 10.1021/acs.jafc.3c08829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Here, we present a method for Salmonella detection using clustered regularly interspaced short palindromic repeats associated with the CRISPR-associated protein 12a-hybridization chain reaction (CRISPR/Cas12a-HCR) system combined with polymerase chain reaction/recombinase-assisted amplification (PCR/RAA) technology. The approach relies on the Salmonella invA gene as a biorecognition element and its amplification through PCR and RAA. In the presence of the target gene, Cas12a, guided by crRNA, recognizes and cleaves the amplification product, initiating the HCR. Fluorescently labeled single-stranded DNA (ssDNA) H1 and H2 were introduced, and the Salmonella concentration was determined based on the fluorescence intensity from the triggered HCR. Both assays demonstrate high specificity, sensitivity, simplicity, and rapidity. The detection range was 2 × 101-2 × 109 CFU/mL, with an LOD of 20 CFU/mL, and the entire process enabled specific and rapid Salmonella detection within 85-105 min. Field-incurred spiked recovery tests were conducted in mutton and beef samples using both assays, demonstrating satisfactory recovery and accuracy in animal-derived foods. By combining CRISPR/Cas12a with hybridization chain reaction technology, this study presents a rapid and sensitive Salmonella detection method that is crucial for identifying pathogenic bacteria and monitoring food safety.
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Affiliation(s)
- Yuanshang Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Pengfei Du
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiting Wang
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Yaobo Liu
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Yanli Ma
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Peng Hu
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Jianfang Cao
- Institute of Food & Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Agro-Products Processing Technology, Key Laboratory of Novel Food Resources Processing, Ministry of Agriculture, Jinan 250100, China
| | - Xiaohong Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
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11
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Tang X, Lu M, Wang J, Man S, Peng W, Ma L. Recent Advances of DNA-Templated Metal Nanoclusters for Food Safety Detection: From Synthesis, Applications, Challenges, and Beyond. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5542-5554. [PMID: 38377578 DOI: 10.1021/acs.jafc.3c09621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Food safety concerns have become a significant threat to human health and well-being, catching global attention in recent years. As a result, it is imperative to research conceptually novel biosensing and effective techniques for food matrices detection. Currently, DNA-templated metal nanoclusters (DNA-MNCs) are considered as one of the most promising nanomaterials due to their excellent properties in biosensing. While DNA-MNCs have garnered increasing interest, the reviews of design strategies, applications, and futuristic prospects for biosensing have been hardly found especially in food safety. The synthesis of DNA-MNCs and their use as biosensing materials in food contamination detection, including pathogenic bacteria, toxins, heavy metals, residues of pesticides, and others were comprehensively reviewed. In addition, we summarize the properties of DNA-MNCs briefly and discuss the challenges and future trends. The application of DNA-MNCs powered biosensing has been demonstrated and actively studied, which is a promising paradigm for food safety testing that can supplement or even replace current existing methods. Despite the challenges of difficulty regulating accurately, poor stability, low quantum yield, and difficult commercial transformation, the application prospects of DNA-MNCs biosensors are promising. This review aims to provide insights and directions for the future development of DNA-MNCs based food detection technology.
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Affiliation(s)
- Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiajing Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Weipan Peng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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12
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Yang R, Xie S, Zhou B, Guo M, Fan J, Su F, Ji Z, Chen Y, Li B. Postamplifying Cas12a Activation through Hybridization Chain Reaction-Triggered Fluorescent Nanocluster Formation for Ultrasensitive Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:9890-9899. [PMID: 38353672 DOI: 10.1021/acsami.3c18732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
CRISPR/Cas12a-based biosensing is advancing rapidly; however, achieving sensitive and cost-effective reporting of Cas12a activation remains a challenge. In response, we have developed a label-free system capable of postamplifying Cas12a activation by integrating hybridization chain reaction (HCR) and DNA-copper nanoclusters (DNA-CuNCs). The trans-cleavage of Cas12a triggers a silenced HCR, leading to the in situ assembly of fluorescent DNA-CuNCs, allowing for the turn-on reporting of Cas12a activation. Without preamplification, this assay can detect DNA with a detection limit of 5 fM. Furthermore, when coupled with preamplification, the system achieves exceptional sensitivity, detecting the monkeypox virus (MPXV) plasmid at 1 copy in human serum. In a MPXV pseudovirus-based validation test, the obtained results are in agreement with those obtained by qPCR, reinforcing the robustness of this method. Our study represents the first effort to manipulate DNA-CuNC formation on HCR for highly sensitive and cost-effective reporting of Cas12a, resulting in an efficient synthetic biology-enabled sensing platform for biosafety applications.
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Affiliation(s)
- Runlin Yang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
- School of Public Health, Xiamen University, Xiamen 361102, China
| | - Bin Zhou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Mingming Guo
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Jun Fan
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Fengli Su
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Zhirun Ji
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing 211166, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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13
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Duan M, Zhao Y, Liu Y, He Y, Dai R, Chen J, Li X, Jia F. A low-background and wash-free signal amplification F-CRISPR biosensor for sensitive quantitative and visible qualitative detection of Salmonella Typhimurium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168905. [PMID: 38016549 DOI: 10.1016/j.scitotenv.2023.168905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023]
Abstract
In traditional CRISPR-based biosensors, the cleavage-induced signal generation is insufficient because only a signals is generated at a CRISPR-induced cleavage. Herein, we developed an improved CRISPR/Cas12a-based biosensor with an enlarged signal generation which integrated the hybridization chain reaction (HCR) and low-background Förster Resonance Energy Transfer (FRET) signal output mode. The HCR with nucleic acid self-assembly capability was used as a signal carrier to load more signaling molecules. To get the best signal amplification, three different fluorescence signal output modes (fluorescence recovery, FRET and low-background FRET) generated by two fluoresceins, FAM and Cy5, were fully investigated and compared. The results indicated that the low-background FRET signal output mode with the strictest signal generation conditions yielded the highest signal-to-noise ratio (S/N) (19.17) and the most obvious fluorescence color change (from red to yellow). In optimal conditions, the proposed biosensor was successfully applied for Salmonella Typhimurium (S. Typhimurium) detection with 6 h (including 4 h for sample pre-treatment) from the initial target processing to the final detection result. The qualitative sensitivity, reliant on color changes, was 103 CFU/mL. The quantitative sensitivity, calculated by the fluorescence value, were 1.62 × 101 CFU/mL, 3.72 × 102 CFU/mL, and 8.71 × 102 CFU/mL in buffer solution, S. Typhimurium-spiked milk samples, and S.Typhimurium-spiked chicken samples, respectively. The excellent detection performance of the proposed biosensor endowed its great application potential in food and environment safety monitoring.
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Affiliation(s)
- Miaolin Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yijie Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yana Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ruitong Dai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xingmin Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Fei Jia
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
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14
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Higuera-Ciapara I, Benitez-Vindiola M, Figueroa-Yañez LJ, Martínez-Benavidez E. Polyphenols and CRISPR as Quorum Quenching Agents in Antibiotic-Resistant Foodborne Human Pathogens ( Salmonella Typhimurium, Campylobacter jejuni and Escherichia coli 0157:H7). Foods 2024; 13:584. [PMID: 38397561 PMCID: PMC10888066 DOI: 10.3390/foods13040584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 02/25/2024] Open
Abstract
Antibiotic resistance in foodborne pathogens is an increasing threat to global human health. Among the most prevalent antibiotic-resistant bacteria are Salmonella enterica serovar Typhimurium, Campylobacter jejuni and E. coli 0157:H7. Control of these and other pathogens requires innovative approaches, i.e., discovering new molecules that will inactivate them, or render them less virulent without inducing resistance. Recently, several polyphenol molecules have been shown to possess such characteristics. Also, the use of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) approaches has recently been proposed for such purpose. This review summarizes the main findings regarding the application of both approaches to control the above-mentioned foodborne pathogens by relying on Quorum Sensing interference (Quorum Quenching) mechanisms and highlights the avenues needed for further research.
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Affiliation(s)
| | - Marieva Benitez-Vindiola
- Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico;
| | - Luis J. Figueroa-Yañez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Jalisco, Mexico; (L.J.F.-Y.); (E.M.-B.)
| | - Evelin Martínez-Benavidez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Jalisco, Mexico; (L.J.F.-Y.); (E.M.-B.)
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15
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Higuera-Ciapara I, Benitez-Vindiola M, Figueroa-Yañez LJ, Martínez-Benavidez E. Polyphenols and CRISPR as Quorum Quenching Agents in Antibiotic-Resistant Foodborne Human Pathogens (Salmonella Typhimurium, Campylobacter jejuni and Escherichia coli 0157:H7). Foods 2024; 13:584. [DOI: https:/doi.org/10.3390/foods13040584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Antibiotic resistance in foodborne pathogens is an increasing threat to global human health. Among the most prevalent antibiotic-resistant bacteria are Salmonella enterica serovar Typhimurium, Campylobacter jejuni and E. coli 0157:H7. Control of these and other pathogens requires innovative approaches, i.e., discovering new molecules that will inactivate them, or render them less virulent without inducing resistance. Recently, several polyphenol molecules have been shown to possess such characteristics. Also, the use of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) approaches has recently been proposed for such purpose. This review summarizes the main findings regarding the application of both approaches to control the above-mentioned foodborne pathogens by relying on Quorum Sensing interference (Quorum Quenching) mechanisms and highlights the avenues needed for further research.
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Affiliation(s)
| | | | - Luis J. Figueroa-Yañez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Jalisco, Mexico
| | - Evelin Martínez-Benavidez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Jalisco, Mexico
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16
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Kasputis T, He Y, Ci Q, Chen J. On-Site Fluorescent Detection of Sepsis-Inducing Bacteria using a Graphene-Oxide CRISPR-Cas12a (GO-CRISPR) System. Anal Chem 2024; 96:2676-2683. [PMID: 38290431 PMCID: PMC10867801 DOI: 10.1021/acs.analchem.3c05459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Sepsis is an extremely dangerous medical condition that emanates from the body's response to a pre-existing infection. Early detection of sepsis-inducing bacterial infections can greatly enhance the treatment process and potentially prevent the onset of sepsis. However, current point-of-care (POC) sensors are often complex and costly or lack the ideal sensitivity for effective bacterial detection. Therefore, it is crucial to develop rapid and sensitive biosensors for the on-site detection of sepsis-inducing bacteria. Herein, we developed a graphene oxide CRISPR-Cas12a (GO-CRISPR) biosensor for the detection of sepsis-inducing bacteria in human serum. In this strategy, single-stranded (ssDNA) FAM probes were quenched with single-layer graphene oxide (GO). Target-activated Cas12a trans-cleavage was utilized for the degradation of the ssDNA probes, detaching the short ssDNA probes from GO and recovering the fluorescent signals. Under optimal conditions, we employed our GO-CRISPR system for the detection of Salmonella Typhimurium (S. Typhimurium) with a detection sensitivity of as low as 3 × 103 CFU/mL in human serum, as well as a good detection specificity toward other competing bacteria. In addition, the GO-CRISPR biosensor exhibited excellent sensitivity to the detection of S. Typhimurium in spiked human serum. The GO-CRISPR system offers superior rapidity for the detection of sepsis-inducing bacteria and has the potential to enhance the early detection of bacterial infections in resource-limited settings, expediting the response for patients at risk of sepsis.
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Affiliation(s)
- Tom Kasputis
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Yawen He
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Qiaoqiao Ci
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Juhong Chen
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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17
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Li B, Zhai G, Dong Y, Wang L, Ma P. Recent progress on the CRISPR/Cas system in optical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:798-816. [PMID: 38259224 DOI: 10.1039/d3ay02147e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein systems are adaptive immune systems unique to archaea and bacteria, with the characteristics of targeted recognition and gene editing to resist the invasion of foreign nucleic acids. Biosensors combined with the CRISPR/Cas system and optical detection technology have attracted much attention in medical diagnoses, food safety, agricultural progress, and environmental monitoring owing to their good sensitivity, high selectivity, and fast detection efficiency. In this review, we introduce the mechanism of CRISPR/Cas systems and developments in this area, followed by summarizing recent progress on CRISPR/Cas system-based optical biosensors combined with colorimetric, fluorescence, electrochemiluminescence and surface-enhanced Raman scattering optical techniques in various fields. Finally, we discuss the challenges and future perspectives of CRISPR/Cas systems in optical biosensors.
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Affiliation(s)
- Bingqian Li
- School of Special Education and Rehabilitation, Binzhou Medical University, Yantai 264003, China.
| | - Guangyu Zhai
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yaru Dong
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Lan Wang
- School of Special Education and Rehabilitation, Binzhou Medical University, Yantai 264003, China.
| | - Peng Ma
- School of Basic Medicine, Binzhou Medical University, Yantai 264003, China.
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18
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Pang L, Pi X, Zhao Q, Man C, Yang X, Jiang Y. Optical nanosensors based on noble metal nanoclusters for detecting food contaminants: A review. Compr Rev Food Sci Food Saf 2024; 23:e13295. [PMID: 38284598 DOI: 10.1111/1541-4337.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/02/2023] [Accepted: 12/16/2023] [Indexed: 01/30/2024]
Abstract
Food contaminants present a significant threat to public health. In response to escalating global concerns regarding food safety, there is a growing demand for straightforward, rapid, and sensitive detection technologies. Noble metal nanoclusters (NMNCs) have garnered considerable attention due to their superior attributes compared to other optical materials. These attributes include high catalytic activity, excellent biocompatibility, and outstanding photoluminescence properties. These features render NMNCs promising candidates for crafting nanosensors for food contaminant detection, offering the potential for the development of uncomplicated, swift, sensitive, user-friendly, and cost-effective detection approaches. This review investigates optical nanosensors based on NMNCs, including the synthesis methodologies of NMNCs, sensing strategies, and their applications in detecting food contaminants. Furthermore, it involves a comparative assessment of the applications of NMNCs in optical sensing and their performance. Ultimately, this paper imparts fresh perspectives on the forthcoming challenges. Hitherto, optical (particularly fluorescent) nanosensors founded on NMNCs have demonstrated exceptional sensing capabilities in the realm of food contaminant detection. To enhance sensing performance, future research should prioritize atomically precise NMNCs synthesis, augmentation of catalytic activity and optical properties, development of high-throughput and multimode sensing, integration of NMNCs with microfluidic devices, and the optimization of NMNCs storage, shelf life, and transportation conditions.
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Affiliation(s)
- Lidong Pang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaowen Pi
- College of Food Science, Southwest University, Chongqing, China
| | - Qianyu Zhao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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19
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Li Y, Liu Y, Tang X, Qiao J, Kou J, Man S, Zhu L, Ma L. CRISPR/Cas-Powered Amplification-Free Detection of Nucleic Acids: Current State of the Art, Challenges, and Futuristic Perspectives. ACS Sens 2023; 8:4420-4441. [PMID: 37978935 DOI: 10.1021/acssensors.3c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
CRISPR/Cas system is becoming an increasingly influential technology that has been repositioned in nucleic acid detection. A preamplification step is usually required to improve the sensitivity of CRISPR/Cas-based detection. The striking biological features of CRISPR/Cas, including programmability, high sensitivity and sequence specificity, and single-base resolution. More strikingly, the target-activated trans-cleavage could act as a biocatalytic signal transductor and amplifier, thereby empowering it to potentially perform nucleic acid detection without a preamplification step. The reports of such work are on the rise, which is not only scientifically significant but also promising for futuristic end-user applications. This review started with the introduction of the detection methods of nucleic acids and the CRISPR/Cas-based diagnostics (CRISPR-Dx). Next, we objectively discussed the pros and cons of preamplification steps for CRISPR-Dx. We then illustrated and highlighted the recently developed strategies for CRISPR/Cas-powered amplification-free detection that can be realized through the uses of ultralocalized reactors, cascade reactions, ultrasensitive detection systems, or others. Lastly, the challenges and futuristic perspectives were proposed. It can be expected that this work not only makes the researchers better understand the current strategies for this emerging field, but also provides insight for designing novel CRISPR-Dx without a preamplification step to win practicable use in the near future.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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20
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Li Y, Zhao Z, Liu Y, Wang N, Man S, Ma L, Wang S. CRISPR/Cas System: The Accelerator for the Development of Non-nucleic Acid Target Detection in Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13577-13594. [PMID: 37656446 DOI: 10.1021/acs.jafc.3c03619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Non-nucleic acid targets have posed a serious challenge to food safety. The detection of non-nucleic acid targets can enable us to monitor food contamination in a timely manner. In recent years, the CRISPR/Cas system has been extensively explored in biosensing. However, there is a lack of a summary of CRISPR/Cas-powered detection tailored to non-nucleic acid targets involved in food safety. This review comprehensively summarizes the recent advances on the construction of CRISPR/Cas-powered detection and the promising applications in the field of food safety related non-nucleic acid targets. The current challenges and futuristic perspectives are also proposed accordingly. The rapidly evolving CRISPR/Cas system has provided a powerful propellant for non-nucleic acid target detection via integration with aptamer and/or DNAzyme. Compared with traditional analytical methods, CRISPR/Cas-powered detection is conceptually novel, essentially eliminates the dependence on large instruments, and also demonstrates the capability for rapid, accurate, sensitive, and on-site testing.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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21
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Preechakasedkit P, Panphut W, Lomae A, Wonsawat W, Citterio D, Ruecha N. Dual Colorimetric/Electrochemical Detection of Salmonella typhimurium Using a Laser-Induced Graphene Integrated Lateral Flow Immunoassay Strip. Anal Chem 2023; 95:13904-13912. [PMID: 37638540 DOI: 10.1021/acs.analchem.3c02252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Foodborne illnesses caused by the ingestion of contaminated foods or beverages are a serious concern due to the millions of reported cases per year. It is essential to develop sensitive and rapid detection methods of foodborne pathogens to ensure food safety for producers and consumers. Unfortunately, current detection techniques still suffer from time-consuming operations and the need for highly skilled personnel. Here, we introduce a highly sensitive dual colorimetric/electrochemical detection approach for Salmonella enterica serovar typhimurium (S. typhimurium) based on a laser-induced graphene-integrated lateral flow immunoassay (LIG-LFIA) strip. The LIG electrode was fabricated by laser engraving on a polyimide tape containing a pseudo silver/silver chloride reference electrode from silver sintering and chlorination. Using double-sided tape inserted into the strip, automatic sequential reagent delivery was enabled for the dual-mode signal readout by single-sample loading. A gold-deposited gold nanoparticle strategy was first employed to simultaneously obtain a colorimetric signal for early screening and a signal turn-on electrochemical response for high-sensitivity and -quantitative analysis. A superior performance of the strip was established, characterized by a short analysis time (12 min assay +15 min sample preparation), a broad working concentration range (1 cfu/10 mL to 108 cfu/mL), and the lowest limit of detection (1 ± 0.5 cfu/10 mL; mean ± standard deviation, n = 3) among reported multimode S. typhimurium detection schemes. The strip was successfully applied in the analysis of various food products without any bacterial enrichment or amplification required, and the results were comparable to those of the standard culture method.
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Affiliation(s)
- Pattarachaya Preechakasedkit
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Rd., Pathumwan, Bangkok 10330, Thailand
| | - Wattana Panphut
- Department of Industrial Microbiology, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Nok Street, Dusit, Bangkok 10300, Thailand
| | - Atchara Lomae
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Rd., Pathumwan, Bangkok 10330, Thailand
| | - Wanida Wonsawat
- Department of Chemistry, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Nok Street, Dusit, Bangkok 10300, Thailand
| | - Daniel Citterio
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Nipapan Ruecha
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Rd., Pathumwan, Bangkok 10330, Thailand
- Center of Excellence for Food and Water Risk Analysis (FAWRA), Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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22
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Qiao J, Zhao Z, Li Y, Lu M, Man S, Ye S, Zhang Q, Ma L. Recent advances of food safety detection by nucleic acid isothermal amplification integrated with CRISPR/Cas. Crit Rev Food Sci Nutr 2023:1-22. [PMID: 37691410 DOI: 10.1080/10408398.2023.2246558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Food safety problems have become one of the most important public health issues worldwide. Therefore, the development of rapid, effective and robust detection is of great importance. Amongst a range of methods, nucleic acid isothermal amplification (NAIA) plays a great role in food safety detection. However, the widespread application remains limited due to a few shortcomings. CRISPR/Cas system has emerged as a powerful tool in nucleic acid detection, which could be readily integrated with NAIA to improve the detection sensitivity, specificity, adaptability versatility and dependability. However, currently there was a lack of a comprehensive summary regarding the integration of NAIA and CRISPR/Cas in the field of food safety detection. In this review, the recent advances in food safety detection based on CRISPR/Cas-integrated NAIA were comprehensively reviewed. To begin with, the development of NAIA was summarized. Then, the types and working principles of CRISPR/Cas were introduced. The applications of the integration of NAIA and CRISPR/Cas for food safety were mainly introduced and objectively discussed. Lastly, current challenges and future opportunities were proposed. In summary, this technology is expected to become an important approach for food safety detection, leading to a safer and more reliable food industry.
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Affiliation(s)
- Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shengying Ye
- Pharmacy Department, The 983th Hospital of the Joint Logistics Support Force of the, Chinese People's Liberation Army, Tianjin, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
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23
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de Dieu Habimana J, Mukama O, Amissah OB, Sun Y, Karangwa E, Liu Y, Mugisha S, Cheng N, Wang L, Chen J, Deng S, Huang R, Li Z. A Rationally Designed CRISPR/Cas12a Assay Using a Multimodal Reporter for Various Readouts. Anal Chem 2023; 95:11741-11750. [PMID: 37504509 DOI: 10.1021/acs.analchem.3c01876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The CRISPR/Cas systems offer a programmable platform for nucleic acid detection, and CRISPR/Cas-based diagnostics (CRISPR-Dx) have demonstrated the ability to target nucleic acids with greater accuracy and flexibility. However, due to the configuration of the reporter and the underlying labeling mechanism, almost all reported CRISPR-Dx rely on a single-option readout, resulting in limitations in end-point result readouts. This is also associated with high reagent consumption and delays in diagnostic reports due to protocol differences. Herein, we report for the first time a rationally designed Cas12a-based multimodal universal reporter (CAMURE) with improved sensitivity that harnesses a dual-mode reporting system, facilitating options in end-point readouts. Through systematic configurations and optimizations, our novel universal reporter achieved a 10-fold sensitivity enhancement compared to the DETECTR reporter. Our unique and versatile reporter could be paired with various readouts, conveying the same diagnostic results. We applied our novel reporter for the detection of staphylococcal enterotoxin A due to its high implication in staphylococcal food poisoning. Integrated with loop-mediated isothermal amplification, our multimodal reporter achieved 10 CFU/mL sensitivity and excellent specificity using a real-time fluorimeter, in-tube fluorescence, and lateral flow strip readouts. We also propose, using artificially contaminated milk samples, a fast (2-5 min) Triton X-100 DNA extraction approach with a comparable yield to the commercial extraction kit. Our CAMURE could be leveraged to detect all gene-encoding SEs by simply reprogramming the guide RNA and could also be applied to the detection of other infections and disease biomarkers.
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Affiliation(s)
- Jean de Dieu Habimana
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Omar Mukama
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
- Department of Biology, College of Science and Technology, University of Rwanda, Avenue de l'armée, Kigali 3900, Rwanda
| | - Obed Boadi Amissah
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yirong Sun
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Eric Karangwa
- Research and Development, AAFUD Industry (Zhuhai) Co. Ltd., Zhuhai 519085, China
| | - Yujie Liu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Samson Mugisha
- Department of Pathology, University of California, San Diego, 9500 Gilman, La Jolla, California 92093, United States
| | - Na Cheng
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Ling Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Jianlin Chen
- Department of Gynecology & Obstetrics, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Sihao Deng
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Rongqi Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
- Guangzhou Qiyuan Biomedical Co., Ltd., Guangzhou 510530, China
| | - Zhiyuan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- GZMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou 511436, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou 511436, China
- Guangzhou Qiyuan Biomedical Co., Ltd., Guangzhou 510530, China
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24
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Fredrick D, Yourston L, Krasnoslobodtsev AV. Detection of cancer-associated miRNA using a fluorescence switch of AgNC@NA and guanine-rich overhang sequences. LUMINESCENCE 2023; 38:1385-1392. [PMID: 36843363 DOI: 10.1002/bio.4471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/03/2023] [Accepted: 02/18/2023] [Indexed: 02/28/2023]
Abstract
DNA-templated silver nanoclusters (AgNC@DNA) are a novel type of nanomaterial with advantageous optical properties. Only a few atoms in size, the fluorescence of nanoclusters can be tuned using DNA overhangs. In this study, we explored the properties of AgNCs manufactured on a short single-stranded (dC)12 when adjacent G-rich sequences (dGN , with N = 3-15) were added. The 'red' emission of AgNC@dC12 with λMAX = 660 nm dramatically changed upon the addition of a G-rich overhang with NG = 15. The pattern of the emission-excitation matrix (EEM) suggested the emergence of two new emissive states at λMAX = 575 nm and λMAX = 710 nm. The appearance of these peaks provides an effective way to design biosensors capable of detecting specific nucleic acid sequences with low fluorescence backgrounds. We used this property to construct an NA-based switch that brings AgNC and the G overhang near one another, turning 'ON' the new fluorescence peaks only when a specific miRNA sequence is present. Next, we tested this detection switch on miR-371, which is overexpressed in prostate cancer. The results presented provide evidence that this novel fluorescent switch is both sensitive and specific with a limit of detection close to 22 picomoles of the target miR-371 molecule.
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Affiliation(s)
- Dylan Fredrick
- Department of Physics, University of Nebraska Omaha, 6001 Dodge Street, Omaha, Nebraska, USA
| | - Liam Yourston
- Department of Physics, University of Nebraska Omaha, 6001 Dodge Street, Omaha, Nebraska, USA
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25
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Ma L, Zhang W, Yin L, Li Y, Zhuang J, Shen L, Man S. A SERS-signalled, CRISPR/Cas-powered bioassay for amplification-free and anti-interference detection of SARS-CoV-2 in foods and environmental samples using a single tube-in-tube vessel. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131195. [PMID: 36963196 PMCID: PMC10005974 DOI: 10.1016/j.jhazmat.2023.131195] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
The pandemic of COVID-19 creates an imperative need for sensitive and portable detection of SARS-CoV-2. We devised a SERS-read, CRISPR/Cas-powered nanobioassay, termed as OVER-SARS-CoV-2 (One-Vessel Enhanced RNA test on SARS-CoV-2), which enabled supersensitive, ultrafast, accurate and portable detection of SARS-CoV-2 in a single vessel in an amplification-free and anti-interference manner. The SERS nanoprobes were constructed by conjugating gold nanoparticles with Raman reporting molecular and single-stranded DNA (ssDNA) probes, whose aggregation-to-dispersion changes can be finely tuned by target-activated Cas12a though trans-cleavage of linker ssDNA. As such, the nucleic acid signals could be dexterously converted and amplified to SERS signals. By customizing an ingenious vessel, the steps of RNA reverse transcription, Cas12a trans-cleavage and SERS nanoprobes crosslinking can be integrated into a single and disposal vessel. It was proved that our proposed nanobioassay was able to detect SARS-CoV-2 as low as 200 copies/mL without any pre-amplification within 45 min. In addition, the proposed nanobioassay was confirmed by clinical swab samples and challenged for SARS-CoV-2 detection in simulated complex environmental and food samples. This work enriches the arsenal of CRISPR-based diagnostics (CRISPR-Dx) and provides a novel and robust platform for SARS-CoV-2 decentralized detection, which can be put into practice in the near future.
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Affiliation(s)
- Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition, Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Wenlu Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition, Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Lijuan Yin
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition, Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition, Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jianwen Zhuang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition, Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Liang Shen
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441000, China.
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition, Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
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26
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Danai L, Rolband LA, Perdomo VA, Skelly E, Kim T, Afonin KA. Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters. Nanomedicine (Lond) 2023; 18:769-782. [PMID: 37345552 PMCID: PMC10308257 DOI: 10.2217/nnm-2023-0082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023] Open
Abstract
Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.
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Affiliation(s)
- Leyla Danai
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lewis A Rolband
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Elizabeth Skelly
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Taejin Kim
- Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV 25801, USA
| | - Kirill A Afonin
- Department of Chemistry, Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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27
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Ma L, Liao D, Zhao Z, Kou J, Guo H, Xiong X, Man S. Sensitive Small Molecule Aptasensing based on Hybridization Chain Reaction and CRISPR/Cas12a Using a Portable 3D-Printed Visualizer. ACS Sens 2023; 8:1076-1084. [PMID: 36651835 DOI: 10.1021/acssensors.2c02097] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Next-generation biosensing tools based on CRISPR/Cas have revolutionized the molecular detection. A number of CRISPR/Cas-based biosensors have been reported for the detection of nucleic acid targets. The establishment of efficient methods for non-nucleic acid target detection would further broaden the scope of this technique, but up to now, the concerning research is limited. In the current study, we reported a versatile biosensing platform for non-nucleic acid small-molecule detection called SMART-Cas12a (small-molecule aptamer regulated test using CRISPR/Cas12a). Simply, hybridization chain reaction cascade signal amplification was first trigged by functional nucleic acid (aptamer) through target binding. Then, the CRISPR/Cas system was integrated to recognize the amplified products followed by activation of the trans-cleavage. As such, the target can be ingeniously converted to nucleic acid signals and then fluorescent signals that can be readily visualized and analyzed by a customized 3D-printed visualizer with the help of a home-made App-enabled smartphone. Adenosine triphosphate was selected as a model target, and under the optimized conditions, we achieved fine analytical performance with a linear range from 0.1 to 750 μM and a detection limit of 1.0 nM. The satisfactory selectivity and recoveries that we have obtained further demonstrated this method to be suitable for a complex sample environment. The sample-to-answer time was less than 100 min. Our work not only expanded the reach of the CRISPR-Cas system in biosensing but also provided a prototype method that can be generalized for detecting a wider range of analytes with desirable adaptability, sensitivity, specificity, and on-site capability.
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Affiliation(s)
- Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Dan Liao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Haoyu Guo
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xin Xiong
- College of Artificial Intelligence, Tianjin University of Science and Technology, Tianjin 3000457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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Chen H, Zhou X, Wang M, Ren L. Towards Point of Care CRISPR-Based Diagnostics: From Method to Device. J Funct Biomater 2023; 14:jfb14020097. [PMID: 36826896 PMCID: PMC9967495 DOI: 10.3390/jfb14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Rapid, accurate, and portable on-site detection is critical in the face of public health emergencies. Infectious disease control and public health emergency policymaking can both be aided by effective and trustworthy point of care tests (POCT). A very promising POCT method appears to be the clustered regularly interspaced short palindromic repeats and associated protein (CRISPR/Cas)-based molecular diagnosis. For on-site detection, CRISPR/Cas-based detection can be combined with multiple signal sensing methods and integrated into smart devices. In this review, sensing methods for CRISPR/Cas-based diagnostics are introduced and the advanced strategies and recent advances in CRISPR/Cas-based POCT are reviewed. Finally, the future perspectives of CRISPR and POCT are summarized and prospected.
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Affiliation(s)
- Haoxiang Chen
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
| | - Xi Zhou
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
| | - Miao Wang
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
| | - Lei Ren
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, China
- State Key Lab of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
- Correspondence:
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29
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Zhang X, Peng Y, Yao L, Shang H, Zheng Z, Chen W, Xu J. Self-Assembly of Multivalent Aptamer-Tethered DNA Monolayers Dedicated to a Fluorescence Polarization-Responsive Circular Isothermal Strand Displacement Amplification for Salmonella Assay. Anal Chem 2023; 95:2570-2578. [PMID: 36653941 DOI: 10.1021/acs.analchem.2c05448] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Pathogenic bacteria are pathogens widely spread that are capable of causing mild to life-threatening diseases in human beings or other organisms. Rationally organizing the simple helical motif of double-stranded DNA (dsDNA) tiles into designed ensemble structures with architecturally defined collective properties could lead to promising biosensing applications for pathogen detection. In this work, we facilely engineered multivalent hairpin aptamer probe-tethered DNA monolayers (MHAP-DNA monolayers) and applied them to build a fluorescence polarization-responsive circular isothermal strand displacement amplification (FP-CSDA) for Salmonella assay. In this system, the MHAP-DNA monolayers were constructed based on a dsDNA tile-directed self-assembly. A FAM-labeled reporting probe (RPFAM) with an inherent low FP signal serves as the signaling unit. The presence of target Salmonella leads to the trapping of F RPFAM into the super DNA monolayers via a target-triggered CSDA to peel off the tethered hairpin-structured aptamer probes (HAPs) responsible for the binding of RPFAM. As a result, the FP signal of the FAM fluorophore can be remarkably amplified due to the recycling of target Salmonella and the capacity of structural DNA materials to strongly restrict the free rotation of the FAM fluorophore but without a fluorescence quenching effect. Experimental results demonstrate that the FP assay is able to detect Salmonella with a low limit of detection (LOD) of 7.2 × 100 CFU/mL and high specificity. As a proof-of-concept study, we envision our study using DNA nanoarchitecture as the foundation to modulate CSDA-based FP assays, promising to open up a new avenue for disease diagnosis, food safety detection, and biochemical studies.
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Affiliation(s)
- Xinlei Zhang
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yubo Peng
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Li Yao
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Huijie Shang
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhi Zheng
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China
| | - Wei Chen
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jianguo Xu
- Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.,Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, China
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30
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Alshatteri AH, Omer KM. Dual-Nanocluster of Copper and Silver as a Ratiometric-Based Smartphone-Assisted Visual Detection of Biothiols. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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