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Kong F, Wang C, Peng S, Chen Z, Huang Y, Zhang J, Wang J, Wang D. CRISPR-Hg: Rapid and visual detection of Hg 2+ based on PCR coupled with CRISPR/Cas12a. Talanta 2024; 277:126379. [PMID: 38852343 DOI: 10.1016/j.talanta.2024.126379] [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: 02/05/2024] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Mercury (Hg) is a notorious toxic heavy metal, causing neurotoxicity and liver damage, posing grave threats to human health and environmental safety. There is an urgent imperative for developing novel Hg2+ detection methods. In this work, we developed a CRISPR-based method for Hg2+ detection named CRISPR-Hg. A CRISPR/Cas12a system was employed and could be activated by the PCR product, generating fluorescence signals based on the trans-cleavage activity. CRISPR-Hg exhibited remarkable selectivity and specificity, achieving a detection limit of 10 pM and minimal interference with background signals. This approach has been successfully applied to detect Hg2+ in real samples, including water, soil, and mushroom. Ulteriorly, a portable device was devised to streamline the readout of fluorescence signals by a smartphone within 30 min. We offer an affordable, highly selective and visually interpretable method for Hg2+ detection, with the potential for broad application in Hg2+ monitoring for food safety and public health.
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Affiliation(s)
- Fange Kong
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China.
| | - Chunxia Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China.
| | - Shichao Peng
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China.
| | - Zhengrui Chen
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China.
| | - Yibing Huang
- School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Jicheng Zhang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, United States.
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Di Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China.
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2
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Fang Y, Nie L, Wang S, Liu S, Li H, Yu R. A universal fluorescence biosensor based on rolling circle amplification and locking probe for DNA detection. Mikrochim Acta 2024; 191:437. [PMID: 38951284 DOI: 10.1007/s00604-024-06501-2] [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: 04/03/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
A stable DNA signal amplification sensor was developed on account of rolling circle amplification (RCA). This sensor includes target DNA-controlled rolling circle amplification technology and locking probe DNA replacement technology, which can be used to detect DNA fragments with genetic information, thus constructing a biosensor for universal detection of DNA. This study takes the homologous DNA of human immunodeficiency virus (HIV) and let-7a as examples to describe this biosensor. The padlock probe is first cyclized by T4 DNA ligase in response to the target's reaction with it. Then, rolling cycle amplification is initiated by Phi29 DNA polymerase, resulting in the formation of a lengthy chain with several triggers. These triggers can open the locked probe LP1 with the fluorescence signal turned off, so that it can continue to react with H2 to form a stable H1-H2 double strand. This regulates the distance between B-DNA modified by the quenching group and H1 modified by fluorescent group, and the fluorescence signal is recovered.
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Affiliation(s)
- Ying Fang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China
| | - Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China
| | - Shiwen Liu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China.
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, P. R. China.
| | - Hongbo Li
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P.R. China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P.R. China
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3
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Saleh EAM, Ali E, Muxamadovna GM, Kassem AF, Kaur I, Kumar A, Jabbar HS, Alwaily ER, Elawady A, Omran AA. CRISPR/Cas-based colorimetric biosensors: a promising tool for the diagnosis of bacterial foodborne pathogens in food products. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3448-3463. [PMID: 38804827 DOI: 10.1039/d4ay00578c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Some physical phenomena and various chemical substances newly introduced in nanotechnology have allowed scientists to develop valuable devices in the field of food sciences. Regarding such progress, the identification of foodborne pathogenic microorganisms is an imperative subject nowadays. These bacterial species have been found to cause severe health impacts after food ingestion and can result in high mortality in acute cases. The rapid detection of foodborne bacterial species at low concentrations is in high demand in recent diagnostics. CRISPR/Cas-mediated biosensors possess the potential to overcome several challenges in classical assays such as complex pretreatments, long turnaround time, and insensitivity. Among them, colorimetric nanoprobes based on the CRISPR strategy afford promising devices for POCT (point-of-care testing) since they can be visualized with the naked eye and do not require diagnostic apparatus. In this study, we briefly classify and discuss the working principles of the different CRISPR/Cas protein agents that have been employed in biosensors so far. We assess the current status of the CRISPR system, specifically focusing on colorimetric biosensing platforms. We discuss the utilization of each Cas effector in the detection of foodborne pathogens and examine the restrictions of the existing technology. The challenges and future opportunities are also indicated and addressed.
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Affiliation(s)
- Ebraheem Abdu Musad Saleh
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia.
| | - Eyhab Ali
- Al-Zahraa University for Women, Karbala, Iraq
| | | | - Asmaa F Kassem
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka-560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | - Abhinav Kumar
- Department of Nuclear and Renewable Energy, Ural Federal University Named After the First President of Russia Boris Yeltsin, Yekaterinburg 620002, Russia
| | - Hijran Sanaan Jabbar
- Department of Chemistry, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Enas R Alwaily
- Microbiology Research Group, College of Pharmacy, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Elawady
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq
| | - Alaa A Omran
- Department of Engineering, AL-Nisour University College, Baghdad, Iraq
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4
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Li Z, Feng W, Zhu Z, Lu S, Lin M, Dong J, Wang Z, Liu F, Chen Q. Cas-OPRAD: a one-pot RPA/PCR CRISPR/Cas12 assay for on-site Phytophthora root rot detection. Front Microbiol 2024; 15:1390422. [PMID: 38903797 PMCID: PMC11188302 DOI: 10.3389/fmicb.2024.1390422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Phytophthora sojae is a devastating plant pathogen that causes soybean Phytophthora root rot worldwide. Early on-site and accurate detection of the causal pathogen is critical for successful management. In this study, we have developed a novel and specific one-pot RPA/PCR-CRISPR/Cas12 assay for on-site detection (Cas-OPRAD) of Phytophthora root rot (P. sojae). Compared to the traditional RPA/PCR detection methods, the Cas-OPRAD assay has significant detection performance. The Cas-OPRAD platform has excellent specificity to distinguish 33 P. sojae from closely related oomycetes or fungal species. The PCR-Cas12a assay had a consistent detection limit of 100 pg. μL-1, while the RPA-Cas12a assay achieved a detection limit of 10 pg. μL-1. Furthermore, the Cas-OPRAD assay was equipped with a lateral flow assay for on-site diagnosis and enabled the visual detection of P. sojae on the infected field soybean samples. This assay provides a simple, efficient, rapid (<1 h), and visual detection platform for diagnosing Phytophthora root rot based on the one-pot CRISPR/Cas12a assay. Our work provides important methods for early and accurate on-site detection of Phytophthora root rot in the field or customs fields.
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Affiliation(s)
- Zhiting Li
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Zaobing Zhu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Shengdan Lu
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Mingze Lin
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Jiali Dong
- Sanya Institute of China Agricultural University, Sanya, China
| | - Zhixin Wang
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Post-Entry Quarantine Center for Tropical Plant, Haikou, China
| | - Fuxiu Liu
- Post-Entry Quarantine Center for Tropical Plant, Haikou, China
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
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5
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Dong J, Feng W, Lin M, Chen S, Liu X, Wang X, Chen Q. Comparative Evaluation of PCR-Based, LAMP and RPA-CRISPR/Cas12a Assays for the Rapid Detection of Diaporthe aspalathi. Int J Mol Sci 2024; 25:5773. [PMID: 38891961 PMCID: PMC11172161 DOI: 10.3390/ijms25115773] [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: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Southern stem canker (SSC) of soybean, attributable to the fungal pathogen Diaporthe aspalathi, results in considerable losses of soybean in the field and has damaged production in several of the main soybean-producing countries worldwide. Early and precise identification of the causal pathogen is imperative for effective disease management. In this study, we performed an RPA-CRISPR/Cas12a, as well as LAMP, PCR and real-time PCR assays to verify and compare their sensitivity, specificity and simplicity and the practicality of the reactions. We screened crRNAs targeting a specific single-copy gene, and optimized the reagent concentrations, incubation temperatures and times for the conventional PCR, real-time PCR, LAMP, RPA and Cas12a cleavage stages for the detection of D. aspalathi. In comparison with the PCR-based assays, two thermostatic detection technologies, LAMP and RPA-CRISPR/Cas12a, led to higher specificity and sensitivity. The sensitivity of the LAMP assay could reach 0.01 ng μL-1 genomic DNA, and was 10 times more sensitive than real-time PCR (0.1 ng μL-1) and 100 times more sensitive than conventional PCR assay (1.0 ng μL-1); the reaction was completed within 1 h. The sensitivity of the RPA-CRISPR/Cas12a assay reached 0.1 ng μL-1 genomic DNA, and was 10 times more sensitive than conventional PCR (1.0 ng μL-1), with a 30 min reaction time. Furthermore, the feasibility of the two thermostatic methods was validated using infected soybean leaf and seeding samples. The rapid, visual one-pot detection assay developed could be operated by non-expert personnel without specialized equipment. This study provides a valuable diagnostic platform for the on-site detection of SSC or for use in resource-limited areas.
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Affiliation(s)
- Jiali Dong
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Sanya Institute of China Agricultural University, Sanya 572025, China;
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Mingze Lin
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Shuzhe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaozhen Liu
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaodan Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China;
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
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6
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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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7
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Lei X, Cao S, Liu T, Wu Y, Yu S. Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection. Talanta 2024; 271:125663. [PMID: 38232570 DOI: 10.1016/j.talanta.2024.125663] [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: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.
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Affiliation(s)
- Xueying Lei
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Shengnan Cao
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Tao Liu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Yongjun Wu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Songcheng Yu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China.
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8
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Zhang Q, Hu J, Li DL, Qiu JG, Jiang BH, Zhang CY. Construction of single-molecule counting-based biosensors for DNA-modifying enzymes: A review. Anal Chim Acta 2024; 1298:342395. [PMID: 38462345 DOI: 10.1016/j.aca.2024.342395] [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: 12/10/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
DNA-modifying enzymes act as critical regulators in a wide range of genetic functions (e.g., DNA damage & repair, DNA replication), and their aberrant expression may interfere with regular genetic functions and induce various malignant diseases including cancers. DNA-modifying enzymes have emerged as the potential biomarkers in early diagnosis of diseases and new therapeutic targets in genomic research. Consequently, the development of highly specific and sensitive biosensors for the detection of DNA-modifying enzymes is of great importance for basic biomedical research, disease diagnosis, and drug discovery. Single-molecule fluorescence detection has been widely implemented in the field of molecular diagnosis due to its simplicity, high sensitivity, visualization capability, and low sample consumption. In this paper, we summarize the recent advances in single-molecule counting-based biosensors for DNA-modifying enzyme (i.e, alkaline phosphatase, DNA methyltransferase, DNA glycosylase, flap endonuclease 1, and telomerase) assays in the past four years (2019 - 2023). We highlight the principles and applications of these biosensors, and give new insight into the future challenges and perspectives in the development of single-molecule counting-based biosensors.
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Affiliation(s)
- Qian Zhang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China; College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Jian-Ge Qiu
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bing-Hua Jiang
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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9
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Zhao L, Wang H, Chen X, Wang L, Abulaizi W, Yang Y, Li B, Wang C, Bai X. Agarose Hydrogel-Boosted One-Tube RPA-CRISPR/Cas12a Assay for Robust Point-of-Care Detection of Zoonotic Nematode Anisakis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8257-8268. [PMID: 38530904 DOI: 10.1021/acs.jafc.4c00204] [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: 03/28/2024]
Abstract
Rapid and accurate detection of the zoonotic nematode Anisakis is poised to control its epidemic. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-associated assay shows great potential in the detection of pathogenic microorganisms. The one-tube method integrated the CRISPR system with the recombinase polymerase amplification (RPA) system to avoid the risk of aerosol pollution; however, it suffers from low sensitivity due to the incompatibility of the two systems and additional manual operations. Therefore, in the present study, the agarose hydrogel boosted one-tube RPA-CRISPR/Cas12a assay was constructed by adding the CRISPR system to the agarose hydrogel, which avoided the initially low amplification efficiency of RPA caused by the cleavage of Cas12a and achieved reaction continuity. The sensitivity was 10-fold higher than that of the one-tube RPA-CRISPR/Cas12a system. This method was used for Anisakis detection within 80 min from the sample to result, achieving point-of-care testing (POCT) through a smartphone and a portable device. This study provided a novel toolbox for POCT with significant application value in preventing Anisakis infection.
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Affiliation(s)
- Lianjing Zhao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Haolu Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiuqin Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liping Wang
- Jiashi County Hospitalof Uygur Medicine, Xinjiang Uyghur Autonomous Region 830057, China
| | - Wulamujiang Abulaizi
- Jiashi County Hospitalof Uygur Medicine, Xinjiang Uyghur Autonomous Region 830057, China
| | - Yaming Yang
- Yunnan Institute of Parasitic Diseases, Puer 665000, China
| | - Benfu Li
- Yunnan Institute of Parasitic Diseases, Puer 665000, China
| | - Cunzhou Wang
- Jiashi County Hospitalof Uygur Medicine, Xinjiang Uyghur Autonomous Region 830057, China
| | - Xue Bai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
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10
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Sun S, Yang H, Wu Z, Zhang S, Xu J, Shi P. CRISPR/Cas systems combined with DNA nanostructures for biomedical applications. Chem Commun (Camb) 2024; 60:3098-3117. [PMID: 38406926 DOI: 10.1039/d4cc00290c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
DNA nanostructures are easy to design and construct, have good biocompatibility, and show great potential in biosensing and drug delivery. Numerous distinctive and versatile DNA nanostructures have been developed and explored for biomedical applications. In addition to DNA nanostructures that are completely assembled from DNA, composite DNA nanostructures obtained by combining DNA with other organic or inorganic materials are also widely used in related research. The CRISPR/Cas system has attracted great attention as a powerful gene editing technology and is also widely used in biomedical diagnosis. Many researchers are committed to exploring new possibilities by combining DNA nanostructures with CRISPR/Cas systems. These explorations provide support for the development of new detection methods and cargo delivery pathways, provide inspiration for improving relevant gene editing platforms, and further expand the application scope of DNA nanostructures and CRISPR/Cas systems. This paper mainly reviews the design principles and biomedical applications of CRISPR/Cas combined with DNA nanostructures based on the types of DNA nanostructures. Finally, the application status, challenges and development prospects of CRISPR/Cas combined with DNA nanostructures in detection and delivery are summarized. It is expected that this review will enable researchers to better understand the current state of the field and provide insights into the application of CRISPR/Cas systems and the development of DNA nanostructures.
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Affiliation(s)
- Shujuan Sun
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Haoqi Yang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Ziyong Wu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Jingjuan Xu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P. R. China.
| | - Pengfei Shi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
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11
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Li X, Dang Z, Tang W, Zhang H, Shao J, Jiang R, Zhang X, Huang F. Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a. BIOSENSORS 2024; 14:145. [PMID: 38534252 DOI: 10.3390/bios14030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.
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Affiliation(s)
- Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jianwei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rui Jiang
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
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12
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Zhou Z, Liang L, Liao C, Pan L, Wang C, Ma J, Yi X, Tan M, Li X, Wei G. A multiplex RPA coupled with CRISPR-Cas12a system for rapid and cost-effective identification of carbapenem-resistant Acinetobacter baumannii. Front Microbiol 2024; 15:1359976. [PMID: 38516017 PMCID: PMC10956356 DOI: 10.3389/fmicb.2024.1359976] [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: 12/22/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a severe nosocomial threat, prompting a need for efficient detection methods. Traditional approaches, such as bacterial culture and PCR, are time-consuming and cumbersome. The CRISPR-based gene editing system offered a potential approach for point-of-care testing of CRAB. Methods We integrated recombinase polymerase amplification (RPA) and CRISPR-Cas12a system to swiftly diagnose CRAB-associated genes, OXA-51 and OXA-23. This multiplex RPA-CRISPR-Cas12a system eliminates bulky instruments, ensuring a simplified UV lamp-based outcome interpretation. Results Operating at 37°C to 40°C, the entire process achieves CRAB diagnosis within 90 minutes. Detection limits for OXA-51 and OXA-23 genes are 1.3 × 10-6 ng/μL, exhibiting exclusive CRAB detection without cross-reactivity to common pathogens. Notably, the platform shows 100% concordance with PCR when testing 30 clinical Acinetobacter baumannii strains. Conclusion In conclusion, our multiplex RPA coupled with the CRISPR-Cas12a system provides a fast and sensitive CRAB detection method, overcoming limitations of traditional approaches and holding promise for efficient point-of-care testing.
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Affiliation(s)
- Zihan Zhou
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
| | - Lina Liang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
| | - Chuan Liao
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
| | - Lele Pan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
| | - Chunfang Wang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
| | - Jiangmei Ma
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Meiying Tan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
| | - Xuebin Li
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, Guangxi, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, Guangxi, China
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13
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Wang Q, Ren Y, Meng T, Yang X, Lu L, Yang H, Hou H, Negahdary M, Wan Y, Song F, Li J. Cas14a1-advanced LAMP for ultrasensitive and visual Pathogen diagnostic. Talanta 2024; 269:125458. [PMID: 38008027 DOI: 10.1016/j.talanta.2023.125458] [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: 04/12/2023] [Revised: 09/06/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas enzymes have been widely applied for biosensor development, combined with various isothermal amplification strategies (IAS) to boost sensitivity and specificity. Currently, the unstable assay and tedious manipulation usually hinder its practical applications. Here, a Cas14a1-advanced LAMP assay (CALA) combined with Rapid Extraction of Bacterial Genomic DNA (REBGD) is proposed for pathogen detection. For rapid CALA, a single stranded fluorescence reporter and ssDNA-gold nanoparticles (AuNPs) are used as signal indicators to establish ultrasensitive and visual platforms. This assay displays precise detection of bacteria, which can achieve an ultrasensitive limit of detection (LOD) 10 aM target genomic DNA. Furthermore, the high reliability of pathogen diagnostic for contrived samples is validated through the rapid visual CALA platform, demonstrating the promising practical testing availability of pathogen detection.
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Affiliation(s)
- Qingwei Wang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Yihua Ren
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Tian Meng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Xiufen Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Lin Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Hao Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou 450001, China, Beijing Institute of Life Science and Technology, Beijing, China
| | - Masoud Negahdary
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
| | - Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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14
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Liu R, Wang X, Wang S, Xie L, Zhao P, Li L, Ge S, Yu J. Rolling circle amplification assisted CRISPR/Cas12a dual-cleavage photoelectrochemical biosensor for highly sensitive detection of miRNA-21. Anal Chim Acta 2024; 1287:342125. [PMID: 38182395 DOI: 10.1016/j.aca.2023.342125] [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: 09/26/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND MicroRNA-21 has been determined to be the only microRNA overexpressed in 11 types of solid tumors, making it an excellent candidate as a biomarker for disease diagnosis and therapy. Photoelectrochemical (PEC) biosensors have been widely used for quantification of microRNA-21. However, most PEC biosensing processes still suffer from some problems, such as the difficulty of avoiding the influence of interferents in complex matrices and the false-positive signals. There is a pressing need for establishing a sensitive and stable PEC method to detect microRNA-21. RESULTS Herein, a nicking endonuclease-mediated rolling circle amplification (RCA)-assisted CRISPR/Cas12a PEC biosensor was fabricated for ultrasensitive detection of microRNA-21. The p-p type heterojunction PbS QDs/Co3O4 polyhedra were prepared as the quencher, thus the initial PEC signal attained the "off" state. Furthermore, the target was specifically identified and amplified by the RCA process. Then, its product single-stranded DNA S1 activated the cis- and trans-cleavage abilities of CRISPR/Cas12a, leading to almost all of the PbS QDs/Co3O4 polyhedra to leave the electrode surface, the p-n semiconductor quenching effect to be disrupted, and the signal achieving the "super-on" state. This pattern of PEC signal changed from "off" to "on" eliminated the interference of false-positive signals. The proposed PEC biosensor presented a satisfactory linear relationship ranging from 1 fM to 10 nM with a detection limit of 0.76 fM (3 Sb/N). SIGNIFICANCE AND NOVELTY With innovatively synthesized PbS QDs/Co3O4 polyhedra as the effective quencher for PEC signal, the CRISPR/Cas12a dual-cleavage PEC biosensor possessed excellent selectivity, stability and repeatability. Furthermore, the detection of various miRNAs can be realized by changing the relevant base sequences in the constructed PEC biosensor. It also provides a powerful strategy for early clinical diagnosis and biomedical research.
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Affiliation(s)
- Ruifang Liu
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, China
| | - Xuefeng Wang
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, China
| | - Shujing Wang
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, China
| | - Li Xie
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Peini Zhao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Li Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research(iAIR), University of Jinan, Jinan, 250022, China.
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
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15
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Talebian S, Dehghani F, Weiss PS, Conde J. Evolution of CRISPR-enabled biosensors for amplification-free nucleic acid detection. Trends Biotechnol 2024; 42:10-13. [PMID: 37516612 DOI: 10.1016/j.tibtech.2023.07.004] [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: 05/31/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
CRISPR biosensors enable rapid and accurate detection of nucleic acids without resorting to target amplification. Specifically, these systems facilitate the simultaneous detection of multiple nucleic acid targets with single-base specificity. This is an invaluable asset that can ultimately facilitate accurate diagnoses of biologically complex diseases.
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Affiliation(s)
- Sepehr Talebian
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia; Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia.
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia; Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - João Conde
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal.
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16
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Safenkova IV, Samokhvalov AV, Serebrennikova KV, Eremin SA, Zherdev AV, Dzantiev BB. DNA Probes for Cas12a-Based Assay with Fluorescence Anisotropy Enhanced Due to Anchors and Salts. BIOSENSORS 2023; 13:1034. [PMID: 38131794 PMCID: PMC10741848 DOI: 10.3390/bios13121034] [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: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
CRISPR/Cas12a is a potent biosensing tool known for its high specificity in DNA analysis. Cas12a recognizes the target DNA and acquires nuclease activity toward single-stranded DNA (ssDNA) probes. We present a straightforward and versatile approach to transforming common Cas12a-cleavable DNA probes into enhancing tools for fluorescence anisotropy (FA) measurements. Our study involved investigating 13 ssDNA probes with linear and hairpin structures, each featuring fluorescein at one end and a rotation-slowing tool (anchor) at the other. All anchors induced FA changes compared to fluorescein, ranging from 24 to 110 mr. Significant FA increases (up to 180 mr) were obtained by adding divalent metal salts (Mg2+, Ca2+, Ba2+), which influenced the rigidity and compactness of the DNA probes. The specific Cas12a-based recognition of double-stranded DNA (dsDNA) fragments of the bacterial phytopathogen Erwinia amylovora allowed us to determine the optimal set (probe structure, anchor, concentration of divalent ion) for FA-based detection. The best sensitivity was obtained using a hairpin structure with dC10 in the loop and streptavidin located near the fluorescein at the stem in the presence of 100 mM Mg2+. The detection limit of the dsDNA target was equal to 0.8 pM, which was eight times more sensitive compared to the common fluorescence-based method. The enhancing set ensured detection of single cells of E. amylovora per reaction in an analysis based on CRISPR/Cas12a with recombinase polymerase amplification. Our approach is universal and easy to implement. Combining FA with Cas12a offers enhanced sensitivity and signal reliability and could be applied to different DNA and RNA analytes.
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Affiliation(s)
- Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Kseniya V. Serebrennikova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Sergei A. Eremin
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
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17
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Yin W, Zhuang J, Li J, Xia L, Hu K, Yin J, Mu Y. Digital Recombinase Polymerase Amplification, Digital Loop-Mediated Isothermal Amplification, and Digital CRISPR-Cas Assisted Assay: Current Status, Challenges, and Perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303398. [PMID: 37612816 DOI: 10.1002/smll.202303398] [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: 04/22/2023] [Revised: 07/29/2023] [Indexed: 08/25/2023]
Abstract
Digital nucleic acid detection based on microfluidics technology can quantify the initial amount of nucleic acid in the sample with low equipment requirements and simple operations, which can be widely used in clinical and in vitro diagnosis. Recently, isothermal amplification technologies such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats-CRISPR associated proteins (CRISPR-Cas) assisted technologies have become a hot spot of attention and state-of-the-art digital nucleic acid chips have provided a powerful tool for these technologies. Herein, isothermal amplification technologies including RPA, LAMP, and CRISPR-Cas assisted methods, based on digital nucleic acid microfluidics chips recently, have been reviewed. Moreover, the challenges of digital isothermal amplification and possible strategies to address them are discussed. Finally, future directions of digital isothermal amplification technology, such as microfluidic chip and device manufacturing, multiplex detection, and one-pot detection, are outlined.
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Affiliation(s)
- Weihong Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Jianjian Zhuang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310006, P. R. China
| | - Jiale Li
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Kai Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
- School of information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
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18
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Li T, Cheng N. Sensitive and Portable Signal Readout Strategies Boost Point-of-Care CRISPR/Cas12a Biosensors. ACS Sens 2023; 8:3988-4007. [PMID: 37870387 DOI: 10.1021/acssensors.3c01338] [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: 10/24/2023]
Abstract
Point-of-care (POC) detection is getting more and more attention in many fields due to its accuracy and on-site test property. The CRISPR/Cas12a system is endowed with excellent sensitivity, target identification specificity, and signal amplification ability in biosensing because of its unique trans-cleavage ability. As a result, a lot of research has been made to develop CRISPR/Cas12a-based biosensors. In this review, we focused on signal readout strategies and summarized recent sensitivity-improving strategies in fluorescence, colorimetric, and electrochemical signaling. Then we introduced novel portability-improving strategies based on lateral flow assays (LFAs), microfluidic chips, simplified instruments, and one-pot design. In the end, we also provide our outlook for the future development of CRISPR/Cas12a biosensors.
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Affiliation(s)
- Tong Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Nan Cheng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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19
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Yun D, Jung C. MiRNA-Responsive CRISPR-Cas System via a DNA Regulator. BIOSENSORS 2023; 13:975. [PMID: 37998150 PMCID: PMC10669420 DOI: 10.3390/bios13110975] [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: 09/26/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)- CRISPR-associated protein 9 (Cas9) genome editing technology is widely used for gene editing because it provides versatility in genetic manipulation. Several methods for regulating CRISPR activity already exist for accurate editing, but these require complex engineering. Thus, a simple and convenient regulatory system is required. In this study, we devised a CRISPR activation system using a DNA regulator that can be activated by miRNAs. The designed regulator was divided into two parts. The inhibition component consisted of the protospacer-adjacent motif (PAM) and seed sequence, which are important for Cas9 target recognition and bind to the ribonucleoprotein (RNP) complex for inhibition. The miRNA recognition component has a single-stranded toehold DNA for target miRNA binding and a partial double-stranded DNA complementary to the remaining miRNA sequence. In the presence of target miRNAs, the structure of the regulator is disrupted by the miRNAs, leading to its dissociation from the RNP complex and subsequent restoration of CRISPR activity. This method is easy to design and can be applied to various miRNAs via simple sequence manipulation. Therefore, this strategy provides a general platform for controlled genome editing.
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Affiliation(s)
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea;
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20
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Li QN, Wang DX, Han GM, Liu B, Tang AN, Kong DM. Low-Background CRISPR/Cas12a Sensors for Versatile Live-Cell Biosensing. Anal Chem 2023; 95:15725-15735. [PMID: 37819747 DOI: 10.1021/acs.analchem.3c03131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The trans-cleavage activity of CRISPR/Cas12a has been widely used in biosensing. However, many CRISPR/Cas12a-based biosensors, especially those that work in "on-off-on" mode, usually suffer from high background and thus impossible intracellular application. Herein, this problem is efficiently overcome by elaborately designing the activator strand (AS) of CRISPR/Cas12a using the "RESET" effect found by our group. The activation ability of the as-designed AS to CRISPR/Cas12a can be easily inhibited, thus assuring a low background for subsequent biosensing applications, which not only benefits the detection sensitivity improvement of CRISPR/Cas12a-based biosensors but also promotes their applications in live cells as well as makes it possible to design high-performance biosensors with greatly improved flexibility, thus achieving the analysis of a wide range of targets. As examples, by using different strategies such as strand displacement, strand cleavage, and aptamer-substrate interaction to reactivate the inhibited enzyme activity, several CRISPR/Cas12a-based biosensing systems are developed for the sensitive and specific detection of different targets, including nucleic acid (miR-21), biological small molecules (ATP), and enzymes (hOGG1), giving the detection limits of 0.96 pM, 8.6 μM, and 8.3 × 10-5 U/mL, respectively. Thanks to the low background, these biosensors are demonstrated to work well for the accurate imaging analysis of different biomolecules in live cells. Moreover, we also demonstrate that these sensing systems can be easily combined with lateral flow assay (LFA), thus holding great potential in point-of-care testing, especially in poorly equipped or nonlaboratory environments.
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Affiliation(s)
- Qing-Nan Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Gui-Mei Han
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Bo Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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21
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Campuzano S, Pingarrón JM. Electrochemical Affinity Biosensors: Pervasive Devices with Exciting Alliances and Horizons Ahead. ACS Sens 2023; 8:3276-3293. [PMID: 37534629 PMCID: PMC10521145 DOI: 10.1021/acssensors.3c01172] [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: 06/12/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
Electrochemical affinity biosensors are evolving at breakneck speed, strengthening and colonizing more and more niches and drawing unimaginable roadmaps that increasingly make them protagonists of our daily lives. They achieve this by combining their intrinsic attributes with those acquired by leveraging the significant advances that occurred in (nano)materials technology, bio(nano)materials and nature-inspired receptors, gene editing and amplification technologies, and signal detection and processing techniques. The aim of this Perspective is to provide, with the support of recent representative and illustrative literature, an updated and critical view of the repertoire of opportunities, innovations, and applications offered by electrochemical affinity biosensors fueled by the key alliances indicated. In addition, the imminent challenges that these biodevices must face and the new directions in which they are envisioned as key players are discussed.
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Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica,
Facultad de Ciencias Químicas, Universidad
Complutense de Madrid, 28040 Madrid, España
| | - José M. Pingarrón
- Departamento de Química Analítica,
Facultad de Ciencias Químicas, Universidad
Complutense de Madrid, 28040 Madrid, España
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22
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Xiang X, Xing G, Liu Y, Wen Q, Wei Y, Lu J, Chen Y, Ji Y, Chen S, Liu T, Shang Y. Immunomagnetic Separation Combined with RCA-CRISPR/Cas12a for the Detection of Salmonella typhimurium on a Figure-Actuated Microfluidic Biosensor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13518-13526. [PMID: 37658470 DOI: 10.1021/acs.jafc.3c03799] [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: 09/03/2023]
Abstract
A figure-actuated microfluidic biosensor was developed for the rapid and sensitive detection of Salmonella typhimurium using immunomagnetic separation to separate target bacteria and rolling circle amplification (RCA) combined with CRISPR/Cas12a to amplify the detection signal. The magnetic nanoparticles (MNPs) modified with the capture antibodies (MNPs@Ab1) and RCA primer linked with recognized antibodies (primer@Ab2) were first used to react with S. typhimurium, resulting in the formation of MNPs@Ab1-S. typhimurium-primer@Ab2 complexes. Then, the RCA and CRISPR/Cas12a reagents were successively pumped into the chamber and incubated at the appropriate conditions. With the help of a 3D-printed signal detector, the fluorescence signal was collected and analyzed using the smartphone APP for the determination of bacterial concentration. This biosensor exhibited a wide linear range for the detection of S. typhimurium with a low limit of detection of 1.93 × 102 CFU/mL and a mean recovery of about 106% in the spiked milk sample.
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Affiliation(s)
- Xinran Xiang
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Gaowa Xing
- Xining Urban Vocational & Technical College, Xining 810000, China
| | - Yuting Liu
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Qianyu Wen
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuhuan Wei
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Jiaran Lu
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuanyuan Chen
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuhan Ji
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Shuhan Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tingting Liu
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuting Shang
- Department of Chemistry, Tsinghua University, Beijing 100084, PR China
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23
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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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24
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Zhang J, Jiang L, Li H, Yuan R, Yang X. Construction of a SERS platform for sensitive detection of aflatoxin B1 based on CRISPR strategy. Food Chem 2023; 415:135768. [PMID: 36848834 DOI: 10.1016/j.foodchem.2023.135768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/04/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
Aflatoxin B1, a pathogen in the aflatoxin family, has attracted much attention due to the harmfulness in production and life. However, the common methods like high performance liquid chromatography used for detection of AFB1 have deficiency in complicated pretreatment processes, and the purification effect is not ideal. Herein, a SERS platform based on CRISPR strategy was designed for sensitive detection of AFB1. By synthesizing core-shell nanoparticles embedded with Raman silent region dye molecules, Prussian blue (PB), the detection of the sensor reduced background interference and the SERS signal was calibrated. At the same time, the high-efficiency reverse cleavage activity of cas12a was used to convert non-nucleic acid targets into nucleic acid, so as to achieve the effect of sensitive detection of AFB1 with a detection limit of 3.55 pg/mL. This study provides a new thought for SERS detection of non-nucleic acid targets in the future.
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Affiliation(s)
- Jiale Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China
| | - Lingling Jiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China
| | - Hongying Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China
| | - Xia Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University) Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China.
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25
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Yu L, Peng Y, Sheng M, Wang Q, Huang J, Yang X. Sensitive and Amplification-Free Electrochemiluminescence Biosensor for HPV-16 Detection Based on CRISPR/Cas12a and DNA Tetrahedron Nanostructures. ACS Sens 2023; 8:2852-2858. [PMID: 37402133 DOI: 10.1021/acssensors.3c00806] [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: 07/05/2023]
Abstract
Rapid and accurate detection of biomarkers was very important for early screening and treatment of diseases. Herein, a sensitive and amplification-free electrochemiluminescence (ECL) biosensor based on CRISPR/Cas12a and DNA tetrahedron nanostructures (TDNs) was constructed. Briefly, 3D TDN was self-assembled on the Au nanoparticle-deposited glassy carbon electrode surface to construct the biosensing interface. The presence of the target would activate the trans-cleavage activity of Cas12a-crRNA duplex to cleave the single-stranded DNA signal probe on the vertex of TDN, causing the Ru(bpy)32+ to fall from the electrode surface and weakened the ECL signal. Thus, the CRISPR/Cas12a system transduced the change of target concentration into an ECL signal enabling the detection of HPV-16. The specific recognition of CRISPR/Cas12a to HPV-16 made the biosensor have good selectivity, while the TDN-modified sensing interface could reduce the cleaving steric resistance and improve the cleaving performance of CRISPR/Cas12a. In addition, the pretreated biosensor could complete sample detection within 100 min with a detection limit of 8.86 fM, indicating that the developed biosensor possesses the potential application prospect for fast and sensitive nucleic acid detection.
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Affiliation(s)
- Linying Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Yao Peng
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Mengting Sheng
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Qian Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, Anhui, China
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26
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Tiwari PK, Ko TH, Dubey R, Chouhan M, Tsai LW, Singh HN, Chaubey KK, Dayal D, Chiang CW, Kumar S. CRISPR/Cas9 as a therapeutic tool for triple negative breast cancer: from bench to clinics. Front Mol Biosci 2023; 10:1214489. [PMID: 37469704 PMCID: PMC10352522 DOI: 10.3389/fmolb.2023.1214489] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a third-generation genome editing method that has revolutionized the world with its high throughput results. It has been used in the treatment of various biological diseases and infections. Various bacteria and other prokaryotes such as archaea also have CRISPR/Cas9 systems to guard themselves against bacteriophage. Reportedly, CRISPR/Cas9-based strategy may inhibit the growth and development of triple-negative breast cancer (TNBC) via targeting the potentially altered resistance genes, transcription, and epigenetic regulation. These therapeutic activities could help with the complex issues such as drug resistance which is observed even in TNBC. Currently, various methods have been utilized for the delivery of CRISPR/Cas9 into the targeted cell such as physical (microinjection, electroporation, and hydrodynamic mode), viral (adeno-associated virus and lentivirus), and non-viral (liposomes and lipid nano-particles). Although different models have been developed to investigate the molecular causes of TNBC, but the lack of sensitive and targeted delivery methods for in-vivo genome editing tools limits their clinical application. Therefore, based on the available evidences, this review comprehensively highlighted the advancement, challenges limitations, and prospects of CRISPR/Cas9 for the treatment of TNBC. We also underscored how integrating artificial intelligence and machine learning could improve CRISPR/Cas9 strategies in TNBC therapy.
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Affiliation(s)
- Prashant Kumar Tiwari
- Biological and Bio-Computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Tin-Hsien Ko
- Department of Orthopedics, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Mandeep Chouhan
- Biological and Bio-Computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei City, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei City, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei City, Taiwan
| | - Himanshu Narayan Singh
- Department of Systems Biology, Columbia University Irving Medical Centre, New York, NY, United States
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Deen Dayal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Chih-Wei Chiang
- Department of Orthopedics, Taipei Medical University Hospital, Taipei City, Taiwan
- Department of Orthopedic Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei City, Taiwan
| | - Sanjay Kumar
- Biological and Bio-Computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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27
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Ivanov AV, Safenkova IV, Zherdev AV, Wan Y, Dzantiev BB. Comparison of Single-Stranded DNA Probes Conjugated with Magnetic Particles for Trans-Cleavage in Cas12a-Based Biosensors. BIOSENSORS 2023; 13:700. [PMID: 37504099 PMCID: PMC10376970 DOI: 10.3390/bios13070700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Biosensors based on endonuclease Cas12 provide high specificity in pathogen detection. Sensitive detection using Cas12-based assays can be achieved using trans-cleaved DNA probes attached to simply separated carriers, such as magnetic particles (MPs). The aim of this work was to compare polyA, polyC, and polyT single-stranded (ss) DNA with different lengths (from 10 to 145 nt) as trans-target probes were immobilized on streptavidin-covered MPs. Each ssDNA probe was labeled using fluorescein (5') and biotin (3'). To compare the probes, we used guide RNAs that were programmed for the recognition of two bacterial pathogens: Dickeya solani (causing blackleg and soft rot) and Erwinia amylovora (causing fire blight). The Cas12 was activated by targeting double-stranded DNA fragments of D. solani or E. amylovora and cleaved the MP-ssDNA conjugates. The considered probes demonstrated basically different dependencies in terms of cleavage efficiency. PolyC was the most effective probe when compared to polyA or polyT probes of the same length. The minimal acceptable length for the cleavage follows the row: polyC < polyT < polyA. The efficiencies of polyC and polyT probes with optimal length were proven for the DNA targets' detection of D. solani and E. amylovora. The regularities found can be used in Cas12a-based detection of viruses, bacteria, and other DNA/RNA-containing analytes.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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28
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Peng X, He Y, Zhao J, Tan K, Yuan R, Chen S. CRISPR/Cas12a-Mediated Aptasensor Based on Tris-(8-hydroxyquinoline)aluminum Microcrystals with Crystallization-Induced Enhanced Electrochemiluminescence for Acetamiprid Analysis. Anal Chem 2023. [PMID: 37339328 DOI: 10.1021/acs.analchem.3c01485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Improving the electrochemiluminescence (ECL) efficiency of luminophores has always been the goal of the ECL field. Herein, a novel crystallization-induced enhanced ECL (CIE ECL) strategy was exploited to significantly enhance the ECL efficiency of metal complex tris-(8-hydroxyquinoline)aluminum (Alq3). Alq3 monomers self-assembled and directionally grew to form Alq3 microcrystals (Alq3 MCs) in the presence of sodium dodecyl sulfate. The highly ordered crystal structure of Alq3 MCs not only constrained the intramolecular rotation of Alq3 monomers to decrease nonradiative transition but also accelerated the electron transfer between Alq3 MCs and coreactant tripropylamine to increase radiative transition, thus leading to a CIE ECL effect. Alq3 MCs exhibited brilliant anode ECL emission, which was 210-fold stronger than that of Alq3 monomers. The exceptional CIE ECL performance of Alq3 MCs coupled the efficient trans-cleavage activity of CRISPR/Cas12a assisted by rolling circle amplification and catalytic hairpin assembly to fabricate a CRISPR/Cas12a-mediated aptasensor for acetamiprid (ACE) detection. The limit of detection was as low as 0.79 fM. This work not only innovatively exploited a CIE ECL strategy to enhance the ECL efficiency of metal complexes but also integrated CRISPR/Cas12a with a dual amplification strategy for the ultrasensitive monitoring of pesticides such as ACE.
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Affiliation(s)
- Xiaoge Peng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, Sichuan 400715, P. R. China
| | - Ying He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, Sichuan 400715, P. R. China
| | - Jinwen Zhao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, Sichuan 400715, P. R. China
| | - Kejun Tan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, Sichuan 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, Sichuan 400715, P. R. China
| | - Shihong Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, Sichuan 400715, P. R. China
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29
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Wang X, Jing S, Wang W, Wang J. Direct and noninvasive fluorescence analysis of an RNA-protein interaction based on a CRISPR/Cas12a-powered assay. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 299:122884. [PMID: 37210856 DOI: 10.1016/j.saa.2023.122884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/25/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
RNA-protein interactions (RPIs) play critical roles in gene transcription and protein expression, but current analytical methods for RPIs are mainly performed in an invasive manner, involving special RNA/protein labeling, hampering access to intact and precise information on RPIs. In this work, we present the first CRISPR/Cas12a-based fluorescence assay for the direct analysis of RPIs without RNA/protein labeling steps. Select vascular endothelial growth factor 165 (VEGF165)/its RNA aptamer interaction as a model, the RNA sequence simultaneously serves as both the aptamer of VEGF165 and crRNA of CRISPR/Cas12a system, and the presence of VEGF165 facilitates VEGF165/its RNA aptamer interaction, thus prohibiting the formation of Cas12a-crRNA-DNA ternary complex along with low fluorescence signal. The assay showed a detection limit of 0.23 pg mL-1, and good performance in serum-spiked samples with an RSD of 0.4 %-13.1 %. This simple and selective strategy opens the door for establishing CRISPR/Cas-based biosensors for gaining intact information on RPIs, and shows widespread potential for other RPIs analysis.
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Affiliation(s)
- Xueliang Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China
| | - Shaozhen Jing
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China
| | - Wanhe Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China.
| | - Jing Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China.
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30
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Zhou M, Li X, Wen H, Huang B, Ren J, Zhang J. The construction of CRISPR/Cas9-mediated FRET 16S rDNA sensor for detection of Mycobacterium tuberculosis. Analyst 2023; 148:2308-2315. [PMID: 37083189 DOI: 10.1039/d3an00462g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The simple and efficient detection of nucleic acids is important in the diagnosis of tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis). However, base mismatch will lead to false positive and false negative nucleic acid test, which seriously interferes with the accuracy of the final results. Herein, we demonstrated a CRISPR/Cas-9-mediated fluorescent strategy utilizing fluorescence resonance energy transfer (FRET) for the detection of bacteria. High-variable region of M. tuberculosis 16S rDNA fragment was used as the target, and CRISPR/Cas9 was used as the recognition element. The binding of the P1 probe of upconversion nanoparticles (UCNPs) @SiO2-P1 and the P2 probe of Fe3O4@Au-P2 caused the fluorescence quenching of UCNPs. In the presence of the target, the P2 probe hybridized with the target to form double-stranded DNA (dsDNA), which was recognized and cleaved by CRISPR/Cas9, resulting in the breaking of the P1-P2 duplex linkage. UCNPs moved away from Fe3O4@Au under a magnetic field, and the fluorescence signal was restored; bacteria were detected under the excitation of a 980 nm laser source. Using the CRISPR/Cas-9-mediated system, the sensor could distinguish single-base mismatches in 10 bases from the protospacer adjacent motif (PAM) region. The limit of detection (LOD) was 20 CFU mL-1 and the detection time was 2 h. It developed a new way of accurate nucleic acid detection for disease diagnosis.
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Affiliation(s)
- Ming Zhou
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, P. R. China.
| | - Xin Li
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, P. R. China.
| | - Herui Wen
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, P. R. China.
| | - Bin Huang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, P. R. China.
| | - Jiali Ren
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Changsha, 410004, P. R. China.
| | - Jialin Zhang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, P. R. China.
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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31
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Hao J, Xie L, Yang T, Huo Z, Liu G, Liu Y, Xiong W, Zeng Z. Naked-eye on-site detection platform for Pasteurella multocida based on the CRISPR-Cas12a system coupled with recombinase polymerase amplification. Talanta 2023; 255:124220. [PMID: 36621165 DOI: 10.1016/j.talanta.2022.124220] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/08/2022] [Accepted: 12/25/2022] [Indexed: 01/04/2023]
Abstract
Pasteurella multocida (P. multocida) is an important pathogenic bacterium that poses a serious threat to the development of the livestock economy and human health. Currently, the existing methods for P. multocida detection are time-consuming and require complex professional operations, limiting the application of field detection. In the study, we presented a single-pot naked-eye CRISPR-Cas12a platform (Cas12a-NEye) for the detection of P. multocida. The round tube cover allowed more Cas12a detection solution to be temporarily stored than the flat cap, enabling single-pot assays and avoiding aerosol contamination. The positive samples generated obvious red using naked eye using no excitation light and the negative samples generated blue. The limit of detection (LOD) was a single copy, without cross-reactivity with other closely related bacteria. Furthermore, we validated this platform using 16 P. multocida clinical lung samples and obtained consistent results with the real-time quantitative polymerase chain reaction (qPCR) method. The entire experimental process included rapid DNA extraction (<1 h) and Cas12a-NEye assay (25 min), which was accomplished within 1.5 h. Thus, this "sample-to-answer" platform has significant potential for P. multocida detection.
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Affiliation(s)
- Jie Hao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China
| | - Tianmu Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China
| | - Zhipeng Huo
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China
| | - Guifang Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China
| | - Yahong Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China; National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China; National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou 510642, China.
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, 510642, China; National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou 510642, China.
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32
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Zhang Q, Zhang X, Zou X, Ma F, Zhang CY. CRISPR/Cas-Based MicroRNA Biosensors. Chemistry 2023; 29:e202203412. [PMID: 36477884 DOI: 10.1002/chem.202203412] [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: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
As important post-transcriptional regulators, microRNAs (miRNAs) play irreplaceable roles in diverse cellular functions. Dysregulated miRNA expression is implicated in various diseases including cancers, and thus miRNAs have become the valuable biomarkers for disease monitoring. Recently, clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) system has shown great promise for the development of next-generation biosensors because of its precise localization capability, good fidelity, and high cleavage activity. Herein, we review recent advance in development of CRISPR/Cas-based biosensors for miRNA detection. We summarize the principles, features, and performance of these miRNA biosensors, and further highlight the remaining challenges and future directions.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, 528458, P.R. China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University Institution, Nanjing, 211189, P.R. China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
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Yi JY, Kim M, Ahn JH, Kim BG, Son J, Sung C. CRISPR/deadCas9-based high-throughput gene doping analysis (HiGDA): A proof of concept for exogenous human erythropoietin gene doping detection. Talanta 2023; 258:124455. [PMID: 36933297 DOI: 10.1016/j.talanta.2023.124455] [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: 11/30/2022] [Revised: 03/07/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
A genetic approach targeted toward improving athletic performance is called gene doping and is prohibited by the World Anti-Doping Agency. Currently, the clustered regularly interspaced short palindromic repeats-associated protein (Cas)-related assays have been utilized to detect genetic deficiencies or mutations. Among the Cas proteins, deadCas9 (dCas9), a nuclease-deficient mutant of Cas9, acts as a DNA binding protein with a target-specific single guide RNA. On the basis of the principles, we developed a dCas9-based high-throughput gene doping analysis for exogenous gene detection. The assay comprises two distinctive dCas9s, a magnetic bead immobilized capture dCas9 for exogenous gene isolation and a biotinylated dCas9 with streptavidin-polyHRP that enables rapid signal amplification. For efficient biotin labeling via maleimide-thiol chemistry, two cysteine residues of dCas9 were structurally validated, and the Cys574 residue was identified as an essential labeling site. As a result, we succeeded in detecting the target gene in a concentration as low as 12.3 fM (7.41 × 105 copies) and up to 10 nM (6.07 × 1011 copies) in a whole blood sample within 1 h with HiGDA. Assuming an exogenous gene transfer scenario, we added a direct blood amplification step to establish a rapid analytical procedure while detecting target genes with high sensitivity. Finally, we detected the exogenous human erythropoietin gene at concentrations as low as 2.5 copies within 90 min in 5 μL of the blood sample. Herein, we propose that HiGDA is a very fast, highly sensitive, and practical detection method for actual doping field in the future.
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Affiliation(s)
- Joon-Yeop Yi
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea; Interdisciplinary Program of Bioengineering, Seoul National University, Seoul, 08826, South Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Minyoung Kim
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Jung Ho Ahn
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Byung-Gee Kim
- Interdisciplinary Program of Bioengineering, Seoul National University, Seoul, 08826, South Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea; Bio-Max/N-Bio Institute, Seoul National University, Seoul, 08826, South Korea; School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, South Korea; Institute for Sustainable Development (ISD), Seoul National University, Seoul, 08826, South Korea
| | - Junghyun Son
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Changmin Sung
- Doping Control Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea.
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34
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CRISPR-Cas assisted diagnostics: A broad application biosensing approach. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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35
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Ma L, Wang J, Li Y, Liao D, Zhang W, Han X, Man S. A ratiometric fluorescent biosensing platform for ultrasensitive detection of Salmonella typhimurium via CRISPR/Cas12a and silver nanoclusters. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130234. [PMID: 36372024 DOI: 10.1016/j.jhazmat.2022.130234] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Rapid, sensitive and specific detection of bacteria is of great importance. Herein, we developed a versatile biosensing platform for ultrasensitive detection of pathogenic bacteria, termed as SCENT-Cas (Silver nanoCluster Empowered Nucleic acids Test using CRISPR/Cas12a). Simply, the species-specific invA gene of Salmonella typhimurium (S. typhi) was isothermally amplified using LAMP, which subsequently triggered the trans-cleavage of CRISPR/Cas12a. The trans-cleavage degraded any single-stranded DNA (ssDNA) non-specifically. A DNA-templated AgNCs probe was then employed, in which green fluorescence emissive AgNCs effectively converted to red fluorescence emissive AgNCs when placed in close vicinity to a pre-designed converter ssDNA. As such, the trans-cleavage was utilized for shredding converter ssDNA, enabling the green-to-red fluorescent change to form a ratiometric biosensing platform. With this strategy, target nucleic acid was dexterously converted into ratiometric fluorescence that was recorded to detect as low as 1 CFU/mL S. typhi with a dynamic range from 1 to 108 CFU/mL. To our knowledge, this is the first report regarding the use of ratiometric fluorescence in CRISPR/Cas-based detection, which minimizes interference and improves reliability. Lastly, this proposed strategy was challenged by detecting S. typhi contamination in real food samples. Our work enriches CRISPR/Cas toolbox in biosensing by providing a desirable method for bacterial detection.
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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.
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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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36
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Liu Y, Wang F, Ge S, Zhang L, Zhang Z, Liu Y, Zhang Y, Ge S, Yu J. Programmable T-Junction Structure-Assisted CRISPR/Cas12a Electrochemiluminescence Biosensor for Detection of Sa-16S rDNA. ACS APPLIED MATERIALS & INTERFACES 2023; 15:617-625. [PMID: 36537539 DOI: 10.1021/acsami.2c18930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Herein, a strand displacement amplification (SDA)-assisted CRISPR/Cas12a (LbCpf1) electrochemiluminescence (ECL) biosensor was fabricated for ultrasensitive identification of Staphylococcus aureus (Sa)-16S rDNA. A porphyrinic Zr metal-organic framework (MOF) (PCN-224) nanomaterial was prepared as the coreactant accelerator, which promoted the conversion of S2O82- and SO4*-, thus enhancing the reaction with CdS quantum dots (QDs) and amplifying the ECL emission signal. Meanwhile, with the presence of Sa-16S rDNA, the auxiliary probes and primers stimulated the SDA reaction under the action of Klenow fragment (3'-5' exo-) and Nt. BbvCI specifically recognized Sa-16S rDNA to form a defective T-junction structure and generated second primers to initiate the cycles. Such a structure transformed the input signal (Sa-16S rDNA) into substantial single-stranded DNA products (SP) through SDA. SP acted as activators and activated arbitrary side chain cleavage of CRISPR/Cas12a (trans-cleavage) and further realized effective annihilation of ECL signals. This ECL platform demonstrated desirable assay performance for Sa-16S rDNA with a wide response range of 1 fM to 10 nM, and the limit of detection was 0.437 fM (S/N = 3), showing good sensitivity and specificity. Therefore, the method not only expanded the applications of CRISPR/Cas12a but also opened up a novel strategy for clinical diagnosis.
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Affiliation(s)
- Yaqi Liu
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan250022, P. R. China
| | - Fengyi Wang
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan250022, P. R. China
| | - Shuo Ge
- Department of Medical Laboratory, Shandong Medical College, Jinan250002, P. R. China
| | - Lu Zhang
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan250022, P. R. China
| | - Zuhao Zhang
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan250022, P. R. China
| | - Yunqing Liu
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan250022, P. R. China
| | - Yan Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan250022, P. R. China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan250022, P. R. China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan250022, P. R. China
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37
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Lin C, Huang Q, Tian M, Luo F, Wang J, Qiu B, Yang S, Lin Z. Electrochemiluminescence biosensor for DNA adenine methylation methyltransferase based on CRISPR/Cas12a trans-cleavage-induced dual signal enhancement. Talanta 2023; 251:123748. [PMID: 35921742 DOI: 10.1016/j.talanta.2022.123748] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/30/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022]
Abstract
In this work, an electrochemiluminescence (ECL) biosensor with dual signal enhancement was constructed and used for DNA adenine methylation methyltransferase (Dam MTase) detection. At present of Dam MTase, restriction endonuclease (DPnI) cleaves hairpin DNA (HP) and releases the HP stem end as a single strand that can activate CRISPR/Cas12a trans-cleavage activity. Assisted by trans-cleavage, the distance between the signal quenching factor ferrocene (Fc) and the ECL signal unit increased, and the repulsion between the signal unit and the Indium Tin Oxides (ITO) electrode decreased. The above results resulted in an enhanced ECL signal. ECL intensity has a good linear relationship with the logarithm of Dam MTase concentration in the range of 5-70 U/mL with a detection limit of 23.4 mU/mL. The proposed biosensor was successfully utilized to detect of Dam MTase in serum samples.
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Affiliation(s)
- Cuiying Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Qingqing Huang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Mengjian Tian
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Fang Luo
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Jian Wang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Shuofei Yang
- Department of Vascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Pujian Road 160, Shanghai, 200127, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China.
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38
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Green CM, Spangler J, Susumu K, Stenger DA, Medintz IL, Díaz SA. Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases. ACS NANO 2022; 16:20693-20704. [PMID: 36378103 DOI: 10.1021/acsnano.2c07749] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Joseph Spangler
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
- Jacobs Corporation, Hanover, Maryland21076, United States
| | - David A Stenger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C.20375, United States
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39
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Shang Y, Xing G, Liu X, Lin H, Lin JM. Fully Integrated Microfluidic Biosensor with Finger Actuation for the Ultrasensitive Detection of Escherichia coli O157:H7. Anal Chem 2022; 94:16787-16795. [DOI: 10.1021/acs.analchem.2c03686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Yuting Shang
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - Gaowa Xing
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - Xuejiao Liu
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - Haifeng Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - Jin-Ming Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, PR China
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40
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Recent advances on CRISPR/Cas system-enabled portable detection devices for on-site agri-food safety assay. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Ma W, Liu M, Xie S, Liu B, Jiang L, Zhang X, Yuan X. CRISPR/Cas12a system responsive DNA hydrogel for label-free detection of non-glucose targets with a portable personal glucose meter. Anal Chim Acta 2022; 1231:340439. [DOI: 10.1016/j.aca.2022.340439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/01/2022]
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42
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Zhou M, Wang H, Li C, Yan C, Qin P, Huang L. CRISPR/Cas9 mediated triple signal amplification platform for high selective and sensitive detection of single base mutations. Anal Chim Acta 2022; 1230:340421. [DOI: 10.1016/j.aca.2022.340421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/29/2022] [Accepted: 09/18/2022] [Indexed: 11/25/2022]
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43
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Huang Z, Liu S, Pei X, Li S, He Y, Tong Y, Liu G. Fluorescence Signal-Readout of CRISPR/Cas Biosensors for Nucleic Acid Detection. BIOSENSORS 2022; 12:bios12100779. [PMID: 36290917 PMCID: PMC9599699 DOI: 10.3390/bios12100779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/27/2022] [Accepted: 09/07/2022] [Indexed: 05/25/2023]
Abstract
The CRISPR/Cas system is now being used extensively in nucleic acid detection applications, particularly after the trans-cleavage activity of several Cas effectors was found. A CRISPR/Cas system combined with multiple signal-readout techniques has been developed for various molecular diagnostics applications. Fluorescence is now a widely utilized dominant read-out technique in CRISPR biosensors. An in-depth understanding of various fluorescence readout types and variables affecting the fluorescence signals can facilitate better experimental designs to effectively improve the analytical performance. There are the following two commonly used types of CRISPR/Cas detection modes: the first is based on binding activity, such as Cas9 and dCas9; the second is based on cleavage activity, such as Cas12a, Cas12b, Cas13, and Cas14. In this review, fluorescence signal-readout strategies from the last 5 years based on the binding activity and cleavage activity of the CRISPR/Cas system with fundamentals and examples are fully discussed. A detailed comparison of the available fluorescent reporter sequences and design principles is summarized. Current challenges and further applications of CRISPR-based detection methods will be discussed according to the most recent developments.
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Affiliation(s)
- Zhaohe Huang
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Sitong Liu
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Xiaojing Pei
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Shujing Li
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yifan He
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yigang Tong
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100029, China
| | - Guoqi Liu
- Biotecnovo (Beijing) Co., Ltd., Beijing Economic and Technological Development Zone, Beijing 100176, China
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Shu X, Zhang D, Li X, Zheng Q, Cai X, Ding S, Yan Y. Integrating CRISPR-Cas12a with a crRNA-Mediated Catalytic Network for the Development of a Modular and Sensitive Aptasensor. ACS Synth Biol 2022; 11:2829-2836. [PMID: 35946354 DOI: 10.1021/acssynbio.2c00224] [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: 11/28/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a, which exhibits excellent target DNA-activated trans-cleavage activity under the guidance of a programmable CRISPR RNA (crRNA), has shown great promise in next-generation biosensing technology. However, current CRISPR-Cas12a-based biosensors usually improve sensitivity by the initial nucleic acid amplification, while the distinct programmability and predictability of the crRNA-guided target binding process has not been fully exploited. Herein, we, for the first time, propose a modular and sensitive CRISPR-Cas12a fluorometric aptasensor by integrating an enzyme-free and robust crRNA-mediated catalytic nucleic acid network, namely, Cas12a-CMCAN, in which crRNA acts as an initiator to actuate cascade toehold-mediated strand displacement reactions (TM-SDRs). As a proof of concept, adenosine triphosphate (ATP) was selected as a model target. Owing to the multiturnover of CRISPR-Cas12a trans-cleavage and the inherent recycling amplification network, this method achieved a limit of detection value of 0.16 μM (20-fold lower than direct Cas12a-based ATP detection) with a linear range from 0.30 to 175 μM. In addition, Cas12a-CMCAN can be successfully employed to detect ATP levels in diluted human serum samples. Considering the simplicity, sensitivity, and easy to tune many targets by changing aptamer sequences, the Cas12a-CMCAN sensing method is expected to offer a heuristic idea for the development of CRISPR-Cas12a-based biosensors and unlock its potential for general and convenient molecule diagnostics.
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Affiliation(s)
- Xiaojia Shu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Decai Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Xingrong Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Qingyuan Zheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoying Cai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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Taghdisi SM, Ramezani M, Alibolandi M, Khademi Z, Hajihasani MM, Alinezhad Nameghi M, khakshour Abdolabadi A, Rahimi H, Abnous K, Danesh NM. A highly sensitive fluorescent aptasensor for detection of prostate specific antigen based on the integration of a DNA structure and CRISPR-Cas12a. Anal Chim Acta 2022; 1219:340031. [DOI: 10.1016/j.aca.2022.340031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022]
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46
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Xie Z, Chen S, Zhang W, Zhao S, Zhao Z, Wang X, Huang Y, Yi G. A novel fluorescence amplification strategy combining cascade primer exchange reaction with CRISPR/Cas12a system for ultrasensitive detection of RNase H activity. Biosens Bioelectron 2022; 206:114135. [DOI: 10.1016/j.bios.2022.114135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 12/16/2022]
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47
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Ma JY, Wang SY, Du YC, Wang DX, Tang AN, Wang J, Kong DM. "RESET" Effect: Random Extending Sequences Enhance the Trans-Cleavage Activity of CRISPR/Cas12a. Anal Chem 2022; 94:8050-8057. [PMID: 35615910 DOI: 10.1021/acs.analchem.2c01401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The trans-cleavage activity of CRISPR/Cas12a has been widely used in biosensing applications. However, the lack of exploration on the fundamental properties of CRISPR/Cas12a not only discourages further in-depth studies of the CRISPR/Cas12a system but also limits the design space of CRISPR/Cas12a-based applications. Herein, a "RESET" effect (random extending sequences enhance trans-cleavage activity) is discovered for the activation of CRISPR/Cas12a trans-cleavage activity. That is, a single-stranded DNA, which is too short to work as the activator, can efficiently activate CRISPR/Cas12a after being extended a random sequence from its 3'-end, even when the random sequence folds into secondary structures. The finding of the "RESET" effect enriches the CRISPR/Cas12a-based sensing strategies. Based on this effect, two CRISPR/Cas12a-based biosensors are designed for the sensitive and specific detection of two biologically important enzymes.
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Affiliation(s)
- Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Si-Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China.,School of Medical Laboratory, College of Medical Technology, Tianjin Medical University, Guangdong Road, Tianjin 300203, People's Republic of China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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48
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Dai B, Xiang A, Qu D, Chen G, Wang L, Wang W, Zhai D, Wang L, Lu Z. Rapid and Sensitive Assay of Helicobacter pylori With One-Tube RPA-CRISPR/Cas12 by Portable Array Detector for Visible Analysis of Thermostatic Nucleic Acid Amplification. Front Microbiol 2022; 13:858247. [PMID: 35586866 PMCID: PMC9108776 DOI: 10.3389/fmicb.2022.858247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2022] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori (H. pylori) has infected more than half of the world’s population and is still a threat to human health. The urea breath test, despite being widely used in clinical diagnosis, still faces huge challenges in the immediate detection of H. pylori. Thus, a rapid, sensitive, and highly specific point of care diagnosis is particularly important for preventing the further transmission of H. pylori and for real-time monitoring of the disease in a given population. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have been applied to various types of nucleic acid testing; however, there are often shortcomings of complex operation and high signal transmission background. In this study, we proposed a new platform for the assay of H. pylori using one-tube-based CRISPR/Cas12a diagnostic methods and designed a detector for this platform, which is a portable array detector for visible analysis of thermostatic nucleic acid amplification (Pad-VATA). By incorporating isothermal recombinase polymerase amplification, our platform could detect the conserved gene fragments of H. pylori with a constant low as 2 copies/μl. The assay process can be performed at a single temperature in about 30 min and integrated into the reactor in the palm-sized Pad-VATA to facilitate rapid diagnosis of H. pylori. We also verified the accuracy of our platform using 10 clinical samples and found that the platform can quickly detect H. pylori infection in a given population. We believe that this fast, convenient, efficient, and inexpensive screening and diagnostic platform can be widely used in various settings, including homes and clinics.
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Affiliation(s)
- Bing Dai
- The College of Life Sciences, Northwest University, Xi’an, China
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - An Xiang
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - Di Qu
- The College of Life Sciences, Northwest University, Xi’an, China
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - Guo Chen
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - Li Wang
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - Wenwen Wang
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - Dongsheng Zhai
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
| | - Lei Wang
- Department of Gastrointestinal Surgery, General Hospital of Ningxia Medical University, Ningxia, China
- *Correspondence: Lei Wang,
| | - Zifan Lu
- Department of Biopharmaceutics, State Key Laboratory of Cancer Biology, Air Force Medical University, Xi’an, China
- Zifan Lu,
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49
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Chi Z, Wu Y, Chen L, Yang H, Khan MR, Busquets R, Huang N, Lin X, Deng R, Yang W, Huang J. CRISPR-Cas14a-integrated strand displacement amplification for rapid and isothermal detection of cholangiocarcinoma associated circulating microRNAs. Anal Chim Acta 2022; 1205:339763. [DOI: 10.1016/j.aca.2022.339763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/23/2022]
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50
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Fu R, Wang Y, Liu Y, Liu H, Zhao Q, Zhang Y, Wang C, Li Z, Jiao B, He Y. CRISPR-Cas12a based fluorescence assay for organophosphorus pesticides in agricultural products. Food Chem 2022; 387:132919. [PMID: 35421656 DOI: 10.1016/j.foodchem.2022.132919] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 12/26/2022]
Abstract
Herein, we propose a sensitive fluorescent assay for organophosphorus pesticides (OPs) detection based on a novel strategy of activating the CRISPR-Cas12a system. Specifically, acetylcholinesterase (AChE) hydrolyzes acetylthiocholine into thiocholine (TCh). Subsequently, TCh induces the degradation of MnO2 nanosheets and generates sufficient Mn2+ ions to activate the Mn2+-dependent DNAzyme. Then, as the catalytic product of activated DNAzyme, the short DNA strand activates the CRISPR-Cas12a system to cleave the fluorophore-quencher-labeled DNA reporter (FQ) probe effectively; thus, increasing the fluorescence intensity (FI) in the solution. However, in the presence of OPs, the activity of AChE is suppressed, resulting in a decrease in FI. Under optimized conditions, the limits of detection for paraoxon, dichlorvos, and demeton were 270, 406, and 218 pg/mL, respectively. Benefiting from the outstanding MnO2 nanosheets properties and three rounds of enzymatic signal amplification, the proposed fluorescence assay holds great potential for the detection of OPs in agricultural products.
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Affiliation(s)
- Ruijie Fu
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Yiwen Wang
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Yanlin Liu
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Haoran Liu
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Qiyang Zhao
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Yaohai Zhang
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Chengqiu Wang
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Zhixia Li
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China
| | - Bining Jiao
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China.
| | - Yue He
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing), Ministry of Agriculture, Citrus Research Institute, Southwest University, Chongqing 400712, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China.
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