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Ding L, Wang X, Chen X, Xu X, Wei W, Yang L, Ji Y, Wu J, Xu J, Peng C. Development of a novel Cas13a/Cas12a-mediated 'one-pot' dual detection assay for genetically modified crops. J Adv Res 2024:S2090-1232(24)00311-4. [PMID: 39084403 DOI: 10.1016/j.jare.2024.07.027] [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: 04/12/2024] [Revised: 07/10/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024] Open
Abstract
INTRODUCTION Genetically modified (GM) crops have been widely cultivated across the world and the development of rapid, ultrasensitive, visual multiplex detection platforms that are suitable for field deployment is critical for GM organism regulation. OBJECTIVE In this study, we developed a novel one-pot system, termed MR-DCA (Multiplex RPA and Dual CRISPR assay), for the simultaneous detection of CaMV35S and NOS genetic targets in GM crops. This innovative approach combined Multiplex RPA (recombinase polymerase amplification) with the Dual CRISPR (clustered regularly interspaced short palindromic repeat) assay technique, to provide a streamlined and efficient method for GM crop detection. METHODS The RPA reaction used for amplification CaMV35S and NOS targets was contained in the tube base, while the dual CRISPR enzymes were placed in the tube cap. Following centrifugation, the dual CRISPR (Cas13a/Cas12a) detection system was initiated. Fluorescence visualization was used to measure CaMV35S through the FAM channel and NOS through the HEX channel. When using lateral flow strips, CaMV35S was detected using rabbit anti-digoxin (blue line), whilst NOS was identified using anti-mouse FITC (red line). Line intensity was quantified using Image J and depicted graphically. RESULTS Detection of the targets was completed in 35 min, with a limit of detection as low as 20 copies. In addition, two analysis systems were developed and they performed well in the MR-DCA assay. In an analysis of 24 blind samples from GM crops with a wide genomic range, MR-DCA gave consistent results with the quantitative PCR method, which indicated high accuracy, applicability and semi-quantitative ability. CONCLUSION The development of MR-DCA represents a significant advancement in the field of GM detection, offering a rapid, sensitive and portable method for multiple target detection that can be used in resource-limited environments.
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Affiliation(s)
- Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Chen Q, Wu J, Tang C, Wang Y. CRISPR-based platforms for the specific and dual detection of defoliating/nondefoliating strains of Verticillium dahliae. PEST MANAGEMENT SCIENCE 2024; 80:2042-2052. [PMID: 38117128 DOI: 10.1002/ps.7940] [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: 10/02/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Verticillium dahliae is a soil-borne pathogenic fungus that causes Verticillium wilt disease on more than 400 plant species worldwide. Because of its broad host range and its ability to survive long term in the soil, there are few effective control measures for V. dahliae once it has become established. Accurate, sensitive, and rapid detection of V. dahliae is crucial for limiting pathogen entry into new regional environments and early management of Verticillium wilt. RESULTS In this study, we developed a method to detect V. dahliae based on recombinase polymerase amplification (RPA) and CRISPR/Cas technology and used fluorescence and lateral flow test strips to monitor the outcomes. Through the establishment and optimization of RPA-CRISPR/Cas13a detection, the sensitivity of the fluorescence method was 1 am for genomic DNA (gDNA) within 20 min, whereas the sensitivity of the lateral flow strip method was 100 am for gDNA in 30 min. The field applicability of RPA-CRISPR/Cas13a was also validated by the detection of V. dahliae on smoke trees (Cotinus coggygria) in Xiangshan Park, Beijing, China. Finally, diplex detection for defoliating and nondefoliating pathotypes of V. dahliae was established by combining CRISPR-Cas12a/Cas13a with specific target genes. CONCLUSION Taken together, this study achieved rapid, sensitive, and accurate detection of V. dahliae and the differentiation of defoliating and nondefoliating pathotypes and provides potential for field-deployable diagnostic tools for rapid and ultrasensitive detection. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Jin Wu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Chen Tang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Yonglin Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
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Chaudhary V, Kumar M, Chauhan C, Sirohi U, Srivastav AL, Rani L. Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120326. [PMID: 38387349 DOI: 10.1016/j.jenvman.2024.120326] [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: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.
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Affiliation(s)
- Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar-Pradesh, India
| | - Mukesh Kumar
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Chetan Chauhan
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Ujjwal Sirohi
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Lal Srivastav
- Chitkara University School of Engineering and Technology, Chitkara University, Himachal Pradesh, India.
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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Sun X, Lei R, Zhang H, Chen W, Jia Q, Guo X, Zhang Y, Wu P, Wang X. Rapid and sensitive detection of two fungal pathogens in soybeans using the recombinase polymerase amplification/CRISPR-Cas12a method for potential on-site disease diagnosis. PEST MANAGEMENT SCIENCE 2024; 80:1168-1181. [PMID: 37874890 DOI: 10.1002/ps.7847] [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: 01/12/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Diaporthe aspalathi and Diaporthe caulivora are two of the fungal pathogens causing soybean stem canker (SSC) in soybean, which is one of the most widespread diseases in soybean growing regions and can cause 100% loss of yield. Current methods for the detection of fungal pathogens, including morphological identification and molecular detection, are mostly limited by the need for professional laboratories and staff. To develop a detection method for potential on-site diagnosis for two of the fungal pathogens causing SSC, we designed a rapid assay combining recombinase polymerase amplification (RPA) and CRISPR-Cas12a-based diagnostics to specifically detect D. aspalathi and D. caulivora. RESULTS The translation elongation factor 1-alpha gene was employed as the target gene to evaluate the specificity and sensitivity of this assay. The RPA/CRISPR-Cas12a system has excellent specificity to distinguish D. aspalathi and D. caulivora from closely related species. The sensitivities of RPA/CRISPR-Cas12a-based fluorescence detection and lateral flow assay for D. aspalathi and D. caulivora are 14.5 copies and 24.6 copies, respectively. This assay can detect hyphae in inoculated soybean stems at 12 days after inoculation and has a recovery as high as 86% for hyphae-spiked soybean seed powder. The total time from DNA extraction to detection was not more than 60 min. CONCLUSION The method developed for rapid detection of plant pathogens includes DNA extraction with magnetic beads or rapid DNA extraction, isothermal nucleic acid amplification at 39 °C, CRISPR-Cas12a cleavage reaction at 37 °C, and lateral flow assay or endpoint fluorescence visualization at room temperature. The RPA and CRISPR-Cas12a reagents can be preloaded in the microcentrifuge tube to simplify the procedures in the field. Both RPA and CRISPR-Cas12a reaction can be realized on a portable incubator, and the results are visualized using lateral flow strips or portable flashlight. This method requires minimal equipment and operator training, and has promising applications for rapid on-site disease screening, port inspection, or controlling fungal pathogen transmission in crop. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiwen Sun
- Chinese Academy of Inspection and Quarantine, Beijing, China
- Shenyang Agricultural University, Shenyang, China
| | - Rong Lei
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | | | - Wujian Chen
- Technical Center of Hangzhou Customs, Hangzhou, China
| | - Qianwen Jia
- School of Life and Health, Dalian University, Dalian, China
| | - Xing Guo
- School of Life and Health, Dalian University, Dalian, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Pinshan Wu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xinyi Wang
- School of Life and Health, Dalian University, Dalian, China
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Zhou XM, Shen ZY, Wu YX, Lin S, Wang MD, Xu T, Wang LL, Sadiq S, Jiao XH, Wu P. Development of a rapid visual detection technology for BmNPV based on CRISPR/Cas13a system. J Invertebr Pathol 2024; 203:108072. [PMID: 38341022 DOI: 10.1016/j.jip.2024.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Pathogenic microorganism of silkworm are important factors that threaten the high-quality development of sericulture. Among them, Bombyx mori nucleopolyhedrovirus (BmNPV) caused diseases often lead to frequent outbreaks and high mortality, resulting in huge losses to sericultural industry. Current molecular detection methods for BmNPV require expensive equipment and sikilled technical personnel. As a result, the most commonly detection method for silkworm egg production enterprises involves observing the presence of polyhedra under a microscope. However, this method has low accuracy and sensitivity. There is an urgent need to develop a new detection technology with high sensitivity, high specificity, and applicability for silkworm farms, silkworm egg production enterprises and quarantine departments. In this study, we successfully established the CRISPR/Cas13a BmNPV visualized detection technology by combining Recombinase Polymerase Amplification (RPA) technology and CRISPR/Cas13a system. This technology is based on microplate lateral, flow test strips and portable fluorescence detector. The detection sensitivity can reach up to 1 copies/μL for positive standard plasmid and 1 fg/μL for BmNPV genome in 30-45 min, demonstrating high sensitivity. By detecting silkworm tissues infected with different pathogens, we determined that CRISPR/Cas13a detection technology has good specificity. In summary, the newly established nucleic acid detection technology for BmNPV is characterized by high sensitivity, high specificity, low cost and convenience for visualization. It can be applied in field detection and silkworm egg quality monitory system.
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Affiliation(s)
- Xue-Min Zhou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhen-Yu Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yi-Xiang Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Meng-Dong Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Tao Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Lu-Lai Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Samreen Sadiq
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xin-Hao Jiao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China.
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Bao M, Dollery SJ, Yuqing F, Tobin GJ, Du K. Micropillar enhanced FRET-CRISPR biosensor for nucleic acid detection. LAB ON A CHIP 2023; 24:47-55. [PMID: 38019145 PMCID: PMC11221459 DOI: 10.1039/d3lc00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
CRISPR technology has gained widespread adoption for pathogen detection due to its exceptional sensitivity and specificity. Although recent studies have investigated the potential of high-aspect-ratio microstructures in enhancing biochemical applications, their application in CRISPR-based detection has been relatively rare. In this study, we developed a FRET-based biosensor in combination with high-aspect-ratio microstructures and Cas12a-mediated trans-cleavage for detecting HPV 16 DNA fragments. Remarkably, our results show that micropillars with higher density exhibit superior molecular binding capabilities, leading to a tenfold increase in detection sensitivity. Furthermore, we investigated the effectiveness of two surface chemical treatment methods for enhancing the developed FRET assay. A simple and effective approach was also developed to mitigate bubble generation in microfluidic devices, a crucial issue in biochemical reactions within such devices. Overall, this work introduces a novel approach using micropillars for CRISPR-based viral detection and provides valuable insights into optimizing biochemical reactions within microfluidic devices.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | | | - Fnu Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Gregory J Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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Wang B, Yang H. Progress of CRISPR-based programmable RNA manipulation and detection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1804. [PMID: 37282821 DOI: 10.1002/wrna.1804] [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: 06/04/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Prokaryotic clustered regularly interspaced short palindromic repeats and CRISPR associated (CRISPR-Cas) systems provide adaptive immunity by using RNA-guided endonucleases to recognize and eliminate invading foreign nucleic acids. Type II Cas9, type V Cas12, type VI Cas13, and type III Csm/Cmr complexes have been well characterized and developed as programmable platforms for selectively targeting and manipulating RNA molecules of interest in prokaryotic and eukaryotic cells. These Cas effectors exhibit remarkable diversity of ribonucleoprotein (RNP) composition, target recognition and cleavage mechanisms, and self discrimination mechanisms, which are leveraged for various RNA targeting applications. Here, we summarize the current understanding of mechanistic and functional characteristics of these Cas effectors, give an overview on RNA detection and manipulation toolbox established so far including knockdown, editing, imaging, modification, and mapping RNA-protein interactions, and discuss the future directions for CRISPR-based RNA targeting tools. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Beibei Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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Bao M, Dollery SJ, Yuqing F, Tobin GJ, Du K. Micropillar enhanced FRET-CRISPR biosensor for nucleic acid detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554533. [PMID: 37662406 PMCID: PMC10473682 DOI: 10.1101/2023.08.23.554533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
CRISPR technology has gained widespread adoption for pathogen detection due to its exceptional sensitivity and specificity. Although recent studies have investigated the potential of high-aspect-ratio microstructures in enhancing biochemical applications, their application in CRISPR-based detection has been relatively rare. In this study, we developed a FRET-based biosensor in combination with high-aspect-ratio microstructures and Cas12a-mediated trans-cleavage for detecting HPV 16 DNA fragments. Remarkably, our results show that micropillars with higher density exhibit superior molecular binding capabilities, leading to a tenfold increase in detection sensitivity. Furthermore, we investigated the effectiveness of two surface chemical treatment methods for enhancing the developed FRET assay. A simple and effective approach was also developed to mitigate bubble generation in microfluidic devices, a crucial issue in biochemical reactions within such devices. Overall, this work introduces a novel approach using micropillars for CRISPR-based viral detection and provides valuable insights into optimizing biochemical reactions within microfluidic devices.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Stephen J Dollery
- Biological Mimetics, Inc. 124 Byte Drive, Frederick, MD 21702, United States
| | - Fnu Yuqing
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Gregory J Tobin
- Biological Mimetics, Inc. 124 Byte Drive, Frederick, MD 21702, United States
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
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Tanny T, Sallam M, Soda N, Nguyen NT, Alam M, Shiddiky MJA. CRISPR/Cas-Based Diagnostics in Agricultural Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11765-11788. [PMID: 37506507 DOI: 10.1021/acs.jafc.3c00913] [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: 07/30/2023]
Abstract
Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.
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Affiliation(s)
- Tanzena Tanny
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mohamed Sallam
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Mayers Road, Nambour, QLD 4560, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, NSW 2800, Australia
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Tang YN, Jiang D, Wang X, Liu Y, Wei D. Recent progress on rapid diagnosis of COVID-19 by point-of-care testing platforms. CHINESE CHEM LETT 2023:108688. [PMID: 37362324 PMCID: PMC10266891 DOI: 10.1016/j.cclet.2023.108688] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 05/25/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
The outbreak of COVID-19 has drawn great attention around the world. SARS-CoV-2 is a highly infectious virus with occult transmission by many mutations and a long incubation period. In particular, the emergence of asymptomatic infections has made the epidemic even more severe. Therefore, early diagnosis and timely management of suspected cases are essential measures to control the spread of the virus. Developing simple, portable, and accurate diagnostic techniques for SARS-CoV-2 is the key to epidemic prevention. The advantages of point-of-care testing technology make it play an increasingly important role in viral detection and screening. This review summarizes the point-of-care testing platforms developed by nucleic acid detection, immunological detection, and nanomaterial-based biosensors detection. Furthermore, this paper provides a prospect for designing future highly accurate, cheap, and convenient SARS-CoV-2 diagnostic technology.
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Affiliation(s)
- Ya-Nan Tang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dingding Jiang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yunqi Liu
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
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12
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Nouri R, Jiang Y, Politza AJ, Liu T, Greene WH, Zhu Y, Nunez JJ, Lian X, Guan W. STAMP-Based Digital CRISPR-Cas13a for Amplification-Free Quantification of HIV-1 Plasma Viral Loads. ACS NANO 2023; 17:10701-10712. [PMID: 37252938 PMCID: PMC11240847 DOI: 10.1021/acsnano.3c01917] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Quantification of HIV RNA in plasma is critical for identifying the disease progression and monitoring the effectiveness of antiretroviral therapy. While RT-qPCR has been the gold standard for HIV viral load quantification, digital assays could provide an alternative calibration-free absolute quantification method. Here, we reported a Self-digitization Through Automated Membrane-based Partitioning (STAMP) method to digitalize the CRISPR-Cas13 assay (dCRISPR) for amplification-free and absolute quantification of HIV-1 viral RNAs. The HIV-1 Cas13 assay was designed, validated, and optimized. We evaluated the analytical performances with synthetic RNAs. With a membrane that partitions ∼100 nL of reaction mixture (effectively containing 10 nL of input RNA sample), we showed that RNA samples spanning 4 orders of dynamic range between 1 fM (∼6 RNAs) to 10 pM (∼60k RNAs) could be quantified as fast as 30 min. We also examined the end-to-end performance from RNA extraction to STAMP-dCRISPR quantification using 140 μL of both spiked and clinical plasma samples. We demonstrated that the device has a detection limit of approximately 2000 copies/mL and can resolve a viral load change of 3571 copies/mL (equivalent to 3 RNAs in a single membrane) with 90% confidence. Finally, we evaluated the device using 140 μL of 20 patient plasma samples (10 positives and 10 negatives) and benchmarked the performance with RT-PCR. The STAMP-dCRISPR results agree very well with RT-PCR for all negative and high positive samples with Ct < 32. However, the STAMP-dCRISPR is limited in detecting low positive samples with Ct > 32 due to the subsampling errors. Our results demonstrated a digital Cas13 platform that could offer an accessible amplification-free quantification of viral RNAs. By further addressing the subsampling issue with approaches such as preconcentration, this platform could be further exploited for quantitatively determining viral load for an array of infectious diseases.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Wallace H Greene
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Yusheng Zhu
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Jonathan J Nunez
- Department of Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, United States
| | - Xiaojun Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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13
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Peng C, Wang Y, Chen X, Wang X, Ding L, Xu X, Wei W, Yang L, Wu J, Sun M, Xu J. A Localized CRISPR Assay that Detects Short Nucleic Acid Fragments in Unamplified Genetically Modified Samples. ACS Sens 2023; 8:1054-1063. [PMID: 36802509 DOI: 10.1021/acssensors.2c01955] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Detecting short genetically modified (GM) nucleic acid fragments in GM crops and associated products is critically important for the global agriculture industry. Although nucleic acid amplification-based technologies have been widely used for genetically modified organism (GMO) detection, they still struggle to amplify and detect these ultra-short nucleic acid fragments in highly processed products. Here, we used a multiple-CRISPR-derived RNA (crRNA) strategy to detect ultra-short nucleic acid fragments. By combining confinement effects on local concentrations, an amplification-free CRISPR-based short nucleic acid (CRISPRsna) system was established to detect the cauliflower mosaic virus 35S promoter in GM samples. Moreover, we demonstrated assay sensitivity, specificity, and reliability by directly detecting nucleic acid samples from GM crops with a wide genomic range. The CRISPRsna assay avoided possible aerosol contamination from nucleic acid amplification and saved time due to an amplification-free approach. Given that our assay displayed distinct advantages over other technologies in detecting ultra-short nucleic acid fragments, it may have wide applications for detecting GM in highly processed products.
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Affiliation(s)
- Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuling Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Meihao Sun
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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14
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Tao Z, Wang B, Cui Q, Wang P, Dzantiev BB, Wan Y, Wu J, Yang Z. A signal-off Cas14a1-based platform for highly specific detection of methicillin-resistant Staphylococcus aureus. Anal Chim Acta 2023; 1256:341154. [PMID: 37037633 DOI: 10.1016/j.aca.2023.341154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023]
Abstract
Antibiotic usage has become very widespread in aquaculture, and the abuse or overuse of antibiotics has led to the evolution of antibiotic-resistance bacteria, which has adverse effects on aquatic products and ecosystems. Moreover, this evolution can potentially cause harm to human health. Thus, there is an urgent need for diagnostic tools for antibiotic-resistant microorganisms. Herein, we proposed a signal-off Cas14a1-based platform (SOCP) for the detection of methicillin-resistant Staphylococcus aureus (MRSA). In this SOCP, we have designed single-stranded DNA (ssDNA) that not only can activate the trans-cleavage ability of dual Cas14a1-sgRNA complex but also can be used as the primers for the amplified methicilin-resistant gene (mecA). When MRSA is present, the primers can be transformed into products with amplification, leading to the signal decrease of trans-cleavage activity of Cas14a1. The SOCP showed high specificity and fair sensitivity for mecA gene and MRSA. In the detection of real samples, this platform also showed consistent results compared with qPCR. The SOCP could provide an alternative tool for the diagnosis of antibiotic-resistant bacteria in aquaculture, food industry and other fields.
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Affiliation(s)
- Zhenzhen Tao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou, 570228, China
| | - Buhua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou, 570228, China
| | - Qian Cui
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou, 570228, China
| | - Peng Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, 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
| | - Jiajia Wu
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Zhiqing Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou, 570228, China; Rizhao Science and Technology Innovation Service Center, 369 Jining Road, Rizhao, Shandong, China.
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15
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Editing the genome of common cereals (Rice and Wheat): techniques, applications, and industrial aspects. Mol Biol Rep 2023; 50:739-747. [PMID: 36309609 DOI: 10.1007/s11033-022-07664-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/25/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023]
Abstract
Gene editing techniques have made a significant contribution to the development of better crops. Gene editing enables precise changes in the genome of crops, which can introduce new possibilities for altering the crops' traits. Since the last three decades, various gene editing techniques such as meganucleases, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspersed short palindromic repeats (CRISPR)/Cas (CRISPR-associated proteins) have been discovered. In this review, we discuss various gene editing techniques and their applications to common cereals. Further, we elucidate the future of gene-edited crops, their regulatory features, and industrial aspects globally. To achieve this, we perform a comprehensive literature survey using databases such as PubMed, Web of Science, SCOPUS, Google Scholar etc. For the literature search, we used keywords such as gene editing, crop genome modification, CRISPR/Cas, ZFN, TALEN, meganucleases etc. With the advent of the CRISPR/Cas technology in the last decade, the future of gene editing has transitioned into a new dimension. The functionality of CRISPR/Cas in both DNA and RNA has increased through the use of various Cas enzymes and their orthologs. Constant research efforts in this direction have improved the gene editing process for crops by minimizing its off-target effects. Scientists also use computational tools, which help them to design experiments and analyze the results of gene editing experiments in advance. Gene editing has diverse potential applications. In the future, gene editing will open new avenues for solving more agricultural issues and boosting crop production, which may have great industrial prospects.
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16
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Wang Y, Liu L, Liu X, Wu K, Zhu X, Ma L, Su J. An Ultrasensitive PCR-Based CRISPR-Cas13a Method for the Detection of Helicobacter pylori. J Pers Med 2022; 12:jpm12122082. [PMID: 36556302 PMCID: PMC9784247 DOI: 10.3390/jpm12122082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/17/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The rapid and simple detection of Helicobacter pylori (H. pylori) is essential for its clinical eradication. Although various methods for detecting H. pylori have been well established, such as endoscopy in combination with histology or culture, rapid urease test (RUT) and molecular tests using clinical specimens, it is of great importance to develop an ultrasensitive and accurate nucleic acid detection platform and apply it to identify H. pylori. To meet these demands, a novel method based on PCR and CRISPR-Cas13a, called PCR-Cas13a, was developed and validated using the DNA of 84 clinical strains and 71 clinical specimens. PCR primers for the pre-amplification of conservative sequence and CRISPR RNA (crRNA) for the detection of specific sequence were designed according to the principle. The designed primers and crRNA were specific to H. pylori, and the assay showed a high degree of specificity compared with other common pathogens. Our detection system can screen H. pylori with a limit of 2.2 copies/μL within 30 mins after PCR amplification. Using a coincidence analysis with traditional methods, our method exhibited 100% accuracy for the detection of H. pylori. Furthermore, its diagnostic performance was compared, in parallel with a q-PCR. The PCR-Cas13a demonstrates 98% sensitivity and 100% specificity. Moreover, our approach had a lower limit of detection (LOD) than q-PCR. Herein, we present a diagnostic system for the highly sensitive screening of H. pylori and distinguish it from other pathogens. All the results demonstrated that this PCR-based CRISPR assay has wide application prospects for the detection of H. pylori and other slow-growth pathogens.
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Affiliation(s)
- Yaxuan Wang
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Liyang Liu
- Department of Gastroenterology, Jingdong Medical Area, General Hospital of Chinese PLA, Beijing 101149, China
| | - Xiaochuan Liu
- Department of Gastroenterology, Emergency General Hospital, Beijing 100028, China
| | - Kai Wu
- Department of Gastroenterology, The Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xiaoyan Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Liyan Ma
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jianrong Su
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Correspondence:
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17
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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18
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Sánchez E, Ali Z, Islam T, Mahfouz M. A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2418-2429. [PMID: 36072993 PMCID: PMC9674313 DOI: 10.1111/pbi.13924] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/14/2022] [Accepted: 08/28/2022] [Indexed: 05/27/2023]
Abstract
Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.
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Affiliation(s)
- Edith Sánchez
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE)Bangabandhu Sheikh Mujibur Rahman Agricultural UniversityGazipurBangladesh
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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19
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Wei H, Bu S, Wang Z, Zhou H, Li X, Wei J, He X, Wan J. Click Chemistry Actuated Exponential Amplification Reaction Assisted CRISPR-Cas12a for the Electrochemical Detection of MicroRNAs. ACS OMEGA 2022; 7:35515-35522. [PMID: 36249407 PMCID: PMC9558246 DOI: 10.1021/acsomega.2c01930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
MicroRNAs (miRNAs) play a very important role in biological processes and are used as biomarkers for the detection of a variety of diseases, including neurodegenerative diseases, chronic cardiovascular diseases, and cancers. A sensitive point-of-care (POC) method is crucial for detecting miRNAs. Herein, CRISPR-Cas12a combined with the click chemistry actuated exponential amplification reaction was introduced into an electrochemical biosensor for detecting miRNA-21. The target miRNA-21 initiated the click chemistry-exponential amplification reaction in the electrochemical biosensor to produce numerous nucleic acid fragments, which could stimulate the trans-cleavage ability of CRISPR-Cas12a to cleave hairpin DNA electrochemical reporters immobilized on the electrode surface. Under optimal conditions, the minimum detection limit for this electrochemical biosensor was as low as 1 fM. Thus, the proposed electrochemical biosensor allows sensitive and efficient miRNA detection and could be a potential analysis tool for POC test and field molecular diagnostics.
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Affiliation(s)
- Hongguo Wei
- School
of Life Science and Technology, Changchun
University of Science and Technology, Changchun 130022, China
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
| | - Shengjun Bu
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
| | - Ze Wang
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
| | - Hongyu Zhou
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
| | - Xue Li
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
| | - Jiaqi Wei
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
| | - Xiuxia He
- School
of Life Science and Technology, Changchun
University of Science and Technology, Changchun 130022, China
| | - Jiayu Wan
- Institute
of Military Veterinary Medicine, Academy
of Military Medical Sciences, Changchun 130122, China
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20
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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CRISPR-Based Genome Editing and Its Applications in Woody Plants. Int J Mol Sci 2022; 23:ijms231710175. [PMID: 36077571 PMCID: PMC9456532 DOI: 10.3390/ijms231710175] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/31/2022] [Indexed: 12/21/2022] Open
Abstract
CRISPR/Cas-based genome editing technology provides straightforward, proficient, and multifunctional ways for the site-directed modification of organism genomes and genes. The application of CRISPR-based technology in plants has a vast potential value in gene function research, germplasm innovation, and genetic improvement. The complexity of woody plants genome may pose significant challenges in the application and expansion of various new editing techniques, such as Cas9, 12, 13, and 14 effectors, base editing, particularly for timberland species with a long life span, huge genome, and ploidy. Therefore, many novel optimisms have been drawn to molecular breeding research based on woody plants. This review summarizes the recent development of CRISPR/Cas applications for essential traits, including wood properties, flowering, biological stress, abiotic stress, growth, and development in woody plants. We outlined the current problems and future development trends of this technology in germplasm and the improvement of products in woody plants.
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22
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Applications of CRISPR/Cas13-Based RNA Editing in Plants. Cells 2022; 11:cells11172665. [PMID: 36078073 PMCID: PMC9454418 DOI: 10.3390/cells11172665] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is widely used as a genome-editing tool in various organisms, including plants, to elucidate the fundamental understanding of gene function, disease diagnostics, and crop improvement. Among the CRISPR/Cas systems, Cas9 is one of the widely used nucleases for DNA modifications, but manipulation of RNA at the post-transcriptional level is limited. The recently identified type VI CRISPR/Cas systems provide a platform for precise RNA manipulation without permanent changes to the genome. Several studies reported efficient application of Cas13 in RNA studies, such as viral interference, RNA knockdown, and RNA detection in various organisms. Cas13 was also used to produce virus resistance in plants, as most plant viruses are RNA viruses. However, the application of CRISPR/Cas13 to studies of plant RNA biology is still in its infancy. This review discusses the current and prospective applications of CRISPR/Cas13-based RNA editing technologies in plants.
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23
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Increasing disease resistance in host plants through genome editing. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00100-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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24
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Bhardwaj P, Kant R, Behera SP, Dwivedi GR, Singh R. Next-Generation Diagnostic with CRISPR/Cas: Beyond Nucleic Acid Detection. Int J Mol Sci 2022; 23:6052. [PMID: 35682737 PMCID: PMC9180940 DOI: 10.3390/ijms23116052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 02/07/2023] Open
Abstract
The early management, diagnosis, and treatment of emerging and re-emerging infections and the rising burden of non-communicable diseases (NCDs) are necessary. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system has recently acquired popularity as a diagnostic tool due to its ability to target specific genes. It uses Cas enzymes and a guide RNA (gRNA) to cleave target DNA or RNA. The discovery of collateral cleavage in CRISPR-Cas effectors such as Cas12a and Cas13a was intensively repurposed for the development of instrument-free, sensitive, precise and rapid point-of-care diagnostics. CRISPR/Cas demonstrated proficiency in detecting non-nucleic acid targets including protein, analyte, and hormones other than nucleic acid. CRISPR/Cas effectors can provide multiple detections simultaneously. The present review highlights the technical challenges of integrating CRISPR/Cas technology into the onsite assessment of clinical and other specimens, along with current improvements in CRISPR bio-sensing for nucleic acid and non-nucleic acid targets. It also highlights the current applications of CRISPR/Cas technologies.
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Affiliation(s)
| | | | | | - Gaurav Raj Dwivedi
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (R.K.); (S.P.B.)
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (R.K.); (S.P.B.)
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25
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Habimana JDD, Huang R, Muhoza B, Kalisa YN, Han X, Deng W, Li Z. Mechanistic insights of CRISPR/Cas nucleases for programmable targeting and early-stage diagnosis: A review. Biosens Bioelectron 2022; 203:114033. [DOI: 10.1016/j.bios.2022.114033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/21/2022]
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26
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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You H, Gordon CA, MacGregor SR, Cai P, McManus DP. Potential of the CRISPR-Cas system for improved parasite diagnosis: CRISPR-Cas mediated diagnosis in parasitic infections: CRISPR-Cas mediated diagnosis in parasitic infections. Bioessays 2022; 44:e2100286. [PMID: 35142378 DOI: 10.1002/bies.202100286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas technology accelerates development of fast, accurate, and portable diagnostic tools, typified by recent applications in COVID-19 diagnosis. Parasitic helminths cause devastating diseases afflicting 1.5 billion people globally, representing a significant public health and economic burden, especially in developing countries. Currently available diagnostic tests for worm infection are neither sufficiently sensitive nor field-friendly for use in low-endemic or resource-poor settings, leading to underestimation of true prevalence rates. Mass drug administration programs are unsustainable long-term, and diagnostic tools - required to be rapid, specific, sensitive, cost-effective, and user-friendly without specialized equipment and expertise - are urgently needed for rapid mapping of helminthic diseases and monitoring control programs. We describe the key features of the CRISPR-Cas12/13 system and emphasise its potential for the development of effective tools for the diagnosis of parasitic and other neglected tropical diseases (NTDs), a key recommendation of the NTDs 2021-2030 roadmap released by the World Health Organization.
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Affiliation(s)
- Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Catherine A Gordon
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Skye R MacGregor
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Pengfei Cai
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
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28
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Das A, Goswami HN, Whyms CT, Sridhara S, Li H. Structural Principles of CRISPR-Cas Enzymes Used in Nucleic Acid Detection. J Struct Biol 2022; 214:107838. [PMID: 35123001 PMCID: PMC8924977 DOI: 10.1016/j.jsb.2022.107838] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-based technology has revolutionized the field of biomedicine with broad applications in genome editing, therapeutics and diagnostics. While a majority of applications involve the RNA-guided site-specific DNA or RNA cleavage by CRISPR enzymes, recent successes in nucleic acid detection rely on their collateral and non-specific cleavage activated by viral DNA or RNA. Ranging in enzyme composition, the mechanism for distinguishing self- from foreign-nucleic acids, the usage of second messengers, and enzymology, the CRISPR enzymes provide a diverse set of diagnosis tools in further innovations. Structural biology plays an important role in elucidating the mechanisms of these CRISPR enzymes. Here we summarize and compare structures of three types of CRISPR enzymes used in nucleic acid detection captured in their respective functional forms and illustrate the current understanding of their activation mechanism.
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Affiliation(s)
- Anuska Das
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hemant N Goswami
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Charlisa T Whyms
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Sagar Sridhara
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
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29
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Díaz-Galicia E, Grünberg R, Arold ST. How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. BIOSENSORS 2022; 12:53. [PMID: 35200314 PMCID: PMC8869480 DOI: 10.3390/bios12020053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. We provide an overview of the currently described Cas effector systems and review existing Cas-based RNA detection methods. We then propose a set of systematic selection criteria for selecting CRISPR-Cas candidates for new applications. Using this approach, we identify four candidates for in vitro RNA.
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Affiliation(s)
- Escarlet Díaz-Galicia
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, F-34090 Montpellier, France
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Clinical validation of engineered CRISPR/Cas12a for rapid SARS-CoV-2 detection. COMMUNICATIONS MEDICINE 2022; 2:7. [PMID: 35603267 PMCID: PMC9053293 DOI: 10.1038/s43856-021-00066-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
Background The coronavirus disease (COVID-19) caused by SARS-CoV-2 has swept through the globe at an unprecedented rate. CRISPR-based detection technologies have emerged as a rapid and affordable platform that can shape the future of diagnostics. Methods We developed ENHANCEv2 that is composed of a chimeric guide RNA, a modified LbCas12a enzyme, and a dual reporter construct to improve the previously reported ENHANCE system. We validated both ENHANCE and ENHANCEv2 using 62 nasopharyngeal swabs and compared the results to RT-qPCR. We created a lyophilized version of ENHANCEv2 and characterized its detection capability and stability. Results Here we demonstrate that when coupled with an RT-LAMP step, ENHANCE detects COVID-19 samples down to a few copies with 95% accuracy while maintaining a high specificity towards various isolates of SARS-CoV-2 against 31 highly similar and common respiratory pathogens. ENHANCE works robustly in a wide range of magnesium concentrations (3 mM-13 mM), allowing for further assay optimization. Our clinical validation results for both ENHANCE and ENHANCEv2 show 60/62 (96.7%) sample agreement with RT-qPCR results while only using 5 µL of sample and 20 minutes of CRISPR reaction. We show that the lateral flow assay using paper-based strips displays 100% agreement with the fluorescence-based reporter assay during clinical validation. Finally, we demonstrate that a lyophilized version of ENHANCEv2 shows high sensitivity and specificity for SARS-CoV-2 detection while reducing the CRISPR reaction time to as low as 3 minutes while maintaining its detection capability for several weeks upon storage at room temperature. Conclusions CRISPR-based diagnostic platforms offer many advantages as compared to conventional qPCR-based detection methods. Our work here provides clinical validation of ENHANCE and its improved form ENHANCEv2 for the detection of COVID-19. Nguyen et al. describe the clinical validation of the ENHANCE system, a method to detect SARS-CoV-2 based on engineered crRNAs for Cas12a and preceded by an RT-LAMP amplification step. Authors also describe the development and clinical validation of a version of this system, ENHANCEv2, that can be lyophilized and that uses another mutated Cas12a for further signal amplification. The COVID-19 pandemic has underscored the need for rapid and accurate tests to detect SARS-CoV-2 infection. The tests commonly used have limitations, and a detection system based on CRISPR technology could offer a useful alternative. CRISPR is a technology derived from bacteria that can specifically detect pieces of DNA. We have previously developed ENHANCE, a detection system that converts the SARS-CoV-2 genetic material into DNA that is then detected by an engineered CRISPR technology. Here, we develop an improved version of this method, ENHANCEv2, that has an extended shelf life and less need for refrigeration, facilitating transportation of the components required for the test and its use. We show that both ENHANCE and ENHACEv2 can quickly and accurately detect SARS-CoV-2 in swabs from infected people. This is a step towards having more versatile tools to detect SARS-CoV-2 infection quickly and accurately.
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31
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Sohail M, Qin L, Li S, Chen Y, Zaman MH, Zhang X, Li B, Huang H. Molecular reporters for CRISPR/Cas: from design principles to engineering for bioanalytical and diagnostic applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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32
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Mohan C, Easterling M, Yau YY. Gene Editing Technologies for Sugarcane Improvement: Opportunities and Limitations. SUGAR TECH : AN INTERNATIONAL JOURNAL OF SUGAR CROPS & RELATED INDUSTRIES 2022; 24:369-385. [PMID: 34667393 PMCID: PMC8517945 DOI: 10.1007/s12355-021-01045-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/07/2021] [Indexed: 05/05/2023]
Abstract
Plant-based biofuels present a promising alternative to depleting non-renewable fuel resources. One of the benefits of biofuel is reduced environmental impact, including reduction in greenhouse gas emission which causes climate change. Sugarcane is one of the most important bioenergy crops. Sugarcane juice is used to produce table sugar and first-generation biofuel (e.g., bioethanol). Sugarcane bagasse is also a potential material for second-generation cellulosic biofuel production. Researchers worldwide are striving to improve sugarcane biomass yield and quality by a variety of means including biotechnological tools. This paper reviews the use of sugarcane as a feedstock for biofuel production, and gene manipulation tools and approaches, including RNAi and genome-editing tools, such as TALENs and CRISPR-Cas9, for improving its quality. The specific focus here is on CRISPR system because it is low cost, simple in design and versatile compared to other genome-editing tools. The advance of CRISPR-Cas9 technology has transformed plant research with its ability to precisely delete, insert or replace genes in recent years. Lignin is the primary material responsible for biomass recalcitrance in biofuel production. The use of genome editing technology to modify lignin composition and distribution in sugarcane cell wall has been realized. The current and potential applications of genome editing technology for sugarcane improvement are discussed. The advantages and limitations of utilizing RNAi and TALEN techniques in sugarcane improvement are discussed as well.
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Affiliation(s)
- Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mona Easterling
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
- Northeast Campus, Tulsa Community College, 3727 East Apache St, Tulsa, OK 74115 USA
| | - Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
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33
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Novel CRISPR/Cas12a-based genetic diagnostic approach for SLC26A4 mutation-related hereditary hearing loss. Eur J Med Genet 2021; 65:104406. [PMID: 34968750 DOI: 10.1016/j.ejmg.2021.104406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 09/18/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Hereditary hearing loss is a common defect of the auditory nervous system with high-incidence, seriously affecting the quality of life of the patients. The clinical manifestations of SLC26A4 mutation-related hearing loss are congenital sensorineural or mixed deafness. Sensitive and specific SLC26A4 mutation detection in the early clinical stage is key for the early indication of potential hearing loss in the lack of effective treatment. Using clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid detection technology, we designed a fast and sensitive detection system for SLC26A4 pathogenic mutations (c.919-2A > G, c.2168A > G and c.1229C > T). This recombinase-aided amplification-based detection system allows rapid target gene amplification and, in combination with the CRISPR-based nucleic acid testing (NAT) system, mutation site detection. Moreover, mismatches were introduced in CRISPR-derived RNA (crRNA) to increase signal differences between the wild-type genes and mutant genes. A total of 64 samples were examined using this approach and all results were verified using Sanger sequencing. The detection results were consistent with the polymerase chain reaction-Sanger sequencing results. Overall, this CRISPR-based NAT technology provides a sensitive and fast new approach for the detection of hereditary deafness and provides a crRNA optimization strategy for single-nucleotide polymorphism detection, which could be helpful for the clinical diagnosis of SLC26A4 mutation-related hereditary hearing loss.
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34
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Li L, Duan C, Weng J, Qi X, Liu C, Li X, Zhu J, Xie C. A field-deployable method for single and multiplex detection of DNA or RNA from pathogens using Cas12 and Cas13. SCIENCE CHINA. LIFE SCIENCES 2021; 65:1456-1465. [PMID: 34962615 PMCID: PMC8713540 DOI: 10.1007/s11427-021-2028-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/28/2021] [Indexed: 12/26/2022]
Abstract
For some Cas nucleases, trans-cleavage activity triggered by CRISPR/Cas-mediated cis-cleavage upon target nucleic acid recognition has been explored for diagnostic detection. Portable single and multiplex nucleic acid-based detection is needed for crop pathogen management in agriculture. Here, we harnessed and characterized RfxCas13d as an additional CRISPR/Cas nucleic acid detection tool. We systematically characterized AsCas12a, LbCas12a, LwaCas13a, and RfxCas13d combined with isothermal amplification to develop a CRISPR/Cas nucleic acid-based tool for single or multiplex pathogen detection. Our data indicated that sufficient detection sensitivity was achieved with just a few copies of DNA/RNA targets as input. Using this tool, we successfully detected DNA from Fusarium graminearum and Fusarium verticillioides and RNA from rice black-streaked dwarf virus in crude extracts prepared in the field. Our method, from sample preparation to result readout, could be rapidly and easily deployed in the field. This system could be extended to other crop pathogens, including those that currently lack a detection method and have metabolite profiles that make detection challenging. This nucleic acid detection system could also be used for single-nucleotide polymorphism genotyping, transgene detection, and qualitative detection of gene expression in the field.
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Affiliation(s)
- Lina Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Canxing Duan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianfeng Weng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiantao Qi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changlin Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xinhai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jinjie Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Chuanxiao Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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35
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Liu G, Lin Q, Jin S, Gao C. The CRISPR-Cas toolbox and gene editing technologies. Mol Cell 2021; 82:333-347. [PMID: 34968414 DOI: 10.1016/j.molcel.2021.12.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/04/2021] [Accepted: 12/02/2021] [Indexed: 02/08/2023]
Abstract
The emergence of CRISPR-Cas systems has accelerated the development of gene editing technologies, which are widely used in the life sciences. To improve the performance of these systems, workers have engineered and developed a variety of CRISPR-Cas tools with a broader range of targets, higher efficiency and specificity, and greater precision. Moreover, CRISPR-Cas-related technologies have also been expanded beyond making cuts in DNA by introducing functional elements that permit precise gene modification, control gene expression, make epigenetic changes, and so on. In this review, we introduce and summarize the characteristics and applications of different types of CRISPR-Cas tools. We discuss certain limitations of current approaches and future prospects for optimizing CRISPR-Cas systems.
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Affiliation(s)
- Guanwen Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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36
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Yuan M, Ding R, Chen S, Duan G. Advances in Field Detection Based on CRISPR/Cas System. ACS Synth Biol 2021; 10:2824-2832. [PMID: 34714068 DOI: 10.1021/acssynbio.1c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid and accurate diagnostic methods are essential to interrupt outbreaks of infectious diseases such as COVID-19. However, the most commonly used nucleic acid detection method, qPCR or RT-qPCR, takes several hours to complete and requires highly sophisticated equipment. Recently, an emerging nucleic acid detection method based on the CRISPR/Cas system has reduced the reliance on qPCR. It has several important features that make it suitable for on-site POCT (point-of-care testing), including short detection cycles, low cost, high sensitivity, and the ability to be combined with different readout methods. This review briefly introduces the steps of CRISPR/Cas detection and then summarizes the current advances of CRISPR/Cas-based POCT from four steps: nucleic acid extraction, target amplification, CRISPR/Cas-based signal generation, and signal output. Finally, we discuss the advantages and challenges of CRISPR-based POCT and describe the future research perspectives for CRISPR.
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Affiliation(s)
- Mingzhu Yuan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Ronghua Ding
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
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37
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Nouri R, Jiang Y, Tang Z, Lian XL, Guan W. Detection of SARS-CoV-2 with Solid-State CRISPR-Cas12a-Assisted Nanopores. NANO LETTERS 2021; 21:8393-8400. [PMID: 34542296 PMCID: PMC8491552 DOI: 10.1021/acs.nanolett.1c02974] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Indexed: 05/12/2023]
Abstract
The outbreak of the SARS-CoV-2 caused the disease COVID-19 to spread globally. Specific and sensitive detection of SARS-CoV-2 facilitates early intervention and prevents the disease from spreading. Here, we present a solid-state CRISPR-Cas12a-assisted nanopore (SCAN) sensing strategy for the specific detection of SARS-CoV-2. We introduced a nanopore-sized counting method to measure the cleavage ratio of reporters, which is used as a criterion for positive/negative classification. A kinetic cleavage model was developed and validated to predict the reporter size distributions. The model revealed the trade-offs between sensitivity, turnaround time, and false-positive rate of the SARS-CoV-2 SCAN. With preamplification and a 30 min CRISPR Cas12a assay, we achieved excellent specificity against other common human coronaviruses and a limit of detection of 13.5 copies/μL (22.5 aM) of viral RNA at a confidence level of 95%. These results suggested that the SCAN could provide a rapid, sensitive, and specific analysis of SARS-CoV-2.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Zifan Tang
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Huck Institutes of the Life Sciences,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Department of Biology, Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Weihua Guan
- Department of Electrical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
- Department of Biomedical Engineering,
Pennsylvania State University, University Park, Pennsylvania
16802, United States
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38
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Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1694. [PMID: 34553495 DOI: 10.1002/wrna.1694] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cell-free environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Martyna Kordyś
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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39
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Durán-Vinet B, Araya-Castro K, Calderón J, Vergara L, Weber H, Retamales J, Araya-Castro P, Leal-Rojas P. CRISPR/Cas13-Based Platforms for a Potential Next-Generation Diagnosis of Colorectal Cancer through Exosomes Micro-RNA Detection: A Review. Cancers (Basel) 2021; 13:4640. [PMID: 34572866 PMCID: PMC8466426 DOI: 10.3390/cancers13184640] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer with the second highest mortality rate worldwide. CRC is a heterogenous disease with multiple risk factors associated, including obesity, smoking, and use of alcohol. Of total CRC cases, 60% are diagnosed in late stages, where survival can drop to about 10%. CRC screening programs are based primarily on colonoscopy, yet this approach is invasive and has low patient adherence. Therefore, there is a strong incentive for developing molecular-based methods that are minimally invasive and have higher patient adherence. Recent reports have highlighted the importance of extracellular vesicles (EVs), specifically exosomes, as intercellular communication vehicles with a broad cargo, including micro-RNAs (miRNAs). These have been syndicated as robust candidates for diagnosis, primarily for their known activities in cancer cells, including immunoevasion, tumor progression, and angiogenesis, whereas miRNAs are dysregulated by cancer cells and delivered by cancer-derived exosomes (CEx). Quantitative polymerase chain reaction (qPCR) has shown good results detecting specific cancer-derived exosome micro-RNAs (CEx-miRNAs) associated with CRC, but qPCR also has several challenges, including portability and sensitivity/specificity issues regarding experiment design and sample quality. CRISPR/Cas-based platforms have been presented as cost-effective, ultrasensitive, specific, and robust clinical detection tools in the presence of potential inhibitors and capable of delivering quantitative and qualitative real-time data for enhanced decision-making to healthcare teams. Thereby, CRISPR/Cas13-based technologies have become a potential strategy for early CRC diagnosis detecting CEx-miRNAs. Moreover, CRISPR/Cas13-based platforms' ease of use, scalability, and portability also showcase them as a potential point-of-care (POC) technology for CRC early diagnosis. This study presents two potential CRISPR/Cas13-based methodologies with a proposed panel consisting of four CEx-miRNAs, including miR-126, miR-1290, miR-23a, and miR-940, to streamline novel applications which may deliver a potential early diagnosis and prognosis of CRC.
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Affiliation(s)
- Benjamín Durán-Vinet
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco 4780000, Chile; (B.D.-V.); (K.A.-C.); (H.W.)
- Center of Excellence in Translational Medicine (CEMT), Biomedicine and Translational Research Laboratory, Universidad de La Frontera, Temuco 4780000, Chile;
| | - Karla Araya-Castro
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco 4780000, Chile; (B.D.-V.); (K.A.-C.); (H.W.)
- Innovation and Entrepreneurship Institute (iDEAUFRO), Universidad de La Frontera, Temuco 4780000, Chile
| | - Juan Calderón
- Center for Genetics and Genomics, School of Medicine, Institute of Science and Innovation in Medicine (ICIM), Clínica Alemana, Universidad del Desarrollo, Santiago 8320000, Chile;
| | - Luis Vergara
- Center of Excellence in Translational Medicine (CEMT), Biomedicine and Translational Research Laboratory, Universidad de La Frontera, Temuco 4780000, Chile;
- Doctoral Program in Cell and Applied Molecular Biology, Universidad de La Frontera, Temuco 4780000, Chile
| | - Helga Weber
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco 4780000, Chile; (B.D.-V.); (K.A.-C.); (H.W.)
- Center of Excellence in Translational Medicine (CEMT), Biomedicine and Translational Research Laboratory, Universidad de La Frontera, Temuco 4780000, Chile;
| | - Javier Retamales
- Chilean Cooperative Group for Oncologic Research (GOCCHI), Santiago 8320000, Chile;
| | - Paulina Araya-Castro
- School of Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago 8320000, Chile;
| | - Pamela Leal-Rojas
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Temuco 4780000, Chile; (B.D.-V.); (K.A.-C.); (H.W.)
- Center of Excellence in Translational Medicine (CEMT), Biomedicine and Translational Research Laboratory, Universidad de La Frontera, Temuco 4780000, Chile;
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural and Forestry Science, Universidad de La Frontera, Temuco 4780000, Chile
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40
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Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. Nature 2021; 597:720-725. [PMID: 34489594 DOI: 10.1038/s41586-021-03886-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/09/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-Cas interference is mediated by Cas effector nucleases that are either components of multisubunit complexes-in class 1 CRISPR-Cas systems-or domains of a single protein-in class 2 systems1-3. Here we show that the subtype III-E effector Cas7-11 is a single-protein effector in the class 1 CRISPR-Cas systems originating from the fusion of a putative Cas11 domain and multiple Cas7 subunits that are derived from subtype III-D. Cas7-11 from Desulfonema ishimotonii (DiCas7-11), when expressed in Escherichia coli, has substantial RNA interference effectivity against mRNAs and bacteriophages. Similar to many class 2 effectors-and unique among class 1 systems-DiCas7-11 processes pre-CRISPR RNA into mature CRISPR RNA (crRNA) and cleaves RNA at positions defined by the target:spacer duplex, without detectable non-specific activity. We engineered Cas7-11 for RNA knockdown and editing in mammalian cells. We show that Cas7-11 has no effects on cell viability, whereas other RNA-targeting tools (such as short hairpin RNAs and Cas13) show substantial cell toxicity4,5. This study illustrates the evolution of a single-protein effector from multisubunit class 1 effector complexes, expanding our understanding of the diversity of CRISPR systems. Cas7-11 provides the basis for new programmable RNA-targeting tools that are free of collateral activity and cell toxicity.
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41
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Yu T, Zhang S, Matei R, Marx W, Beisel CL, Wei Q. Coupling smartphone and
CRISPR–Cas12a
for digital and multiplexed
nucleic acid
detection. AIChE J 2021. [DOI: 10.1002/aic.17365] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tao Yu
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina USA
| | - Shengwei Zhang
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina USA
| | - Razvan Matei
- Department of Biological Sciences Columbia University New York New York USA
| | - William Marx
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina USA
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina USA
- Helmholtz Institute for RNA‐Based Infection Research (HIRI) Helmholtz Centre for Infection Research (HZI) Würzburg Germany
- Medical Faculty University of Würzburg Würzburg Germany
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina USA
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42
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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43
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Perčulija V, Lin J, Zhang B, Ouyang S. Functional Features and Current Applications of the RNA-Targeting Type VI CRISPR-Cas Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004685. [PMID: 34254038 PMCID: PMC8209922 DOI: 10.1002/advs.202004685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/26/2021] [Indexed: 05/14/2023]
Abstract
CRISPR-Cas systems are a form of prokaryotic adaptive immunity that employs RNA-guided endonucleases (Cas effectors) to cleave foreign genetic elements. Due to their simplicity, targeting programmability, and efficiency, single-effector CRISPR-Cas systems have great potential for application in research, biotechnology, and therapeutics. While DNA-targeting Cas effectors such as Cas9 and Cas12a have become indispensable tools for genome editing in the past decade, the more recent discovery of RNA-targeting CRISPR-Cas systems has opened the door for implementation of CRISPR-Cas technology in RNA manipulation. With an increasing number of studies reporting their application in transcriptome engineering, viral interference, nucleic acid detection, and RNA imaging, type VI CRISPR-Cas systems and the associated Cas13 effectors particularly hold promise as RNA-targeting or RNA-binding tools. However, even though previous structural and biochemical characterization provided a firm basis for leveraging type VI CRISPR-Cas systems into such tools, the lack of comprehension of certain mechanisms underlying their functions hinders more sophisticated and conventional use. This review will summarize current knowledge on structural and mechanistic properties of type VI CRISPR-Cas systems, give an overview on the reported applications, and discuss functional features that need further investigation in order to improve performance of Cas13-based tools.
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Affiliation(s)
- Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- International College of Chinese StudiesFujian Normal UniversityFuzhou350117China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)Qingdao266237China
- National Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
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44
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Gao S, Liu J, Li Z, Ma Y, Wang J. Sensitive detection of foodborne pathogens based on CRISPR-Cas13a. J Food Sci 2021; 86:2615-2625. [PMID: 33931854 DOI: 10.1111/1750-3841.15745] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/12/2022]
Abstract
Salmonella, being one of the most widespread foodborne pathogens, is a compulsory test item required by national food safety standard of China and many other countries. More sensitive and specific Salmonella detection method is still needed since traditional methods are time consuming and highly dependent on enormous manpower and material resources. In this research, a bacteria detection method based on CRISPR-Cas13a system (where CRISPR is Clustered Regularly Interspaced Short Palindromic Repeats) was proposed. The target DNA was amplified by PCR and transcribed into RNA by T7 transcriptase, which can activate the RNase activity of the Cas13a protein. The self-folding quenched fluorescent probe can be cleaved by the activated Cas13a protein to generate fluorescent signal. We named this method as PCF detection (PCR-CRISPR-Fluorescence based nucleic acid detection). In this study, PCF detection showed excellent sensitivity, which can detect Salmonella genomic DNA with a minimum of 101 aM or 10° CFU/ml Salmonella bacteria in 2 hr. It also showed good specificity with no cross-reaction with other common foodborne bacteria. PRACTICAL APPLICATION: The PCF detection method proposed in this article can detect Salmonella sensitively and specifically, providing a novel strategy for the detection of foodborne pathogens in food and has great application potential in other microbial detection fields.
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Affiliation(s)
- Song Gao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jingwen Liu
- Guangzhou Customs Technology Centre, Guangzhou, China
| | - Zhiyong Li
- Guangzhou Customs Technology Centre, Guangzhou, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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45
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Song F, Wei Y, Wang P, Ge X, Li C, Wang A, Yang Z, Wan Y, Li J. Combining tag-specific primer extension and magneto-DNA system for Cas14a-based universal bacterial diagnostic platform. Biosens Bioelectron 2021; 185:113262. [PMID: 33930753 DOI: 10.1016/j.bios.2021.113262] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/14/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022]
Abstract
Nucleic acid-based diagnosis using CRISPR-Cas associated enzymes is essential for rapid infectious disease diagnosis and treatment strategies during a global pandemic. The obstacle has been blossomed CRIPSR-Cas based tools that can monitor wide range of pathogens in clinical samples with ultralow concentrations. Here, a universal nucleic acid magneto-DNA nanoparticle system was exploited for the detection of pathogenic bacteria, based on the collateral cleavage activity of CRISPR-Cas14a and tag-specific primer extension. In the system, the target nucleic acids were amplificated and be separated from mixtures by streptavidin-coated magnetic bead. The collateral cleavage activity of CRISPR-Cas14a can be activated via the tag sequence on the target product. Consequently, the fluorophore quencher reporter can be activated by CRISPR-Cas14a, leading to the increasing response. The exploited universal bacterial diagnostic can distinguish six different bacteria strains with 1 cfu/mL or 1 aM sensitivity, which may provide new strategies to construct fast, accurate, cost-effective and sensitive diagnostic tools in environments with limited resources.
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Affiliation(s)
- Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Yangdao Wei
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Peng Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Xiaolin Ge
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Chaoyang Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Zhiqing Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China; CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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46
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Nouri R, Tang Z, Dong M, Liu T, Kshirsagar A, Guan W. CRISPR-based detection of SARS-CoV-2: A review from sample to result. Biosens Bioelectron 2021; 178:113012. [PMID: 33497879 PMCID: PMC7826142 DOI: 10.1016/j.bios.2021.113012] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/10/2021] [Accepted: 01/17/2021] [Indexed: 12/23/2022]
Abstract
The current pandemic of the 2019 novel coronavirus (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concern. Rapid, affordable, and accurate diagnostics of SARS-CoV-2 is essential for early treatment and control of the disease spread. In the past few years, CRISPR technology has shown great potential for highly sensitive and specific molecular diagnostics. Amid the ongoing COVID-19 pandemic, there is an increasing interest in implementing CRISPR-based diagnostic principles to develop fast and precise methods for detecting SARS-CoV-2. In this work, we reviewed and summarized these CRISPR-based diagnostic systems as well as their characteristics and challenges. We also provided future perspectives of CRISPR-based sensing towards point-of-care molecular diagnosis applications.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, United States.
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47
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Dhar BC, Steimberg N, Mazzoleni G. Point-of-Care Pathogen Detection with CRISPR-based Programmable Nucleic Acid Binding Proteins. ChemMedChem 2021; 16:1566-1575. [PMID: 33258314 DOI: 10.1002/cmdc.202000782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 12/24/2022]
Abstract
The contemporary discovery of extremely versatile engineered nucleic acid-binding proteins has transformed a brave new world in the genome-editing scientific area. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated programmable nucleic acid-binding proteins have brought about a revolution in diagnostic platforms. The groundbreaking finding that bacteria and archaea that harbored prokaryotes have transmitted adaptive immunity through CRISPR and CRISPR-associated (Cas) proteins has driven revolutionary advances in molecular biology. Importantly, advances in gene editing focus how expanding visions in CRISPR-Cas biology are revolutionizing the area of molecular diagnostics for identifying DNA and RNA in emerging microbiological pathogens, for single nucleotide polymorphism (SNP) identifications, and for cell-free mutation. Recent advances, such as improvements in multiplexing and quantitative capabilities as well as instrument-free detection of nucleic acids, will potentially leverage the introduction of these novel technologies to detecting bacteria and viruses at the point of care (POC). In this review, we highlight the fundamental features of CRISPR/Cas-based molecular diagnostic technologies and summarize a vision of the next applications for identifying pathogens in POC settings.
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Affiliation(s)
- Bidhan C Dhar
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC), 205 S Columbia St., Chapel Hill, NC, 27514, USA
| | - Nathalie Steimberg
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.,Interuniversity Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health" (MISTRAL), University of Brescia/ University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Giovanna Mazzoleni
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.,Interuniversity Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health" (MISTRAL), University of Brescia/ University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
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48
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Nguyen LT, Gurijala J, Rananaware SR, Pizzano BLM, Stone BT, Jain PK. CRISPR-ENHANCE: An enhanced nucleic acid detection platform using Cas12a. Methods 2021; 203:116-124. [PMID: 33577982 DOI: 10.1016/j.ymeth.2021.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Rapid detection of nucleic acids is essential for clinical diagnosis of a wide range of infectious and non-infectious diseases. CRISPR-based diagnostic platforms are well-established for rapid and specific detection of nucleic acids but suffer from a low detection sensitivity without a target pre-amplification step. Our recently developed detection system, called CRISPR-ENHANCE, employs engineered crRNAs and optimized conditions to achieve a significantly higher sensitivity and enable femtomolar levels of nucleic acid detection even without target pre-amplification. Using the CRISPR-ENHANCE platform and following the methodology detailed in this paper, nucleic acid detection for low copy numbers can be achieved in less than an hour through either a fluorescence-based detection or a lateral flow assay. The step-by-step instructions provided, in addition to describing how to perform both assays, incorporate details on a LAMP/RT-LAMP-based target amplification step to enable detection of RNA, ssDNA and dsDNA. Furthermore, a protocol for in-house expression and purification of LbCas12a using CL7/lm7-based affinity chromatography, which has been used to achieve a high yield and purity of the enzyme in a single-step, is provided.
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Affiliation(s)
- Long T Nguyen
- Department of Chemical Engineering, University of Florida, United States
| | - Jeevan Gurijala
- Department of Chemical Engineering, University of Florida, United States
| | | | - Brianna L M Pizzano
- Department of Agricultural and Biological Engineering, University of Florida, United States
| | - Brandon T Stone
- Department of Microbiology & Cell Science, University of Florida, United States
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, United States; UF Health Cancer Center, University of Florida, United States.
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49
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Wu H, Chen X, Zhang M, Wang X, Chen Y, Qian C, Wu J, Xu J. Versatile detection with CRISPR/Cas system from applications to challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116150] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Jia F, Li X, Zhang C, Tang X. The expanded development and application of CRISPR system for sensitive nucleotide detection. Protein Cell 2021; 11:624-629. [PMID: 32246439 PMCID: PMC7124133 DOI: 10.1007/s13238-020-00708-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Fengjing Jia
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200000, China
| | - Xuewen Li
- Silicon Gene Tech Co., Ltd., Shanghai, 200124, China
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200000, China.
| | - Xueming Tang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China. .,Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
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