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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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