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Yuan A, Sha R, Xie W, Qu G, Zhang H, Wang H, Le XC, Jiang G, Peng H. RNA-Activated CRISPR/Cas12a Nanorobots Operating in Living Cells. J Am Chem Soc 2024; 146:26657-26666. [PMID: 39183441 DOI: 10.1021/jacs.4c02354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Active clustered regularly interspaced short palindromic repeats (CRISPR/Cas12a) systems possess both cis-cleavage (targeted) and trans-cleavage (collateral) activities, which are useful for genome engineering and diagnostic applications. Both single- and double-stranded DNA can activate crRNA-Cas12a ribonucleoprotein (RNP) to achieve cis- and trans-cleavage enzymatic activities. However, it is not clear whether RNA can activate the CRISPR/Cas12a system and what is critical to the trans-cleavage activity. We report here that RNA can activate the CRISPR/Cas12a system and trigger its trans-cleavage activity. We reveal that the activated crRNA-Cas12a RNP favors the trans-cleavage of longer sequences than commonly used. These new findings of the RNA-activated trans-cleavage capability of Cas12a provided the foundation for the design and construction of CRISPR nanorobots that operate in living cells. We assembled the crRNA-Cas12a RNP and nucleic acid substrates on gold nanoparticles to form CRISPR nanorobots, which dramatically increased the local effective concentration of the substrate in relation to the RNP and the trans-cleavage kinetics. Binding of the target microRNA to the crRNA-Cas12a RNP activated the nanorobots and their trans-cleavage function. The repeated (multiple-turnover) trans-cleavage of the fluorophore-labeled substrates generated amplified fluorescence signals. Sensitive and real-time imaging of specific microRNA in live cells demonstrated the promising potential of the CRISPR nanorobot system for future applications in monitoring and modulating biological functions within living cells.
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Affiliation(s)
- Aijiao Yuan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Sha
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Hongquan Zhang
- Division of Analytical & Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - X Chris Le
- Division of Analytical & Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G2G3, Canada
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Hanyong Peng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Yu L, Zhou Y, Shi XC, Wang GY, Fu ZH, Liang CG, Wang JZ. An amplification-free CRISPR-Cas12a assay for titer determination and composition analysis of the rAAV genome. Mol Ther Methods Clin Dev 2024; 32:101304. [PMID: 39193315 PMCID: PMC11347852 DOI: 10.1016/j.omtm.2024.101304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
The viral genome titer is a crucial indicator for the clinical dosing, manufacturing, and analytical testing of recombinant adeno-associated virus (rAAV) gene therapy products. Although quantitative PCR and digital PCR are the common methods used for quantifying the rAAV genome titer, they are limited by inadequate accuracy and robustness. The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a biosensor is being increasingly used in virus detection; however, there is currently no report on its application in the titer determination of gene therapy products. In the present study, an amplification-free CRISPR-Cas12a assay was developed, optimized, and applied for rAAV genome titer determination. The assay demonstrated high precision and accuracy within the detection range of 4 × 109 and 1011 vg/mL. No significant difference was observed between the Cas12a and qPCR assay results (p < 0.05, t test). Moreover, Cas12a exhibited similar activity on both single-stranded and double-stranded DNA substrates. Based on this characteristic, the titers of positive-sense and negative-sense strands were determined separately, which revealed a significant difference between their titers for an in-house reference AAV5-IN. This study presents the inaugural report of a Cas12a assay developed for the titer determination and composition analysis of the rAAV genome.
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Affiliation(s)
- Lei Yu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning 110016, P.R. China
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
| | - Yong Zhou
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
| | - Xin-chang Shi
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
| | - Guang-yu Wang
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
| | - Zhi-hao Fu
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
| | - Cheng-gang Liang
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
| | - Jun-zhi Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenyang, Liaoning 110016, P.R. China
- State Key Laboratory of Drug Regulatory Science & NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 31 Huatuo St, Daxing District, Beijing 100050, P.R. China
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Mohammad N, Talton L, Dalgan S, Hetzler Z, Steksova A, Wei Q. Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation. Commun Chem 2024; 7:130. [PMID: 38851849 PMCID: PMC11162422 DOI: 10.1038/s42004-024-01214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Most CRISPR-based biosensors rely on labeled reporter molecules and expensive equipment for signal readout. A recent approach quantifies analyte concentration by sizing λ DNA reporters via gel electrophoresis, providing a simple solution for label-free detection. Here, we report an alternative strategy for label-free CRISPR-Cas12a, which relies on Cas12a trans-nicking induced supercoil relaxation of dsDNA plasmid reporters to generate a robust and ratiometric readout. The ratiometric CRISPR (rCRISPR) measures the relative percentage of supercoiled plasmid DNA to the relaxed circular DNA by gel electrophoresis for more accurate target concentration quantification. This simple method is two orders of magnitude more sensitive than the typical fluorescent reporter. This self-referenced strategy solves the potential application limitations of previously demonstrated DNA sizing-based CRISPR-Dx without compromising the sensitivity. Finally, we demonstrated the applicability of rCRISPR for detecting various model DNA targets such as HPV 16 and real AAV samples, highlighting its feasibility for point-of-care CRISPR-Dx applications.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Logan Talton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Selen Dalgan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Anastasiia Steksova
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
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Kim HJ, Cho IS, Choi SR, Jeong RD. Identification of an Isolate of Citrus Tristeza Virus by Nanopore Sequencing in Korea and Development of a CRISPR/Cas12a-Based Assay for Rapid Visual Detection of the Virus. PHYTOPATHOLOGY 2024; 114:1421-1428. [PMID: 38079355 DOI: 10.1094/phyto-10-23-0354-r] [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: 06/06/2024]
Abstract
Citrus tristeza virus (CTV) is a highly destructive viral pathogen posing a significant threat to citrus crops worldwide. Disease management and crop protection strategies necessitate the development of rapid and accurate detection methods. In this study, we employed Oxford Nanopore sequencing to detect CTV in Citrus unshiu samples. Subsequently, we developed a specific and sensitive detection assay combining CRISPR/Cas12a with reverse transcription-recombinase polymerase amplification. The CRISPR-Cas12a assay exhibited exceptional specificity for CTV, surpassing conventional RT-PCR by at least 10-fold in sensitivity. Remarkably, the developed assay detected CTV in field samples, with zero false negatives. This diagnostic approach is user-friendly, cost-effective, and offers tremendous potential for rapid onsite detection of CTV. Therefore, the CRISPR-Cas12a assay plays a significant role in managing and preserving citrus trees that are free from viruses in the industry.
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Affiliation(s)
- Hae-Jun Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Se-Ryung Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Republic of Korea
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5
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Blanluet C, Kuo CJ, Bhattacharya A, Santiago JG. Design and Evaluation of a Robust CRISPR Kinetic Assay for Hot-Spot Genotyping. Anal Chem 2024; 96:7444-7451. [PMID: 38684052 DOI: 10.1021/acs.analchem.3c05657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Next-generation sequencing offers highly multiplexed and accurate detection of nucleic acid sequences but at the expense of complex workflows and high input requirements. The ease of use of CRISPR-Cas12 assays is attractive and may enable highly accurate detection of sequences implicated in, for example, cancer pathogenic variants. CRISPR assays often employ end-point measurements of Cas12 trans-cleavage activity after Cas12 activation by the target; however, end point-based methods can be limited in accuracy and robustness by arbitrary experimental choices. To overcome such limitations, we develop and demonstrate here an accurate assay targeting a mutation of the epidermal growth factor gene implicated in lung cancer (exon 19 deletion). The assay is based on characterizing the kinetics of Cas12 trans-cleavage to discriminate the mutant from wild-type targets. We performed extensive experiments (780 reactions) to calibrate key assay design parameters, including the guide RNA sequence, reporter sequence, reporter concentration, enzyme concentration, and DNA target type. Interestingly, we observed a competitive reaction between the target and reporter molecules that has important consequences for the design of CRISPR assays, which use preamplification to improve sensitivity. Finally, we demonstrate the assay on 18 tumor-extracted amplicons and 100 training iterations with 99% accuracy and discuss discrimination parameters and models to improve wild type versus mutant classification.
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Affiliation(s)
- Charles Blanluet
- CentraleSupelec─Universite Paris-Saclay, 91190 Gif-sur-Yvette, France
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Asmita Bhattacharya
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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6
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Lei X, Cao S, Liu T, Wu Y, Yu S. Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection. Talanta 2024; 271:125663. [PMID: 38232570 DOI: 10.1016/j.talanta.2024.125663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.
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Affiliation(s)
- Xueying Lei
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Shengnan Cao
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Tao Liu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Yongjun Wu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Songcheng Yu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China.
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7
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Sun M, Fang X, Lin B, Mo J, Wang F, Zhou X, Weng X. Locus-specific detection of pseudouridine with CRISPR-Cas13a. Chem Commun (Camb) 2024; 60:4088-4091. [PMID: 38511312 DOI: 10.1039/d4cc00179f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
We combined the CRISPR-Cas13a system with CMC chemical labeling, developing an approach that enables precise identification of pseudouridine (Ψ) sites at specific loci within ribosomal RNA (rRNA), messenger RNA (mRNA) and small nuclear RNAs (snRNA). This method, with good efficiency and simplicity, detects Ψ sites through fluorescence measurement, providing a straightforward and fast validation for targeted Ψ sites of interest.
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Affiliation(s)
- Mei Sun
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Xin Fang
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Bingqian Lin
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
- Wuhan TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
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8
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Lan H, Shu W, Jiang D, Yu L, Xu G. Cas-based bacterial detection: recent advances and perspectives. Analyst 2024; 149:1398-1415. [PMID: 38357966 DOI: 10.1039/d3an02120c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Persistent bacterial infections pose a formidable threat to global health, contributing to widespread challenges in areas such as food safety, medical hygiene, and animal husbandry. Addressing this peril demands the urgent implementation of swift and highly sensitive detection methodologies suitable for point-of-care testing and large-scale screening. These methodologies play a pivotal role in the identification of pathogenic bacteria, discerning drug-resistant strains, and managing and treating diseases. Fortunately, new technology, the CRISPR/Cas system, has emerged. The clustered regularly interspaced short joint repeats (CRISPR) system, which is part of bacterial adaptive immunity, has already played a huge role in the field of gene editing. It has been employed as a diagnostic tool for virus detection, featuring high sensitivity, specificity, and single-nucleotide resolution. When applied to bacterial detection, it also surpasses expectations. In this review, we summarise recent advances in the detection of bacteria such as Mycobacterium tuberculosis (MTB), methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli (E. coli), Salmonella and Acinetobacter baumannii (A. baumannii) using the CRISPR/Cas system. We emphasize the significance and benefits of this methodology, showcasing the capability of diverse effector proteins to swiftly and precisely recognize bacterial pathogens. Furthermore, the CRISPR/Cas system exhibits promise in the identification of antibiotic-resistant strains. Nevertheless, this technology is not without challenges that need to be resolved. For example, CRISPR/Cas systems must overcome natural off-target effects and require high-quality nucleic acid samples to improve sensitivity and specificity. In addition, limited applicability due to the protospacer adjacent motif (PAM) needs to be addressed to increase its versatility. Despite the challenges, we are optimistic about the future of bacterial detection using CRISPR/Cas. We have already highlighted its potential in medical microbiology. As research progresses, this technology will revolutionize the detection of bacterial infections.
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Affiliation(s)
- Huatao Lan
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Weitong Shu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Dan Jiang
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Guangxian Xu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
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Lee HJ, Kim HJ, Cho IS, Jeong RD. Identification of Viruses Infecting Phalaenopsis Orchids Using Nanopore Sequencing and Development of an RT-RPA-CRISPR/Cas12a for Rapid Visual Detection of Nerine Latent Virus. Int J Mol Sci 2024; 25:2666. [PMID: 38473916 DOI: 10.3390/ijms25052666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Phalaenopsis orchids are one of the most popular ornamental plants. More than thirty orchid viruses have been reported, and virus-infected Phalaenopsis orchids significantly lose their commercial value. Therefore, the development of improved viral disease detection methods could be useful for quality control in orchid cultivation. In this study, we first utilized the MinION, a portable sequencing device based on Oxford Nanopore Technologies (ONT) to rapidly detect plant viruses in Phalaenopsis orchids. Nanopore sequencing revealed the presence of three plant viruses in Phalaenopsis orchids: odontoglossum ringspot virus, cymbidium mosaic virus, and nerine latent virus (NeLV). Furthermore, for the first time, we detected NeLV infection in Phalaenopsis orchids using nanopore sequencing and developed the reverse transcription-recombinase polymerase amplification (RT-RPA)-CRISPR/Cas12a method for rapid, instrument-flexible, and accurate diagnosis. The developed RT-RPA-CRISPR/Cas12a technique can confirm NeLV infection in less than 20 min and exhibits no cross-reactivity with other viruses. To determine the sensitivity of RT-RPA-CRISPR/Cas12a for NeLV, we compared it with RT-PCR using serially diluted transcripts and found a detection limit of 10 zg/μL, which is approximately 1000-fold more sensitive. Taken together, the ONT platform offers an efficient strategy for monitoring plant viral pathogens, and the RT-RPA-CRISPR/Cas12a method has great potential as a useful tool for the rapid and sensitive diagnosis of NeLV.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
| | - Hae-Jun Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
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Jang H, Song J, Kim S, Byun JH, Lee KG, Park KH, Woo E, Lim EK, Jung J, Kang T. ANCA: artificial nucleic acid circuit with argonaute protein for one-step isothermal detection of antibiotic-resistant bacteria. Nat Commun 2023; 14:8033. [PMID: 38052830 DOI: 10.1038/s41467-023-43899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Endonucleases have recently widely used in molecular diagnostics. Here, we report a strategy to exploit the properties of Argonaute (Ago) proteins for molecular diagnostics by introducing an artificial nucleic acid circuit with Ago protein (ANCA) method. The ANCA is designed to perform a continuous autocatalytic reaction through cross-catalytic cleavage of the Ago protein, enabling one-step, amplification-free, and isothermal DNA detection. Using the ANCA method, carbapenemase-producing Klebsiella pneumoniae (CPKP) are successfully detected without DNA extraction and amplification steps. In addition, we demonstrate the detection of carbapenem-resistant bacteria in human urine and blood samples using the method. We also demonstrate the direct identification of CPKP swabbed from surfaces using the ANCA method in conjunction with a three-dimensional nanopillar structure. Finally, the ANCA method is applied to detect CPKP in rectal swab specimens from infected patients, achieving sensitivity and specificity of 100% and 100%, respectively. The developed method can contribute to simple, rapid and accurate diagnosis of CPKP, which can help prevent nosocomial infections.
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Affiliation(s)
- Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 175 Cambridge Street, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA, 02114, USA
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kwang-Hyun Park
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Euijeon Woo
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea.
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Mohammad N, Talton L, Hetzler Z, Gongireddy M, Wei Q. Unidirectional trans-cleaving behavior of CRISPR-Cas12a unlocks for an ultrasensitive assay using hybrid DNA reporters containing a 3' toehold. Nucleic Acids Res 2023; 51:9894-9904. [PMID: 37650631 PMCID: PMC10570054 DOI: 10.1093/nar/gkad715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/04/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
CRISPR-Cas12a can induce nonspecific trans-cleavage of dsDNA substrate, including long and stable λ DNA. However, the mechanism behind this is still largely undetermined. In this study, we observed that while trans-activated Cas12a didn't cleave blunt-end dsDNA within a short reaction time, it could degrade dsDNA reporters with a short overhang. More interestingly, we discovered that the location of the overhang also affected the susceptibility of dsDNA substrate to trans-activated Cas12a. Cas12a trans-cleaved 3' overhang dsDNA substrates at least 3 times faster than 5' overhang substrates. We attributed this unique preference of overhang location to the directional trans-cleavage behavior of Cas12a, which may be governed by RuvC and Nuc domains. Utilizing this new finding, we designed a new hybrid DNA reporter as nonoptical substrate for the CRISPR-Cas12a detection platform, which sensitively detected ssDNA targets at sub picomolar level. This study not only unfolded new insight into the trans-cleavage behavior of Cas12a but also demonstrated a sensitive CRISPR-Cas12a assay by using a hybrid dsDNA reporter molecule.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Logan Talton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Megha Gongireddy
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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12
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Hu J, Liang L, He M, Lu Y. Sensitive and Direct Analysis of Pseudomonas aeruginosa through Self-Primer-Assisted Chain Extension and CRISPR-Cas12a-Based Color Reaction. ACS OMEGA 2023; 8:34852-34858. [PMID: 37779973 PMCID: PMC10536833 DOI: 10.1021/acsomega.3c04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a common opportunistic Gram-negative pathogen that may cause infections to immunocompromised patients. However, sensitive and reliable analysis of P. aeruginosa remains a huge challenge. In this method, target recognition assists the formation of a self-primer and initiates single-stranded chain production. The produced single-stranded DNA chain is identified by CRISPR-Cas12a, and consequently, the trans-cleavage activity of the Cas12a enzyme is activated to parallelly digest Ag+ aptamer sequences that are chelated with silver ions (Ag+). The released Ag+ reacted with 3,3',5,5'-tetramethylbenzidine (TMB) for coloring. Compared with the traditional color developing strategies, which mainly rely on the DNA hybridization, the color developing strategy in this approach exhibits a higher efficiency due to the robust trans-cleavage activity of the Cas12a enzyme. Consequently, the method shows a low limit of detection of a wide detection of 5 orders of magnitudes and a low limit of detection of 21 cfu/mL, holding a promising prospect in early diagnosis of infections. Herein, we develop a sensitive and reliable method for direct and colorimetric detection of P. aeruginosa by integrating self-primer-assisted chain production and CRISPR-Cas12a-based color reaction and believe that the established approach will facilitate the development of bacteria-analyzing sensors.
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Affiliation(s)
- Jiangchun Hu
- Science
and Technology Innovation Center, Guangyuan
Central Hospital, Guangyuan
City 628000, Sichuan
Province, China
| | - Ling Liang
- Science
and Technology Innovation Center, Guangyuan
Central Hospital, Guangyuan
City 628000, Sichuan
Province, China
| | - Mingfang He
- Science
and Technology Innovation Center, Guangyuan
Central Hospital, Guangyuan
City 628000, Sichuan
Province, China
| | - Yongping Lu
- Science
and Technology Innovation Center, Guangyuan
Central Hospital, Guangyuan
City 628000, Sichuan
Province, China
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13
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Paenkaew S, Jaito N, Pradit W, Chomdej S, Nganvongpanit K, Siengdee P, Buddhachat K. RPA/CRISPR-cas12a as a specific, sensitive and rapid method for diagnosing Ehrlichia canis and Anaplasma platys in dogs in Thailand. Vet Res Commun 2023; 47:1601-1613. [PMID: 36997812 PMCID: PMC10062689 DOI: 10.1007/s11259-023-10114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
Rickettsial pathogens including Ehrlichia canis and Anaplasma platys are bacteria that cause parasitic infections in dogs such as canine monocytic ehrlichiosis (CME) and canine cyclic thrombocytopenia (CCT), respectively affecting mortality and morbidity worldwide. An accurate, sensitive, and rapid method to diagnose these agents is essential for effective treatment. In this study, a recombinase polymerase amplification (RPA) coupled with CRISPR-Cas12a methods was established to detect E. canis and A. platys infection in dogs based on the 16S rRNA. The optimal condition for DNA amplification by RPA was 37 °C for 20 min, followed by CRISPR-Cas12a digestion at 37 °C for one hour. A combination of RPA and the cas12a detection method did not react with other pathogens and demonstrated strong sensitivity, detecting as low as 100 copies of both E. canis and A. platys. This simultaneous detection method was significantly more sensitive than conventional PCR. The RPA-assisted cas12a assay provides specific, sensitive, rapid, simple and appropriate detection of rickettsial agents in canine blood at the point-of-care for diagnostics, disease prevention and surveillance.
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Affiliation(s)
- Suphaporn Paenkaew
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Nongluck Jaito
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Rd., Klong Luang District, Pathum Thani, 12120, Thailand
| | - Waranee Pradit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Korakot Nganvongpanit
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Puntita Siengdee
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, 10210, Bangkok, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand.
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