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Yuan A, Sha R, Xie W, Qu G, Zhang H, Wang H, Le XC, Jiang G, Peng H. RNA-Activated CRISPR/Cas12a Nanorobots Operating in Living Cells. J Am Chem Soc 2024; 146:26657-26666. [PMID: 39183441 DOI: 10.1021/jacs.4c02354] [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: 08/27/2024]
Abstract
Active clustered regularly interspaced short palindromic repeats (CRISPR/Cas12a) systems possess both cis-cleavage (targeted) and trans-cleavage (collateral) activities, which are useful for genome engineering and diagnostic applications. Both single- and double-stranded DNA can activate crRNA-Cas12a ribonucleoprotein (RNP) to achieve cis- and trans-cleavage enzymatic activities. However, it is not clear whether RNA can activate the CRISPR/Cas12a system and what is critical to the trans-cleavage activity. We report here that RNA can activate the CRISPR/Cas12a system and trigger its trans-cleavage activity. We reveal that the activated crRNA-Cas12a RNP favors the trans-cleavage of longer sequences than commonly used. These new findings of the RNA-activated trans-cleavage capability of Cas12a provided the foundation for the design and construction of CRISPR nanorobots that operate in living cells. We assembled the crRNA-Cas12a RNP and nucleic acid substrates on gold nanoparticles to form CRISPR nanorobots, which dramatically increased the local effective concentration of the substrate in relation to the RNP and the trans-cleavage kinetics. Binding of the target microRNA to the crRNA-Cas12a RNP activated the nanorobots and their trans-cleavage function. The repeated (multiple-turnover) trans-cleavage of the fluorophore-labeled substrates generated amplified fluorescence signals. Sensitive and real-time imaging of specific microRNA in live cells demonstrated the promising potential of the CRISPR nanorobot system for future applications in monitoring and modulating biological functions within living cells.
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Affiliation(s)
- Aijiao Yuan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Sha
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Hongquan Zhang
- Division of Analytical & Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - X Chris Le
- Division of Analytical & Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Hanyong Peng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Chen J, Su H, Kim JH, Liu L, Liu R. Recent advances in the CRISPR/Cas system-based visual detection method. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39345221 DOI: 10.1039/d4ay01147c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Currently, various infectious pathogens and bacterial toxins as well as heavy metal pollution pose severe threats to global environmental health and the socio-economic infrastructure. Therefore, there is a pressing need for rapid, sensitive, and convenient visual molecular detection methods. The rapidly evolving detection approach based on clustered regularly interspaced short palindromic repeats (CRISPR)/associated nucleases (Cas) has opened a new frontier in the field of molecular diagnostics. This paper reviews the development of visual detection methods in recent years based on different Cas and analyzes their advantages and disadvantages as well as the challenges of future research. Firstly, different CRISPR/Cas effectors and their working principles in the diagnosis of various diseases are briefly reviewed. Subsequently, the article focuses on the development of visual readout signals in point-of-care testing using laboratory-based CRISPR/Cas technology, including colorimetric, fluorescence, and lateral flow analysis. Finally, the challenges and prospects of visual detection methods based on CRISPR/Cas technology are discussed.
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Affiliation(s)
- Jinrong Chen
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong 18323, Korea.
- Shandong Province Key Laboratory of Detection Technology of Tumor Markers, Linyi University, Linyi 276005, China.
| | - Hang Su
- Shandong Province Key Laboratory of Detection Technology of Tumor Markers, Linyi University, Linyi 276005, China.
| | - June Hyun Kim
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong 18323, Korea.
| | - Lishang Liu
- Shandong Province Key Laboratory of Detection Technology of Tumor Markers, Linyi University, Linyi 276005, China.
| | - Rui Liu
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong 18323, Korea.
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Lee DG, Min YH, Byun JY, Shin YB. Small Molecule Detection with Ligation-Dependent Light-Up Aptamer Transcriptional Amplification. ACS APPLIED BIO MATERIALS 2024. [PMID: 39315418 DOI: 10.1021/acsabm.4c00987] [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: 09/25/2024]
Abstract
ATP and NAD+ are small biomolecules that participate in a variety of physiological functions and are considered as potential biomarkers for disease diagnosis. In this study, we developed a ligation-dependent light-up aptamer transcriptional amplification assay for the sensitive and selective detection of ATP and NAD+. This assay relies on a specific DNA ligase that catalyzes the ligation of a nicked DNA template in the presence of a specific small molecule. We prepared a nicked template consisting of a duplex fragment with an overhang for the T7 promoter region and a single-stranded DNA with a complementary overhang sequence for the Broccoli aptamer. The nicked template was connected using a DNA ligase in the presence of a specific small molecule. The ligation product was subjected to in vitro transcription to amplify the light-up aptamer-mediated fluorescence signals. By integrating the target-dependent ligation and transcription amplification, significant signal amplification was achieved with 5.9 and 142 pM detection limits for ATP and NAD+, respectively. Moreover, good selectivity to discriminate between the target and its analogues was also realized. The application of this method to biological samples was evaluated using human serum and exhibited excellent recovery values.
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Affiliation(s)
- Deok-Gyu Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305-764, Korea
| | - Yoo-Hong Min
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Ju-Young Byun
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Yong-Beom Shin
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
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4
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Lei W, Hao L, Qiu H, Bian K, Cui T, Zeng W, Zhang Y, Yang W, Zhang B. Quantum-Dot-Encoded Beads-Enhanced CRISPR/Cas-Based Lateral-Flow Assay for the Amplification-Free, Sensitive, and Rapid Detection of Nucleic Acids in Breast Cancer. ACS APPLIED MATERIALS & INTERFACES 2024; 16:44399-44408. [PMID: 39145508 DOI: 10.1021/acsami.4c05388] [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: 08/16/2024]
Abstract
Nucleic acid detection plays a pivotal role in the accurate diagnosis of diseases. The CRISPR/Cas detection system, noted for its significant utility in a variety of applications, often necessitates enhanced sensitivity or specific signal amplification strategies, particularly for detecting low-abundance biomarkers. In this study, we present a quantum-dot-encoded beads (QDB)-energized CRISPR/Cas12-based lateral-flow assay (QDB-CRISPR-LFA). This method enables amplification-free, sensitive, and rapid detection (<40 min) of BRCA-1. We validated our method using contrived reference samples and nucleic acids extracted from tumor cells. The QDB-CRISPR-LFA provides a visual, more rapid alternative to the traditional BRCA-1 real-time RT-PCR assay. Significantly, through the integration of CRISPR's specificity and the high signal output of QDB, the detection threshold for BRCA-1 has been reduced to the femtomolar level, representing an enhancement of 2-4 orders of magnitude over existing CRISPR/Cas detection methods. This advancement underscores the potential of our approach in advancing nucleic acid detection techniques, which is crucial for the early and precise diagnosis of diseases.
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Affiliation(s)
- Wenjing Lei
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Liangwen Hao
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Han Qiu
- Galactophore Department, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou 434200, China
| | - Kexin Bian
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Tianming Cui
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Weiwei Zeng
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Yu Zhang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Weitao Yang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Bingbo Zhang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
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5
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Liu H, Dong J, Duan Z, Xia F, Willner I, Huang F. Light-activated CRISPR-Cas12a for amplified imaging of microRNA in cell cycle phases at single-cell levels. SCIENCE ADVANCES 2024; 10:eadp6166. [PMID: 39047109 PMCID: PMC11268419 DOI: 10.1126/sciadv.adp6166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024]
Abstract
An ortho-nitrobenzyl phosphate ester-caged nucleic acid hairpin structure coupled to the CRISPR-Cas12a complex is introduced as a functional reaction module for the light-induced activation of the CRISPR-Cas12a (LAC12a) machinery toward the amplified fluorescence detection of microRNA-21 (miRNA-21). The LAC12a machinery is applied for the selective, in vitro sensing of miRNA-21 and for the intracellular imaging of miRNA-21 in different cell lines. The LAC12a system is used to image miRNA-21 in different cell cycle phases of MCF-7 cells. Moreover, the LAC12a machinery integrated in cells enables the two-photon laser confocal microscopy-assisted, light-stimulated spatiotemporal, selective activation of the CRISPR-Cas12a miRNA-21 imaging machinery at the single-cell level and the evaluation of relative expression levels of miRNA-21 at distinct cell cycle phases. The method is implemented to map the distribution of cell cycle phases in an array of single cells.
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Affiliation(s)
- Hong Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Jiantong Dong
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Itamar Willner
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fujian Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
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Wei C, Lei X, Yu S. Multiplexed Detection Strategies for Biosensors Based on the CRISPR-Cas System. ACS Synth Biol 2024; 13:1633-1646. [PMID: 38860462 DOI: 10.1021/acssynbio.4c00161] [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: 06/12/2024]
Abstract
A growing number of applications require simultaneous detection of multiplexed nucleic acid targets in a single reaction, which enables higher information density in combination with reduced assay time and cost. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-Cas system have broad applications for the detection of nucleic acids due to their strong specificity, high sensitivity, and excellent programmability. However, realizing multiplexed detection is still challenging for the CRISPR-Cas system due to the nonspecific collateral cleavage activity, limited signal reporting strategies, and possible cross-reactions. In this review, we summarize the principles, strategies, and features of multiplexed detection based on the CRISPR-Cas system and further discuss the challenges and perspective.
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Affiliation(s)
- Cong Wei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
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7
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Zhang C, Zhao X, Huang Z, Li Z, Hu J, Liu R, Lv Y. Highly sensitive detection of aflatoxin B1 byCRISPR/Cas12a-assisted single nanoparticle counting. Food Chem 2024; 443:138557. [PMID: 38280363 DOI: 10.1016/j.foodchem.2024.138557] [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: 09/11/2023] [Revised: 12/28/2023] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) and CRISPR-associated protein (Cas) have gained extensive applications in bioassays. However, CRISPR-based detection platforms are often hampered by limited analytical sensitivity, while nucleic acid-based amplification strategies are usually indispensable for additional signal enhancement with potential risks of amplification leakages. To address these challenges, an amplification-free CRISPR-based bioassay of aflatoxin B1 (AFB1) was proposed by applying single nanoparticle counting. Single-particle mode inductively coupled plasma mass spectrometry (Sp-ICPMS) has been regarded as a sensitive tool for nanoparticle counting since one nanoparticle can generate considerable signals above backgrounds. With AFB1, activator strands were introduced to initiate the trans-cleavage of CRISPR/Cas12a for cutting the nanoparticles-tagged-magnetic beads, which were transduced to nanoparticle count signals after separation. Finally, a pico-mole level limit-of-detections (LODs) with moderate selectivity was achieved. Certified reference materials (CRMs) analysis and recovery tests were conducted with promising results. To our best knowledge, this is the first report of the single particle counting-based CRISPR/Cas12a biosensing study.
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Affiliation(s)
- Chengchao Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Xin Zhao
- Department of Clinical Laboratory, Chengdu Seventh People's Hospital, Chengdu, Sichuan 610041, PR China
| | - Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ziyan Li
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China.
| | - Yi Lv
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
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8
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Qiu M, Yuan Z, Li N, Yang X, Zhang X, Jiang Y, Zhao Q, Man C. Self-assembled bifunctional nanoflower-enabled CRISPR/Cas biosensing platform for dual-readout detection of Salmonella enterica. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134323. [PMID: 38640680 DOI: 10.1016/j.jhazmat.2024.134323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
Sensitive detection and point-of-care test of bacterial pathogens is of great significance in safeguarding the public health worldwide. Inspired by the characteristics of horseradish peroxidase (HRP), we synthesized a hybrid nanoflower with peroxidase-like activity via a three-component self-assembled strategy. Interestingly, the prepared nanozyme not only could act as an alternative to HRP for colorimetric biosensing, but also function as a unique signal probe that could be recognized by a pregnancy test strip. By combining the bifunctional properties of hybrid nanoflower, isothermal amplification of LAMP, and the specific recognition and non-specific cleavage properties of CRISPR/Cas12a system, the dual-readout CRISPR/Cas12a biosensor was developed for sensitive and rapid detection of Salmonella enterica. Moreover, this platform in the detection of Salmonella enterica had limits of detection of 1 cfu/mL (colorimetric assay) in the linear range of 101-108 cfu/mL and 102 cfu/mL (lateral flow assay) in the linear range of 102-108 cfu/mL, respectively. Furthermore, the developed biosensor exhibited good recoveries in the spiked samples (lake water and milk) with varying concentrations of Salmonella enterica. This work provides new insights for the design of multifunctional nanozyme and the development of innovative dual-readout CRISPR/Cas system-based biosensing platform for the detection of pathogens.
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Affiliation(s)
- Manyan Qiu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhiyu Yuan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Nan Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xianlong Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
| | - Qianyu Zhao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
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Zhang D, Jiang S, Xia N, Zhang J, Liu A, Deng D, Zhang C, Sun Y, Chen N, Kang X, Pan Z, Zheng W, Zhu J. Development of visual detection of African swine fever virus using CRISPR/LwCas13a lateral flow strip based on structural protein gene D117L. Vet Microbiol 2024; 293:110073. [PMID: 38579481 DOI: 10.1016/j.vetmic.2024.110073] [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: 01/08/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
African swine fever virus (ASFV) is a large double stranded DNA arbovirus that is highly contagious and seriously endangers domestic and wild pigs. In the past decade, African swine fever (ASF) has spread in many countries in the Caucasus, Russian Federation, Eastern Europe and Asia, causing significant losses to the pig industry. At present, there is a lack of effective vaccine and treatment for ASF. Therefore, the rapid and accurate detection is crucial for ASF prevention and control. In this study, we have developed a portable lateral flow strip (LFS) detection mediated by recombinase polymerase amplification (RPA) and CRISPR/LwCas13a, which is performed at 37 ℃ and visualized by eyes without the need for complex instruments. This RPA-LwCas13a-LFS is based on the ASFV structural protein p17 gene (D117L), with a detection sensitivity up to 2 gene copies. This method is highly specific and has no cross reactivity to 7 other pig viruses. In the detection of two batches of 100 clinical samples, the p17 (D117L) RPA-LwCas13a-LFS had 100% coincidence with conventional quantitative PCR (qPCR). These findings demonstrate the potential of this simple, rapid, sensitive, and specific ASFV detection method for on-site ASFV detection.
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Affiliation(s)
- Desheng Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Sen Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Nengwen Xia
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Jiajia Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Anjing Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Dafu Deng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Chenyang Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Yuxin Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Xilong Kang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Zhiming Pan
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China.
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, PR China; Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, PR China.
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10
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Xia Y, Rao R, Xiong M, He B, Zheng B, Jia Y, Li Y, Yang Y. CRISPR-Powered Strategies for Amplification-Free Diagnostics of Infectious Diseases. Anal Chem 2024; 96:8091-8108. [PMID: 38451204 DOI: 10.1021/acs.analchem.3c04363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Affiliation(s)
- Yupiao Xia
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruotong Rao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengqiu Xiong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bangshun He
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bingxin Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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11
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Shi J, Li S, Shao R, Jiang Y, Qiao Y, Liu J, Zhou Y, Li Y. Electrochemiluminescence aptasensing method for ultrasensitive determination of lipopolysaccharide based on CRISPR-Cas12a accessory cleavage activity. Talanta 2024; 272:125828. [PMID: 38428132 DOI: 10.1016/j.talanta.2024.125828] [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: 10/26/2023] [Revised: 02/17/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
In this study, an ultrasensitive electrochemiluminescence (ECL) aptasensing method was developed for lipopolysaccharide (LPS) determination based on CRISPR-Cas12a accessory cleavage activity. Tris (2,2'-bipyridine) dichlororuthenium (II) (Ru(bpy)32+) was adsorbed on the surface of a glassy carbon electrode (GCE) coated with a mixture of gold nanoparticles (AuNPs) and Nafion film via electrostatic interaction. The obtained ECL platform (Ru(bpy)32+/AuNP/Nafion/GCE) exhibited strong ECL emission. Thiol-functionalized single-stranded DNA (ssDNA) was modified with a ferrocenyl (Fc) group and autonomously assembled on the ECL platform of Ru(bpy)32+/AuNP/Nafion/GCE via thiol-gold bonding, resulting in the quenching of ECL emission. After hybridization of the LPS aptamer strand (AS) with its partial complementary strand (CS), the formed double-stranded DNA (dsDNA) could activate CRISPR-Cas12a to indiscriminately cleave ssDNA-Fc on the surface of Ru(bpy)32+/AuNP/Nafion/GCE, resulting in recovery of the ECL intensity of Ru(bpy)32+ due to the increasing distance between Fc and the electrode surface. The combination of LPS and AS suppressed the formation of dsDNA, inhibited the activation of CRISPR-Cas12a, and prevented further cleavage of ssDNA-Fc. This mechanism aided in upholding the integrity of ssDNA-Fc on the surface of the electrode and was combined with ECL quenching induced by the target. The ECL intensity decreased linearly as the concentration of LPS increased from 1 to 50,000 pg/mL and followed a logarithmic relationship. This method exhibited a remarkably low detection limit of 0.24 pg/mL, which meets the requirement for low-concentration detection of LPS in the human body. The proposed method demonstrates the capacity of CRISPR-Cas12a to perform non-specific cutting of single-stranded DNA and transform the resultant cutting substances into changes in the ECL signal. By amalgamating this approach with the distinct identification abilities of LPS and its aptamers, a simple, responsive, and discriminatory LPS assay was established that holds immense significance for clinical diagnosis.
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Affiliation(s)
- Jiayue Shi
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China
| | - Sijia Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China
| | - Rongguang Shao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China
| | - Yang Jiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China
| | - Yanxia Qiao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China
| | - Jin Liu
- Shaanxi Key Laboratory of Catalysis, School of Chemistry and Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi, 723000, China.
| | - Yaqian Zhou
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China.
| | - Yan Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, China.
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12
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Wu Y, Jin R, Chang Y, Liu M. A high-fidelity DNAzyme-assisted CRISPR/Cas13a system with single-nucleotide resolved specificity. Chem Sci 2024; 15:6934-6942. [PMID: 38725495 PMCID: PMC11077575 DOI: 10.1039/d4sc01501k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 05/12/2024] Open
Abstract
A CRISPR/Cas system represents an innovative tool for developing a new-generation biosensing and diagnostic strategy. However, the off-target issue (i.e., mistaken cleavage of nucleic acid targets and reporters) remains a great challenge for its practical applications. We hypothesize that this issue can be overcome by taking advantage of the site-specific cleavage ability of RNA-cleaving DNAzymes. To test this idea, we propose a DNAzyme Operation Enhances the Specificity of CRISPR/Cas13a strategy (termed DOES-CRISPR) to overcome the problem of relatively poor specificity that is typical of the traditional CRISPR/Cas13a system. The key to the design is that the partial hybridization of the CRISPR RNA (crRNA) with the cleavage fragment of off-target RNA was not able to activate the collateral cleavage activity of Cas13a. We showed that DOES-CRISPR can significantly improve the specificity of traditional CRISPR/Cas13a-based molecular detection by up to ∼43-fold. The broad utility of the strategy is illustrated through engineering three different systems for the detection of microRNAs (miR-17 and let-7e), CYP2C19*17 gene, SARS-Cov-2 variants (Gamma, Delta, and Omicron) and Omicron subtypes (BQ.1 and XBB.1) with single-nucleotide resolved specificity. Finally, clinical evaluation of this assay using 10 patient blood samples demonstrated a clinical sensitivity of 100% and specificity of 100% for genotyping CYP2C19*17, and analyzing 20 throat swab samples provided a diagnostic sensitivity of 95% and specificity of 100% for Omicron detection, and a clinical sensitivity of 92% and specificity of 100% for XBB.1 detection.
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Affiliation(s)
- Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Ruigang Jin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
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13
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Yang C, Du C, Yuan F, Yu P, Wang B, Su C, Zou R, Wang J, Yan X, Sun C, Li H. CRISPR/Cas12a-derived ratiometric fluorescence sensor for high-sensitive Pb 2+ detection based on CDs@ZIF-8 and DNAzyme. Biosens Bioelectron 2024; 251:116089. [PMID: 38354496 DOI: 10.1016/j.bios.2024.116089] [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: 10/15/2023] [Revised: 12/26/2023] [Accepted: 01/28/2024] [Indexed: 02/16/2024]
Abstract
Benefiting from specific target recognition and trans-cleavage capabilities, the CRISPR/Cas12a system has great application prospects in the design of highly sensitive and rapid fluorescence biosensors. The CRISPR/Cas12a-based fluorophore-quencher molecular beacons exhibit single-color emission and are easily exposed to interference from environmental factors. Herein, we design a CRISPR/Cas12a-derived ratiometric fluorescence sensor for Pb2+ detection based on embedded carbon dots@zeolitic imidazolate framework-8 (CDs@ZIF-8) composites and DNAzyme. The functions of ZIF-8 about encapsulating red emissive CDs in the inner cavity and adsorbing DNA on the outer surface are integrated to establish dual fluorescence signals, thereby reducing the possibility of interference and improving sensing accuracy. The presence of Pb2+ is converted into the change of activator by the GR5 DNAzyme to activate the CRISPR/Cas12a system, which provides signal amplification through multiple turnovers of side branch cutting, achieving highly sensitive detection of Pb2+ with a low detection limit of 18 pM. This method has the advantages of simplicity, universality, and excellent quantitative ability, and has broad prospects in sensing applications.
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Affiliation(s)
- Chuanyu Yang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Caiyi Du
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Feiyu Yuan
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Peitong Yu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Boxu Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Changshun Su
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Ruiqi Zou
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Xu Yan
- College of Electronic Science and Engineering, Jilin University, Changchun 130012, China
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China.
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China; Chongqing Research Institute, Jilin University, Chongqing 401123, China.
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14
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Yang S, Zhou L, Fang Z, Wang Y, Zhou G, Jin X, Cao Y, Zhao J. Proximity-Guaranteed DNA Machine for Accurate Identification of Breast Cancer Extracellular Vesicles. ACS Sens 2024; 9:2194-2202. [PMID: 38621146 DOI: 10.1021/acssensors.4c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Breast cancer is one of the most diagnosed cancers worldwide. Precise diagnosis and subtyping have important significance for targeted therapy and prognosis prediction of breast cancer. Herein, we design a proximity-guaranteed DNA machine for accurate identification of breast cancer extracellular vesicles (EVs), which is beneficial to explore the subtype features of breast cancer. In our design, two proximity probes are located close on the same EV through specific recognition of coexisting surface biomarkers, thus being ligated with the help of click chemistry. Then, the ligated product initiates the operation of a DNA machine involving catalytic hairpin assembly and clusters of regularly interspaced short palindromic repeats (CRISPR)-Cas12a-mediated trans-cleavage, which finally generates a significant response that enables the identification of EVs expressing both biomarkers. Principle-of-proof studies are performed using EVs derived from the breast cancer cell line BT474 as the models, confirming the high sensitivity and specificity of the DNA machine. When further applied to clinical samples, the DNA machine is shown to be capable of not only distinguishing breast cancer patients with special subtypes but also realizing the tumor staging regarding the disease progression. Therefore, our work may provide new insights into the subtype-based diagnosis of breast cancer as well as identification of more potential therapeutic targets in the future.
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Affiliation(s)
- Shuang Yang
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Liang Zhou
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhikai Fang
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ying Wang
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 201321, China
| | - Guozhang Zhou
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xi Jin
- Key Laboratory of Breast Cancer, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai 201321, China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, China
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15
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Cao H, Mao K, Yang J, Wu Q, Hu J, Zhang H. High-Throughput μPAD with Cascade Signal Amplification through Dual Enzymes for arsM in Paddy Soil. Anal Chem 2024; 96:6337-6346. [PMID: 38613479 DOI: 10.1021/acs.analchem.3c05958] [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: 04/15/2024]
Abstract
The arsM gene is a critical biomarker for the potential risk of arsenic exposure in paddy soil. However, on-site screening of arsM is limited by the lack of high-throughput point-of-use (POU) methods. Here, a multiplex CRISPR/Cas12a microfluidic paper-based analytical device (μPAD) was constructed for the high-throughput POU analysis of arsM, with cascade amplification driven by coupling crRNA-enhanced Cas12a and horseradish peroxidase (HRP)-modified probes. First, seven crRNAs were designed to recognize arsM, and their LODs and background signal intensities were evaluated. Next, a step-by-step iterative approach was utilized to develop and optimize coupling systems, which improved the sensitivity 32 times and eliminated background signal interference. Then, ssDNA reporters modified with HRP were introduced to further lower the LOD to 16 fM, and the assay results were visible to the naked eye. A multiplex channel microfluidic paper-based chip was developed for the reaction integration and simultaneous detection of 32 samples and generated a recovery rate between 87.70 and 114.05%, simplifying the pretreatment procedures and achieving high-throughput POU analysis. Finally, arsM in Wanshan paddy soil was screened on site, and the arsM abundance ranged from 1.05 × 106 to 6.49 × 107 copies/g; this result was not affected by the environmental indicators detected in the study. Thus, a coupling crRNA-based cascade amplification method for analyzing arsM was constructed, and a microfluidic device was developed that contains many more channels than previous paper chips, greatly improving the analytical performance in paddy soil samples and providing a promising tool for the on-site screening of arsM at large scales.
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Affiliation(s)
- Haorui Cao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Jiajia Yang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Qingqing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiming Hu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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16
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Zhu D, Su T, Sun T, Qin X, Su S, Bai Y, Li F, Zhao D, Shao G, Chao J, Feng Z, Wang L. Enhancing Point-of-Care Diagnosis of African Swine Fever Virus (ASFV) DNA with the CRISPR-Cas12a-Assisted Triplex Amplified Assay. Anal Chem 2024; 96:5178-5187. [PMID: 38500378 DOI: 10.1021/acs.analchem.3c05364] [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: 03/20/2024]
Abstract
Accurate, ultrasensitive, and point-of-care (POC) diagnosis of the African swine fever virus (ASFV) remains imperative to prevent its spread and limit the losses incurred. Herein, we propose a CRISPR-Cas12a-assisted triplex amplified colorimetric assay for ASFV DNA detection with ultrahigh sensitivity and specificity. The specific recognition of recombinase aided amplification (RAA)-amplified ASFV DNA could activate the Cas12a/crRNA/ASFV DNA complex, leading to the digestion of the linker DNA (bio-L1) on magnetic beads (MBs), thereby preventing its binding of gold nanoparticles (AuNPs) network. After magnetic separation, the release of AuNPs network comprising a substantial quantity of AuNPs could lead to a discernible alteration in color and significantly amplify the plasmonic signal, which could be read by spectrophotometers or smartphones. By combining the RAA, CRISPR/Cas12a-assisted cleavage, and AuNPs network-mediated colorimetric amplification together, the assay could detect as low as 0.1 copies/μL ASFV DNA within 1 h. The assay showed an accuracy of 100% for the detection of ASFV DNA in 16 swine tissue fluid samples, demonstrating its potential for on-site diagnosis of ASFV.
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Affiliation(s)
- Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Tong Su
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Tao Sun
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xingcai Qin
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yun Bai
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Fang Li
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Dongming Zhao
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Guoqing Shao
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Zhixin Feng
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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17
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Zhang WQ, Tu YD, Liu H, Liu R, Zhang XJ, Jiang L, Huang Y, Xia F. A Single Set of Well-Designed Aptamer Probes for Reliable On-site Qualitative and Ultra-Sensitive Quantitative Detection. Angew Chem Int Ed Engl 2024; 63:e202316434. [PMID: 38192021 DOI: 10.1002/anie.202316434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/10/2024]
Abstract
Aptamer-based probes are pivotal components in various sensing strategies, owing to their exceptional specificity and versatile programmable structure. Nevertheless, numerous aptamer-based probes usually offer only a single function, limiting their capacity to meet the diverse requirements of multi-faceted sensing systems. Here, we introduced supersandwich DNA probes (SSW-DNA), designed and modified on the outer surface of nanochannels with hydrophobic inner walls, enabling dual functionality: qualitative detection for on-site analysis and quantitative detection for precise analysis. The fragmented DNAs resulting from the target recognition, are subsequently identified through lateral flow assays, enabling robust on-site qualitative detection of microcystin-LR with an impressively low limit of detection (LOD) at 0.01 μg/L. Meanwhile, the nanochannels enable highly sensitive quantification of microcystin-LR through the current analysis, achieving an exceptionally low LOD at 2.5×10-7 μg/L, with a broad dynamic range spanning from 1×10-6 to 1×102 μg/L. Furthermore, the process of target recognition introduces just a single potential error propagation, which reduces the overall risk of errors during the entire qualitative and quantitative detection process. This sensing strategy broadens the scope of applications for aptamer-based composite probes, holding promising implications across diverse fields, such as medical diagnosis, food safety, and environmental protection.
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Affiliation(s)
- Wei-Qi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Yi-Dan Tu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Hong Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Rui Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Xiao-Jin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yu Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
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18
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Li T, Chen D, He X, Li Z, Xu Z, Li R, Zheng B, Hu R, Zhu J, Li Y, Yang Y. Leveraging Cas13a's trans-cleavage on RNA G-quadruplexes for amplification-free RNA detection. Chem Commun (Camb) 2024; 60:3166-3169. [PMID: 38410041 DOI: 10.1039/d3cc06238d] [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: 02/28/2024]
Abstract
In this study, we investigated Cas13a's efficacy in trans-cleaving RNA G-quadruplexes (rG4s) as an alternative to ssRNA reporters in CRISPR-Cas13a diagnostics. Our findings demonstrate enhanced efficiency due to the structural arrangement of rG4s. Implementing a simplified CRISPR-Cas13a system based on rG4, we identified SARS-CoV-2 infections in 25 patient samples within 1 hour without target pre-amplification.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Xiaoling He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheyu Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhichen Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runchen Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingxin Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology-Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan 430071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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19
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He W, Liu X, Na J, Bian H, Zhong L, Li G. Application of CRISPR/Cas13a-based biosensors in serum marker detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1426-1438. [PMID: 38385279 DOI: 10.1039/d3ay01927f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The detection of serum markers is important for the early diagnosis and monitoring of diseases, but conventional detection methods have the problem of low specificity or sensitivity. CRISPR/Cas13a-based biosensors have the characteristics of simple detection methods and high sensitivity, which have a certain potential to solve the problems of conventional detection. This paper focuses on the research progress of CRISPR/Cas13a-based biosensors in serum marker detection, introduces the principles and applications of fluorescence, electrochemistry, colorimetric, and other biosensors based on CRISPR/Cas13a in the detection of serum markers, compares and analyzes the differences between the above CRISPR/Cas13a-based biosensors, and looks forward to the future development direction of CRISPR/Cas13a-based biosensors.
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Affiliation(s)
- Wei He
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China.
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China.
| | - Jintong Na
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China.
| | - Huimin Bian
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China.
| | - Liping Zhong
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China.
| | - Guiyin Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China.
- College of Chemistry, Guangdong University of Petrochemical Technology, Guandu Road, Maoming, Guangdong 525000, China
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20
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Chen H, Feng Y, Liu F, Tan C, Xu N, Jiang Y, Tan Y. Universal smartphone-assisted label-free CRISPR/Cas12a-DNAzyme chemiluminescence biosensing platform for on-site detection of nucleic acid and non-nucleic acid targets. Biosens Bioelectron 2024; 247:115929. [PMID: 38128320 DOI: 10.1016/j.bios.2023.115929] [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: 10/11/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) (CRISPR/Cas) system enables sensitive and specific detection of biomolecules, thanks to its programmability, high fidelity, and powerful signal amplification capabilities. Herein, a universal smartphone-assisted label-free G-quadruplex (G4) DNAzyme-based chemiluminescence CRISPR/Cas12a biosensing platform (G4CLCas) is firstly described that achieves on-site, ultrasensitive visual detection of nucleic acid and non-nucleic acid targets. The G4CLCas-based sensing platform relies on Cas12a trans-cleavage activation that triggers the cleavage of the G4 DNAzyme, resulting in chemiluminescence signals off/on compared to that of the control. Chemiluminescence signals are captured as images that are quantitatively analyzed and visualized using a smartphone-assisted imaging cartridge. Under optimal conditions, G4CLCas achieves a low limit of detection (LOD) of 8.6 aM (∼5.2 copies/μL) for monkeypox virus (MPXV) DNA within the linear concentration range of 10-300 aM and can accurately quantify viral DNA in spiked samples. G4CLCas can also detect non-nucleic acid targets, whereby it achieves a low LOD value of 84.3 nM for adenosine triphosphate (ATP) within the linear concentration range of 2-2000 μM. Here, a label-free, portable, on-site CRISPR/Cas12a chemiluminescence biosensing platform based on the G4 DNAzyme substrates is proposed with potential applications in clinical detection and bioanalytical chemistry research.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China; Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ying Feng
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Feng Liu
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China; Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China; School of Food and Drug, Shenzhen Polytechnic University, Shenzhen, 518055, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China; Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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21
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Chen M, Jiang X, Hu Q, Long J, He J, Wu Y, Wu Z, Niu Y, Jing C, Yang X. Toehold-Containing Three-Way Junction-Initiated Multiple Exponential Amplification and CRISPR/Cas14a Assistant Magnetic Separation Enhanced Visual Detection of Mycobacterium Tuberculosis. ACS Sens 2024; 9:62-72. [PMID: 38126108 DOI: 10.1021/acssensors.3c01622] [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: 12/23/2023]
Abstract
Rapid and simple nucleic acid detection is significant for disease diagnosis and pathogen screening, especially under specific conditions. However, achieving highly sensitive and specific nucleic acid detection to meet the time and equipment demand remains technologically challenging. In this study, we proposed a magnetic separation enhanced colorimetry biosensor based on a toehold-containing three-way junction (TWJ) induced multiple isothermal exponential amplification and the CRISPR/Cas14a (C-TEC) biosensor. The TWJ template was designed as a Y-X-Y structure. In the presence of the target, the formation of toehold-containing TWJ complex induced primer extension, leading to the generation of amplified single-stranded DNA; this amplified DNA could then bind to either the free TWJ template for EXPAR reaction or the toehold of the TWJ complex for toehold-mediated strand displacement, thereby enabling the recycling of the target. The amplification products could trigger CRISPR/Cas14a for efficient trans-cleavage and release the magnetically bound gold nanoparticle probes for colorimetry detection. Using Mycobacterium tuberculosis 16S rDNA as the target, the proposed C-TEC could detect 16S rDNA down to 50 fM by the naked eye and 20.71 fM by UV-vis detector at 520 nm within 90 min under optimal conditions. We successfully applied this biosensor to clinical isolates of Mycobacterium tuberculosis. In addition, the C-TEC biosensor also showed feasibility for the detection of RNA viruses. In conclusion, the proposed C-TEC is a convenient, fast, and versatile platform for visual detection of pathogen DNA/RNA and has potential clinical applications.
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Affiliation(s)
- Mengqi Chen
- Chongqing Medical University, Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing 400016, China
| | - Xue Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qianfang Hu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital, Chongqing Medical University, Chongqing 400016, China
| | - Jinyan Long
- Chongqing Medical University, Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing 400016, China
| | - Jianwei He
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yuchen Wu
- Chongqing Medical University, Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing 400016, China
| | - Zhili Wu
- Chongqing Medical University, Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing 400016, China
| | - Yanhong Niu
- Chongqing Medical University, Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing 400016, China
| | - Chunmei Jing
- Children's Hospital of Chongqing Medical University, Chongqing 400015, China
| | - Xiaolan Yang
- Chongqing Medical University, Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing 400016, China
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22
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Pandit S, Duchow M, Chao W, Capasso A, Samanta D. DNA-Barcoded Plasmonic Nanostructures for Activity-Based Protease Sensing. Angew Chem Int Ed Engl 2024; 63:e202310964. [PMID: 37985161 DOI: 10.1002/anie.202310964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
We report the development of a new class of protease activity sensors called DNA-barcoded plasmonic nanostructures. These probes are comprised of gold nanoparticles functionalized with peptide-DNA conjugates (GPDs), where the peptide is a substrate of the protease of interest. The DNA acts as a barcode identifying the peptide and facilitates signal amplification. Protease-mediated peptide cleavage frees the DNA from the nanoparticle surface, which is subsequently measured via a CRISPR/Cas12a-based assay as a proxy for protease activity. As proof-of-concept, we show activity-based, multiplexed detection of the SARS-CoV-2-associated protease, 3CL, and the apoptosis marker, caspase 3, with high sensitivity and selectivity. GPDs yield >25-fold turn-on signals, 100-fold improved response compared to commercial probes, and detection limits as low as 58 pM at room temperature. Moreover, nanomolar concentrations of proteases can be detected visually by leveraging the aggregation-dependent color change of the gold nanoparticles. We showcase the clinical potential of GPDs by detecting a colorectal cancer-associated protease, cathepsin B, in three different patient-derived cell lines. Taken together, GPDs detect physiologically relevant concentrations of active proteases in challenging biological samples, require minimal sample processing, and offer unmatched multiplexing capabilities (mediated by DNA), making them powerful chemical tools for biosensing and disease diagnostics.
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Affiliation(s)
- Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Mark Duchow
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Wilson Chao
- Department of Biochemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
| | - Anna Capasso
- Department of Oncology, Dell Medical School, The University of Texas at Austin, 1601 Trinity St., Austin, TX 78712, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St., Austin, TX 78712, USA
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23
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Chen S, Yin Y, Pang X, Wang C, Wang L, Wang J, Jia J, Liu X, Xu S, Luo X. Light and endogenous enzyme triggered plasmonic antennas for accurate subcellular molecular imaging with enhanced spatial resolution. Chem Sci 2024; 15:566-572. [PMID: 38179540 PMCID: PMC10762929 DOI: 10.1039/d3sc05728c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Developing accurate tumor-specific molecular imaging approaches holds great potential for evaluating cancer progression. However, traditional molecular imaging approaches still suffer from restricted tumor specificity due to the "off-tumor" signal leakage. In this work, we proposed light and endogenous APE1-triggered plasmonic antennas for accurate tumor-specific subcellular molecular imaging with enhanced spatial resolution. Light activation ensures subcellular molecular imaging and endogenous enzyme activation ensures tumor-specific molecular imaging. In addition, combined with the introduction of plasmon enhanced fluorescence (PEF), off-tumor signal leakage at the subcellular level was effectively reduced, resulting in the significantly enhanced discrimination ratio of tumor/normal cells (∼11.57-fold) which is better than in previous reports, demonstrating great prospects of these plasmonic antennas triggered by light and endogenous enzymes for tumor-specific molecular imaging at the subcellular level.
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Affiliation(s)
- Shuwei Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Yue Yin
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Xiaozhe Pang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Congkai Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Lei Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Junqi Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Jiangfei Jia
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Xinxue Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Shenghao Xu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology Qingdao 266042 P. R. China
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24
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Li Y, Liu Y, Tang X, Qiao J, Kou J, Man S, Zhu L, Ma L. CRISPR/Cas-Powered Amplification-Free Detection of Nucleic Acids: Current State of the Art, Challenges, and Futuristic Perspectives. ACS Sens 2023; 8:4420-4441. [PMID: 37978935 DOI: 10.1021/acssensors.3c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
CRISPR/Cas system is becoming an increasingly influential technology that has been repositioned in nucleic acid detection. A preamplification step is usually required to improve the sensitivity of CRISPR/Cas-based detection. The striking biological features of CRISPR/Cas, including programmability, high sensitivity and sequence specificity, and single-base resolution. More strikingly, the target-activated trans-cleavage could act as a biocatalytic signal transductor and amplifier, thereby empowering it to potentially perform nucleic acid detection without a preamplification step. The reports of such work are on the rise, which is not only scientifically significant but also promising for futuristic end-user applications. This review started with the introduction of the detection methods of nucleic acids and the CRISPR/Cas-based diagnostics (CRISPR-Dx). Next, we objectively discussed the pros and cons of preamplification steps for CRISPR-Dx. We then illustrated and highlighted the recently developed strategies for CRISPR/Cas-powered amplification-free detection that can be realized through the uses of ultralocalized reactors, cascade reactions, ultrasensitive detection systems, or others. Lastly, the challenges and futuristic perspectives were proposed. It can be expected that this work not only makes the researchers better understand the current strategies for this emerging field, but also provides insight for designing novel CRISPR-Dx without a preamplification step to win practicable use in the near future.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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25
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Tang W, Tong T, Wang H, Lu X, Yang C, Wu Y, Wang Y, Liu J, Ding B. A DNA Origami-Based Gene Editing System for Efficient Gene Therapy in Vivo. Angew Chem Int Ed Engl 2023; 62:e202315093. [PMID: 37906116 DOI: 10.1002/anie.202315093] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
DNA nanostructures have played an important role in the development of novel drug delivery systems. Herein, we report a DNA origami-based CRISPR/Cas9 gene editing system for efficient gene therapy in vivo. In our design, a PAM-rich region precisely organized on the surface of DNA origami can easily recruit and load sgRNA/Cas9 complex by PAM-guided assembly and pre-designed DNA/RNA hybridization. After loading the sgRNA/Cas9 complex, the DNA origami can be further rolled up by the locking strands with a disulfide bond. With the incorporation of DNA aptamer and influenza hemagglutinin (HA) peptide, the cargo-loaded DNA origami can realize the targeted delivery and effective endosomal escape. After reduction by GSH, the opened DNA origami can release the sgRNA/Cas9 complex by RNase H cleavage to achieve a pronounced gene editing of a tumor-associated gene for gene therapy in vivo. This rationally developed DNA origami-based gene editing system presents a new avenue for the development of gene therapy.
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Affiliation(s)
- Wantao Tang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ting Tong
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Changping Yang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yushuai Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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26
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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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Chowdhry R, Lu SZ, Lee S, Godhulayyagari S, Ebrahimi SB, Samanta D. Enhancing CRISPR/Cas systems with nanotechnology. Trends Biotechnol 2023; 41:1549-1564. [PMID: 37451945 DOI: 10.1016/j.tibtech.2023.06.005] [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: 04/18/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
CRISPR/Cas systems have revolutionized biology and medicine, and have led to new paradigms in disease diagnostics and therapeutics. However, these complexes suffer from key limitations regarding barriers to cellular entry, stability in biological environments, and off-target effects. Integrating nanotechnology with CRISPR/Cas systems has emerged as a promising strategy to overcome these challenges and has further unlocked structures that accumulate preferentially in tissues of interest, have tunable pharmacological properties, and are activated in response to desired stimuli. Nanomaterials can also enhance CRISPR/Cas-mediated detection platforms by enabling faster, more sensitive, and convenient readouts. We highlight recent advances in this rapidly growing field. We also outline areas that need further development to fully realize the potential of CRISPR technologies.
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Affiliation(s)
- Rupali Chowdhry
- Department of Public Health, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven Z Lu
- Department of Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Seungheon Lee
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Sasha B Ebrahimi
- Drug Product Development - Steriles, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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28
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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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29
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He Y, Hu Q, San S, Kasputis T, Splinter MGD, Yin K, Chen J. CRISPR-based Biosensors for Human Health: A Novel Strategy to Detect Emerging Infectious Diseases. Trends Analyt Chem 2023; 168:117342. [PMID: 37840598 PMCID: PMC10571337 DOI: 10.1016/j.trac.2023.117342] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Infectious diseases (such as sepsis, influenza, and malaria), caused by various pathogenic bacteria and viruses, are widespread across the world. Early and rapid detection of disease-related pathogens is necessary to reduce their spread in the world and prevent their potential global pandemics. The clustered regularly interspaced short palindromic repeats (CRISPR) technology, as the next-generation molecular diagnosis technique, holds immense promise in the detection of infectious diseases because of its remarkable advantages, including supreme flexibility, sensitivity, and specificity. While numerous CRISPR-based biosensors have been developed for application in environmental monitoring, food safety, and point-of-care diagnosis, there remains a critical need to summarize and explore their potential in human health. This review aims to address this gap by focusing on the latest advancements in CRISPR-based biosensors for infectious disease detection. We provide an overview of the current status, pre-amplification methods, the unique feature of each CRISPR system, and the design of CRISPR-based biosensing strategies to detect disease-associated nucleic acids. Last but not least, the review analyzes the current challenges and provides future perspectives, which will contribute to developing more effective CRISPR-based biosensors for human health.
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Affiliation(s)
- Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People’s Republic of China
| | - Samantha San
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tom Kasputis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People’s Republic of China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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30
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Zhu Y, Zhang M, Guo S, Xu H, Jie Z, Tao SC. CRISPR-based diagnostics of different biomolecules from nucleic acids, proteins, and small molecules to exosomes. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1539-1550. [PMID: 37528660 PMCID: PMC10577475 DOI: 10.3724/abbs.2023134] [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: 04/26/2023] [Accepted: 06/29/2023] [Indexed: 08/03/2023] Open
Abstract
CRISPR-based detection technologies have been widely explored for molecular diagnostics. However, the challenge lies in converting the signal of different biomolecules, such as nucleic acids, proteins, small molecules, exosomes, and ions, into a CRISPR-based nucleic acid detection signal. Understanding the detection of different biomolecules using CRISPR technology can aid in the development of practical and promising detection approaches. Unfortunately, existing reviews rarely provide an overview of CRISPR-based molecular diagnostics from the perspective of different biomolecules. Herein, we first introduce the principles and characteristics of various CRISPR nucleases for molecular diagnostics. Then, we focus on summarizing and evaluating the latest advancements in CRISPR-based detection of different biomolecules. Through a comparison of different methods of amplification and signal readout, we discuss how general detection methods can be integrated with CRISPR. Finally, we conclude by identifying opportunities for the improvement of CRISPR in quantitative, amplification-free, multiplex, all-in-one, and point-of-care testing (POCT) purposes.
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Affiliation(s)
- Yuanshou Zhu
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
| | - Meng Zhang
- Department of Pulmonary and Critical Care MedicineShanghai Fifth People’s HospitalFudan UniversityShanghai200240China
| | - Shujuan Guo
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
| | - Hong Xu
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care MedicineShanghai Fifth People’s HospitalFudan UniversityShanghai200240China
- Center of Community-Based Health ResearchFudan UniversityShanghai200240China
| | - Sheng-ce Tao
- Shanghai Center for Systems BiomedicineKey Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Jiao Tong UniversityShanghai200240China
- School of Biomedical EngineeringMed-X Research InstituteShanghai Jiao Tong UniversityShanghai200030China
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31
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Yin W, Hu J, Chen F, Zhu L, Ma Y, Wang N, Wei H, Yang H, Chou SH, He J. Combining hybrid nanoflowers with hybridization chain reaction for highly sensitive detection of SARS-CoV-2 nucleocapsid protein. Anal Chim Acta 2023; 1279:341838. [PMID: 37827653 DOI: 10.1016/j.aca.2023.341838] [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: 08/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND COVID-19 (coronavirus disease 2019) pandemic has had enormous social and economic impacts so far. The nucleocapsid protein (N protein) is highly conserved and is a key antigenic marker for the diagnosis of early SARS-CoV-2 infection. RESULTS In this study, the N protein was first captured by an aptamer (Aptamer 58) coupled to magnetic beads (MBs), which in turn were bound to another DNA sequence containing the aptamer (Aptamer 48-Initiator). After adding 5'-biotinylated hairpin DNA Amplifier 1 and Amplifier 2 with cohesive ends for complementary hybridization, the Initiator in the Aptamer 48-Initiator began to trigger the hybridization chain reaction (HCR), generating multiple biotin-labeled DNA concatamers. When incubated with synthetic streptavidin-invertase-Ca3(PO4)2 hybrid nanoflower (SICa), DNA concatamers could specifically bind to SICa through biotin-streptavidin interaction with high affinity. After adding sucrose, invertase in SICa hydrolyzed sucrose to glucose, whose concentration could be directly read with a portable glucometer, and its concentration was positively correlated with the amount of captured N protein. The method is highly sensitive with a detection limit as low as 1 pg/mL. SIGNIFICANCE We believe this study provided a practical solution for the early detection of SARS-CoV-2 infection, and offered a new method for detecting other viruses through different target proteins.
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Affiliation(s)
- Wen Yin
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Ji Hu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fang Chen
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhu
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nuo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430000, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430000, China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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32
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Li Y, Liu ML, Liang WB, Zhuo Y, He XJ. Spherical nucleic acid enzyme programmed network to accelerate CRISPR assays for electrochemiluminescence biosensing applications. Biosens Bioelectron 2023; 238:115589. [PMID: 37591158 DOI: 10.1016/j.bios.2023.115589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/30/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]
Abstract
Given the targeted binding ability and cleavage activity of the emerging CRISPR/Cas12a assay which transduces the target into its cleavage activity exhibited broadly prospective applications in integrated sensing and actuating system. Here, we elaborated a universal approach to quickly activate CRISPR/Cas12a for low-abundance biomarker detection based on the amplification strategy of a target-induced spherical nucleic acid enzyme (SNAzyme) network that could accelerate the output of activators. Specifically, multifunctional Y-shaped probes and hairpin probes (HPs, which contained the specific sequence of the activators of CRISPR/Cas12a and the substrate chain of DNAzyme) were rationally designed to construct SNAzyme. Target recognition induced disassembly of the Y-shaped probes, which released DNAzyme strands to active DNAzyme and accompanied by SNAzyme self-assembly into SNAzyme network. Interestingly, compared with randomly dispersed SNAzyme, the reaction kinetics of the SNAzyme network enhanced 1.6 times in response to Α-methyl acyl-CoA racemase (AMACR, a biomarker for prostate cancer), which was attributed to the promoted catalytic efficiency of DNAzyme by the confined SNAzyme network. Benefiting from these, the prepared biosensor based on electrochemiluminescence (ECL) platform by loading AuAg nanoclusters (AuAgNCs) into metal-organic framework-5 (MOF-5) exhibited satisfying detection performance for AMACR with a wide linear range (0.001 μg/mL to 100 μg/mL) and a low detection limit (1.0 × 10-4 μg/mL, which exhibited significant potential in clinical diagnoses.
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Affiliation(s)
- Yi Li
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mei-Ling Liu
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, China
| | - Xiao-Jing He
- Department of Radiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Li Y, Zhao Z, Liu Y, Wang N, Man S, Ma L, Wang S. CRISPR/Cas System: The Accelerator for the Development of Non-nucleic Acid Target Detection in Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13577-13594. [PMID: 37656446 DOI: 10.1021/acs.jafc.3c03619] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Non-nucleic acid targets have posed a serious challenge to food safety. The detection of non-nucleic acid targets can enable us to monitor food contamination in a timely manner. In recent years, the CRISPR/Cas system has been extensively explored in biosensing. However, there is a lack of a summary of CRISPR/Cas-powered detection tailored to non-nucleic acid targets involved in food safety. This review comprehensively summarizes the recent advances on the construction of CRISPR/Cas-powered detection and the promising applications in the field of food safety related non-nucleic acid targets. The current challenges and futuristic perspectives are also proposed accordingly. The rapidly evolving CRISPR/Cas system has provided a powerful propellant for non-nucleic acid target detection via integration with aptamer and/or DNAzyme. Compared with traditional analytical methods, CRISPR/Cas-powered detection is conceptually novel, essentially eliminates the dependence on large instruments, and also demonstrates the capability for rapid, accurate, sensitive, and on-site testing.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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Ke X, Hu Y, Chen C, Hu T. A one-tube dual-readout biosensor for detection of nucleic acids and non-nucleic acids using CRISPR-ALP tandem assay. Analyst 2023; 148:4356-4364. [PMID: 37555739 DOI: 10.1039/d3an00918a] [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: 08/10/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have been considered a next-generation molecular diagnosis tool. Single-readout mode has been extensively employed in massive CRISPR/Cas12a-based biosensors. In this work, we propose a one-tube dual-readout biosensor (CRISAT) for the first time for the detection of ultrasensitive nucleic acids and non-nucleic acids developed by harnessing CRISPR-ALP tandem assay. In the presence of a target, Cas12a is activated to randomly cut the single-stranded hyDNA sequence of MB@hyDNA-cALP, thus releasing abundant alkaline phosphatase (ALP) in the supernatant solution. By using 4-aminophenol phosphate as the substrate of ALP, p-aminophenol is produced, which then reacts with N-[3-(trimethoxysilyl)propyl]ethylenediamine or diethylenetriamine to generate silicon-containing polymer carbon dots (Si PCDs) or polymer carbon dots (PCDs) in situ, which can be observed by the naked eye or detected using a fluorescent device in the same solution. Using this strategy, a fluorescence and colorimetry dual-readout nanoplatform for CRISPR-based biosensors can be rationally developed. We ascertain the applicability of CRISAT by detecting the SARS-CoV-2 pseudovirus, achieving superior sensitivity and specificity. With simple modification of crRNAs, the CRISAT platform can also be employed to detect monkeypox virus (MPXV) and non-nucleic acids of adenosine triphosphate (ATP). This work shows great potential for the detection of nucleic acids and non-nucleic acids.
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Affiliation(s)
- Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
| | - Yi Hu
- Hefei National Lab for Physical Sciences at the Microscale and the Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, China
| | - Chuanxia Chen
- School of Materials Science and Engineering, University of Jinan, Jinan, Shandong, 250022, China.
| | - Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
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Nixon SR, Phukan IK, Armijo BJ, Ebrahimi SB, Samanta D. Proximity-Driven DNA Nanosensors. ECS SENSORS PLUS 2023; 2:030601. [PMID: 37424706 PMCID: PMC10323711 DOI: 10.1149/2754-2726/ace068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/12/2023] [Indexed: 07/11/2023]
Abstract
In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.
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Affiliation(s)
- Sara R. Nixon
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Imon Kanta Phukan
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Brian J. Armijo
- Department of Chemistry, Southwestern University, Georgetown, TX 78626, United States of America
| | - Sasha B. Ebrahimi
- Drug Product Development—Steriles, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
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36
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Burkin KM, Ivanov AV, Zherdev AV, Dzantiev BB, Safenkova IV. A Critical Study on DNA Probes Attached to Microplate for CRISPR/Cas12 Trans-Cleavage Activity. BIOSENSORS 2023; 13:824. [PMID: 37622910 PMCID: PMC10452489 DOI: 10.3390/bios13080824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
CRISPR/Cas12-based biosensors are emerging tools for diagnostics. However, their application of heterogeneous formats needs the efficient detection of Cas12 activity. We investigated DNA probes attached to the microplate surface and cleaved by Cas12a. Single-stranded (ss) DNA probes (19 variants) and combined probes with double-stranded (ds) and ssDNA parts (eight variants) were compared. The cleavage efficiency of dsDNA-probes demonstrated a bell-shaped dependence on their length, with a cleavage maximum of 50%. On the other hand, the cleavage efficiency of ssDNA probes increased monotonously, reaching 70%. The most effective ssDNA probes were integrated with fluorescein, antibodies, and peroxidase conjugates as reporters for fluorescent, lateral flow, and chemiluminescent detection. Long ssDNA probes (120-145 nt) proved the best for detecting Cas12a trans-activity for all of the tested variants. We proposed a test system for the detection of the nucleocapsid (N) gene of SARS-CoV-2 based on Cas12 and the ssDNA-probe attached to the microplate surface; its fluorescent limit of detection was 0.86 nM. Being united with pre-amplification using recombinase polymerase, the system reached a detection limit of 0.01 fM, thus confirming the effectiveness of the chosen ssDNA probe for Cas12-based biosensors.
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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, 119071 Moscow, Russia; (K.M.B.); (A.V.I.); (A.V.Z.); (B.B.D.)
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37
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Fei X, Lei C, Ren W, Liu X, Liu C. Regulating the trans-Cleavage Activity of CRISPR/Cas12a by Using an Elongation-Caged Single-Stranded DNA Activator and the Biosensing Applications. Anal Chem 2023; 95:12169-12176. [PMID: 37531567 DOI: 10.1021/acs.analchem.3c02471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
The CRISPR/Cas12a system exhibits extraordinary capability in the field of biosensing and molecular diagnosis due to its trans-cleavage ability. However, it is still desirable for precise control and programmable regulation of Cas12a trans-cleavage activity to promote the in-depth studies and application expansion of Cas12a-based sensing platforms. In this work, we have developed a new and robust CRISPR/Cas12a regulation mechanism by endowing the activator with the function of caging crRNA ingeniously. Specifically, we constructed an integrated elongation-caged activator (EL-activator) by extending the ssDNA activator on the 3'-end. We found that appending only about 8 nt that is complementary to the crRNA repeat region is enough to cage the crRNA spacer/repeat region, thus effectively inhibiting Cas12a trans-cleavage activity. The inner inhibition mechanism was further uncovered after a thorough investigation, demonstrating that the EL-activator works by impeding the conformation of crRNA required for Cas12a recognition and destroying its affinity with Cas12a. By further switching on the elongated moiety on the EL-activator using target biomarkers, the blocked trans-cleavage activity of Cas12a can be rapidly recovered. Finally, a versatile sensing platform was established based on the EL-activator regulation mechanism, expanding the conventional Cas12a system that only directly recognizes DNA to the direct detection of enzymes and RNA biomarkers. This work has enriched the CRISPR/Cas12a regulation toolbox and expanded its sensing applications.
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Affiliation(s)
- Xinrui Fei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Xiaoling Liu
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
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38
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de Dieu Habimana J, Mukama O, Amissah OB, Sun Y, Karangwa E, Liu Y, Mugisha S, Cheng N, Wang L, Chen J, Deng S, Huang R, Li Z. A Rationally Designed CRISPR/Cas12a Assay Using a Multimodal Reporter for Various Readouts. Anal Chem 2023; 95:11741-11750. [PMID: 37504509 DOI: 10.1021/acs.analchem.3c01876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The CRISPR/Cas systems offer a programmable platform for nucleic acid detection, and CRISPR/Cas-based diagnostics (CRISPR-Dx) have demonstrated the ability to target nucleic acids with greater accuracy and flexibility. However, due to the configuration of the reporter and the underlying labeling mechanism, almost all reported CRISPR-Dx rely on a single-option readout, resulting in limitations in end-point result readouts. This is also associated with high reagent consumption and delays in diagnostic reports due to protocol differences. Herein, we report for the first time a rationally designed Cas12a-based multimodal universal reporter (CAMURE) with improved sensitivity that harnesses a dual-mode reporting system, facilitating options in end-point readouts. Through systematic configurations and optimizations, our novel universal reporter achieved a 10-fold sensitivity enhancement compared to the DETECTR reporter. Our unique and versatile reporter could be paired with various readouts, conveying the same diagnostic results. We applied our novel reporter for the detection of staphylococcal enterotoxin A due to its high implication in staphylococcal food poisoning. Integrated with loop-mediated isothermal amplification, our multimodal reporter achieved 10 CFU/mL sensitivity and excellent specificity using a real-time fluorimeter, in-tube fluorescence, and lateral flow strip readouts. We also propose, using artificially contaminated milk samples, a fast (2-5 min) Triton X-100 DNA extraction approach with a comparable yield to the commercial extraction kit. Our CAMURE could be leveraged to detect all gene-encoding SEs by simply reprogramming the guide RNA and could also be applied to the detection of other infections and disease biomarkers.
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Affiliation(s)
- Jean de Dieu Habimana
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Omar Mukama
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
- Department of Biology, College of Science and Technology, University of Rwanda, Avenue de l'armée, Kigali 3900, Rwanda
| | - Obed Boadi Amissah
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yirong Sun
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Eric Karangwa
- Research and Development, AAFUD Industry (Zhuhai) Co. Ltd., Zhuhai 519085, China
| | - Yujie Liu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Samson Mugisha
- Department of Pathology, University of California, San Diego, 9500 Gilman, La Jolla, California 92093, United States
| | - Na Cheng
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Ling Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Jianlin Chen
- Department of Gynecology & Obstetrics, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Sihao Deng
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Rongqi Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
- Guangzhou Qiyuan Biomedical Co., Ltd., Guangzhou 510530, China
| | - Zhiyuan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- GZMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou 511436, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou 511436, China
- Guangzhou Qiyuan Biomedical Co., Ltd., Guangzhou 510530, China
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Sai J, Zhou L, Jiang L, Xue D, Pei R, Liu A, Xu L. Dual Signal Amplification by Urease Catalysis and Silver Nanoparticles for Ultrasensitive Colorimetric Detection of Nucleic Acids. Anal Chem 2023. [PMID: 37464726 DOI: 10.1021/acs.analchem.3c01483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Signal amplification techniques are highly desirable for the analysis of low-level targets that are closely related with diseases and the monitoring of important biological processes. However, it is still challenging to achieve this goal in a facile and economical way. Herein, we developed a novel dual signal amplification strategy by combining urease catalysis with the release of Ag+ from silver nanoparticles (AgNPs). This strategy was used for quantifying a DNA sequence (HIV-1) related with human immunodeficiency virus (HIV). DNA target HIV-1 hybridizes with the capture DNA probe on magnetic beads and the reporter DNA probe on AgNPs, forming a sandwich complex. The captured AgNPs are then transformed into numerous Ag+ ions that inactivate numerous ureases. Without catalytic production of ammonia from urea, the substrate solution shows a low pH 5.8 that will increase otherwise. The pH change is monitored by a pH indicator (phenol red), which allows for colorimetric detection. The proposed approach is sensitive, easy to use, economic, and universal, exhibiting a low detection limit of 9.7 fM (i.e., 1.94 attomoles) and a dynamic linear range of 4 orders for HIV-1 sequence detection.
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Affiliation(s)
- Jialin Sai
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Lu Zhou
- Department of Neurology, Affiliated Taizhou Hospital of Wenzhou Medical University, Linhai 317000, China
| | - Lin Jiang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Dongguo Xue
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
| | - Lijun Xu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, Qingdao 266071, China
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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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41
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Zhu L, Liang Z, Xu Y, Chen Z, Wang J, Zhou L. Ultrasensitive and Rapid Visual Detection of Escherichia coli O157:H7 Based on RAA-CRISPR/Cas12a System. BIOSENSORS 2023; 13:659. [PMID: 37367024 DOI: 10.3390/bios13060659] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
Escherichia coli (E. coli) O157:H7 is a major foodborne and waterborne pathogen that can threaten human health. Due to its high toxicity at low concentrations, it is crucial to establish a time-saving and highly sensitive in situ detection method. Herein, we developed a rapid, ultrasensitive, and visualized method for detecting E. coli O157:H7 based on a combination of Recombinase-Aided Amplification (RAA) and CRISPR/Cas12a technology. The CRISPR/Cas12a-based system was pre-amplified using the RAA method, which showed high sensitivity and enabled detecting as low as ~1 CFU/mL (fluorescence method) and 1 × 102 CFU/mL (lateral flow assay) of E. coli O157:H7, which was much lower than the detection limit of the traditional real-time PCR technology (103 CFU/mL) and ELISA (104~107 CFU/mL). In addition, we demonstrated that this method still has good applicability in practical samples by simulating the detection in real milk and drinking water samples. Importantly, our RAA-CRISPR/Cas12a detection system could complete the overall process (including extraction, amplification, and detection) within 55 min under optimized conditions, which is faster than most other reported sensors, which take several hours to several days. The signal readout could also be visualized by fluorescence generated with a handheld UV lamp or a naked-eye-detected lateral flow assay depending on the DNA reporters used. Because of the advantages of being fast, having high sensitivity, and not requiring sophisticated equipment, this method has a promising application prospect for in situ detection of trace amounts of pathogens.
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Affiliation(s)
- Lishan Zhu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhenda Liang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yongtao Xu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhiquan Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - 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
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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Yang H, Ledesma-Amaro R, Gao H, Ren Y, Deng R. CRISPR-based biosensors for pathogenic biosafety. Biosens Bioelectron 2023; 228:115189. [PMID: 36893718 DOI: 10.1016/j.bios.2023.115189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Pathogenic biosafety is a worldwide concern. Tools for analyzing pathogenic biosafety, that are precise, rapid and field-deployable, are highly demanded. Recently developed biotechnological tools, especially those utilizing CRISPR/Cas systems which can couple with nanotechnologies, have enormous potential to achieve point-of-care (POC) testing for pathogen infection. In this review, we first introduce the working principle of class II CRISPR/Cas system for detecting nucleic acid and non-nucleic acid biomarkers, and highlight the molecular assays that leverage CRISPR technologies for POC detection. We summarize the application of CRISPR tools in detecting pathogens, including pathogenic bacteria, viruses, fungi and parasites and their variants, and highlight the profiling of pathogens' genotypes or phenotypes, such as the viability, and drug-resistance. In addition, we discuss the challenges and opportunities of CRISPR-based biosensors in pathogenic biosafety analysis.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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Mao G, Luo X, Ye S, Wang X, He J, Kong J, Dai J, Yin W, Ma Y. Fluorescence and Colorimetric Analysis of African Swine Fever Virus Based on the RPA-Assisted CRISPR/Cas12a Strategy. Anal Chem 2023; 95:8063-8069. [PMID: 37167072 DOI: 10.1021/acs.analchem.3c01033] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It is well-established that different detection modes are necessary for corresponding applications, which can effectively reduce matrix interference and improve the detection accuracy. Here, we reported a magnetic separation method based on recombinase polymerase amplification (RPA)-assisted clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a for dual-mode analysis of African swine fever virus (ASFV) genes, including colorimetry and fluorescence. The ASFV gene was selected as the initial RPA template to generate the amplicon. The RPA amplicon was then recognized by CRISPR-associated RNA (crRNA), activating the trans-cleavage activity of Cas12a and leading to the nonspecific cleavage of ssDNA as well as a significant release of alkaline phosphatase (ALP) in the ALP-ssDNA modified magnetic bead. The released ALP can catalyze para-nitrophenyl phosphate to generate para-nitrophenol, resulting in substantial changes in absorbance and fluorescence, both of which can be used for detection with the naked eye. This strategy allows the sensitive detection of ASFV DNA, with a 20 copies/mL detection limit; no cross-reactivity with other viruses was observed. A good linear relationship was obtained in serum. In addition, this sensor displayed 100% specificity and sensitivity for clinical sample analysis. This method integrates the high sensitivity of fluorescence with easy readout of colorimetry and enables a simple, low-cost, and highly sensitive dual-mode detection of viral nucleic acid, thereby providing a broad prospect for the practical application in the diagnosis of virus infection.
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Affiliation(s)
- Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Silu Ye
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Liu W, Zhu X, Li L, Wang S, Li CZ, Liang T. Reining in Cas13a activity with N-terminal removable tags expands Cas13a based molecular sensing and enables precise gene interference. Biosens Bioelectron 2023; 227:115138. [PMID: 36809733 DOI: 10.1016/j.bios.2023.115138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Activation of Cas13 is exclusively dependent on crRNA-target RNA hybridization according to the canonical mode of Cas13 action. Upon activation Cas13 can cleave both target RNA and any surrounding RNA. The latter has been well adopted by therapeutic gene interference and biosensor development. This work for the first time, rationale designs and validates a multi-component controlled activation system of Cas13 by N-terminus tagging. A composite SUMO tag comprised of His, Twinstrep, and Smt3 tags fully suppresses target dependent activation of Cas13a by interfering with crRNA docking. The suppression releases upon proteases mediated proteolytic cleavage. The modular composition of the composite tag can be altered to fulfill customized response to alternative proteases. The biosensor SUMO-Cas13a is able to resolve a broad concentration range of protease Ulp1 with a calculated LOD of 48.8pg/μL in aqueous buffer. Further, in accordance with this finding Cas13a was successfully programmed to exert target gene knock down preferentially in SUMO protease high cell types. In summary the discovered regulatory component not only fulfills Cas13a based protease detection for the first time, but also delivers a novel strategy for multi-component controlled activation of Cas13a toward temporal and spacial precision.
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Affiliation(s)
- Wenjun Liu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, 310003, China.
| | - Xuena Zhu
- Department of Pathology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Ling Li
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shanshan Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen-Zhong Li
- Biomedical Engineering Program, The Chinese University of Hong Kong School of Medicine, Shenzhen, 518172, China
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China; The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Zhejiang University Cancer Center, Hangzhou, 310003, China.
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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46
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Pan J, Deng F, Liu Z, Zeng L, Chen J. Construction of molecular logic gates using heavy metal ions as inputs based on catalytic hairpin assembly and CRISPR-Cas12a. Talanta 2023; 255:124210. [PMID: 36566557 DOI: 10.1016/j.talanta.2022.124210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
We successfully constructed several molecular logic gates using heavy metal ions as inputs based on catalytic hairpin assembly (CHA) and CRISPR-Cas12a. The corresponding DNAzymes were used to recognize heavy metal ions (Hg2+, Cd2+, Pb2+, and Mn2+). The specific cleavage between heavy metal ions and DNAzymes leads to the release of the trigger DNA, which can be used to activate CHA through logic computation. The CHA-generated DNA duplexes contain the protospacer adjacent motifs (PAM) sequence, which can be distinguished by CRISPR-Cas12a. The hybridization interactions between the duplexes and gRNA will activate the trans-cleavage capability of Cas12a, which can cleave the single-stranded DNA (ssDNA) reporter. The separation of the fluorescence group and quench group in ssDNA will generate a high fluorescence signal for readout. Using Hg2+ and Cd2+ as the two inputs, several basic logic gates were constructed, including OR, AND, and INHIBT. Using Hg2+, Cd2+, Pb2+, and Mn2+ as the four inputs, cascaded logic gates were further fabricated. With the advantages of scalability, versatility, and logic computing capability, our proposed molecular logic gates can provide an intelligent sensing system for heavy metal ions monitoring.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lingwen Zeng
- Guangdong Langyuan Biotechnology Co., LTD, Foshan, 528313, China; School of Food Science and Engineering, Foshan University, Foshan 528231, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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47
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Sheng C, Zhao J, Yu F, Li L. Enzyme Translocation-Mediated Signal Amplification for Spatially Selective Aptasensing of ATP in Inflammatory Cells. Angew Chem Int Ed Engl 2023; 62:e202217551. [PMID: 36750407 DOI: 10.1002/anie.202217551] [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: 11/29/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 02/09/2023]
Abstract
Amplified ATP imaging in inflammatory cells is highly desirable. However, the spatial selectivity of current amplification methods is limited, that is, signal amplification is performed systemically and not in a disease site-specific manner. Here we present a versatile strategy, termed enzymatically triggerable, aptamer-based signal amplification (ETA-SA), that enables inflammatory cell-specific imaging of ATP through spatially-resolved signal amplification. The ETA-SA leverages a translocated enzyme in inflammatory cells to activate DNA aptamer probes and further drive cascade reactions through the consumption of hairpin fuels, which, however, exerts no ATP response activity in normal cells, leading to a significantly improved sensitivity and spatial specificity for the inflammation-specific ATP imaging in vivo. Benefiting from the improved spatial selectivity, enhanced signal-to-background ratios were achieved for ATP imaging during acute hepatitis.
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Affiliation(s)
- Chuangui Sheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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48
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Chen D, Liang Y, Wang H, Wang H, Su F, Zhang P, Wang S, Liu W, Li Z. CRISPR-Cas-Driven Single Micromotor (Cas-DSM) Enables Direct Detection of Nucleic Acid Biomarkers at the Single-Molecule Level. Anal Chem 2023; 95:5729-5737. [PMID: 36944919 DOI: 10.1021/acs.analchem.2c05767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The target-dependent endonuclease activity (also known as the trans-cleavage activity) of CRISPR-Cas systems has stimulated great interest in the development of nascent sensing strategies for nucleic acid diagnostics. Despite many attempts, the majority of the sensitive CRISPR-Cas diagnostics strategies mainly rely on nucleic acid preamplification, which generally needs complex probes/primers designs, multiple experimental steps, and a longer testing time, as well as introducing the risk of false-positive results. In this work, we propose the CRISPR-Cas-Driven Single Micromotor (Cas-DSM), which can directly detect the nucleic acid targets at a single-molecule level with high specificity. We have demonstrated that the Cas-DSM is a reliable and practical method for the quantitative detection of DNA/RNA in various complex clinical samples as well as in individual cells without any preamplification processes. Due to the excellent features of the CRISPR/Cas system, including constant temperature, simple design, high specificity, and flexible programmability, the Cas-DSM could serve as a simple and universal platform for nucleic acid detection. More importantly, this work will provide a breakthrough for the development of next-generation amplification-free CRISPR/Cas sensing toolboxes.
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Affiliation(s)
- Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yuanwen Liang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Shuhui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
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49
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Su W, Li J, Ji C, Chen C, Wang Y, Dai H, Li F, Liu P. CRISPR/Cas systems for the detection of nucleic acid and non-nucleic acid targets. NANO RESEARCH 2023; 16:1-14. [PMID: 37359078 PMCID: PMC10026200 DOI: 10.1007/s12274-023-5567-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/28/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are becoming powerful tools for disease biomarkers detection. Due to the specific recognition, cis-cleavage and nonspecific trans-cleavage capabilities, CRISPR/Cas systems have implemented the detection of nucleic acid targets (DNA and RNA) as well as non-nucleic acid targets (e.g., proteins, exosomes, cells, and small molecules). In this review, we first summarize the principles and characteristics of various CRISPR/Cas systems, including CRISPR/Cas9, Cas12, Cas13 and Cas14 systems. Then, various types of applications of CRISPR/Cas systems used in detecting nucleic and non-nucleic acid targets are introduced emphatically. Finally, the prospects and challenges of their applications in biosensing are discussed.
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Affiliation(s)
- Weiran Su
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Junru Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Chen Ji
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Congshuo Chen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yuzheng Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Huili Dai
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Fengqin Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China
- Central Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- Micro-Nano Research and Diagnosis Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
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50
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Wang Z, Wei L, Ruan S, Chen Y. CRISPR/Cas12a-Assisted Chemiluminescence Sensor for Aflatoxin B 1 Detection in Cereal Based on Functional Nucleic Acid and In-Pipet Rolling Circle Amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4417-4425. [PMID: 36853759 DOI: 10.1021/acs.jafc.3c00341] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Herein, we report a CRISPR/Cas12a-assisted chemiluminescence sensor for aflatoxin B1 (AFB1) detection based on functional nucleic-acid-mediated target recognition and in-pipet rolling circle amplification-mediated signal amplification. In this sensor, we performed rolling circle amplification on the inside of the pipet to enrich horseradish peroxidase (pipet-poly-HRP). When AFB1 is present, it interacts with functional nucleic acids and results in the release of the activator. The activator is designed to activate the CRISPR/Cas12a system, which cleaves the pipet-poly-HRP to liberate HRP. The freed HRP can then be measured by chemiluminescence to quantify AFB1. This CRISPR/Cas12a-assisted chemiluminescence sensor enables facile, highly sensitive, and specific detection of AFB1, with a linear range from 50 pg/mL to 100 ng/mL and a detection limit of 5.2 pg/mL. Furthermore, it exhibits satisfactory recovery and has successfully challenged AFB1 detection in cereal samples. The proposed sensor offers a novel rapid screening approach that holds great promise for food security monitoring.
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Affiliation(s)
- Zhilong Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Luyu Wei
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Shilong Ruan
- Daye Public Inspection and Test Center, Daye, Hubei 435100, People's Republic of China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, People's Republic of China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
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