1
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Juma KM, Murakami Y, Morimoto K, Takita T, Kojima K, Suzuki K, Yanagihara I, Ikuta S, Fujiwara S, Yasukawa K. Achieving unprecedented stability in lyophilized recombinase polymerase amplification with thermostable pyruvate kinase from Thermotoga maritima. J Biosci Bioeng 2024; 138:29-35. [PMID: 38719683 DOI: 10.1016/j.jbiosc.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 06/11/2024]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. Considering the onsite use of RPA reagents, lyophilized RPA reagents with long storage stability are highly desired. In this study, as one of the approaches to solve this problem, we attempted to use a thermostable pyruvate kinase (PK). PK gene was isolated from a thermophilic bacterium Thermotoga maritima (Tma-PK). Tma-PK was expressed in Escherichia coli and purified from the cells. Tma-PK exhibited higher thermostability than human PK. The purified Tma-PK preparation was applied to RPA as an ATP-regenerating enzyme. Liquid RPA reagent with Tma-PK exhibited the same performance as that with human PK. Lyophilized RPA reagent with Tma-PK exhibited higher performance than that with human PK. Combined with our previous results of RPA reagents of thermostable Pol from a thermophilic bacterium, Aeribacillus pallidus, the results in this study suggest that thermostable enzymes are preferable to mesophilic ones as a component in lyophilized RPA reagents.
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuto Murakami
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka 565-0871, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka 594-1101, Japan
| | - Soichiro Ikuta
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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2
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Patnaik A, Rai SK, Dhaked RK. CRISPR-Cas12a assisted recombinase based strand invading isothermal amplification platform designed for targeted detection of Bacillus anthracis Sterne. Int J Biol Macromol 2024; 263:130216. [PMID: 38378112 DOI: 10.1016/j.ijbiomac.2024.130216] [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: 12/29/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Detection of a pathogen is crucial prior to all prophylaxis and post exposure treatment, as it can prevent further disease manifestation. In this study, we have developed a nucleic acid pre-amplification based CRISPR diagnostic for detection and surveillance of Bacillus anthracis Sterne. Strand Invasion Based isothermal Amplification (SIBA) platform and Cas12a (CRISPR endo-nuclease) was used to develop CRISPR-SIBA, a multifaceted diagnostic platform. SIBA was employed as the isothermal pre-amplification platform. CRISPR-Cas12a based collateral trans-cleavage reaction was used to ensure and enhance the specificity of the system. Efficiency of the detection system was evaluated by detecting Bacillus anthracis Sterne in complex wastewater sample backgrounds. Previously reported, Prophage 3, Cya and Pag genes of Bacillus anthracis were used as targets for this assay. The amplification system provided reliable and specific detection readout, with a sensitivity limit of 100 colony forming units in 40 min. The endpoint fluorescence from CRISPR collateral cleavage reactions gave a detection limit of 105 to 106 CFUs. The experiments conducted in this study provide the evidence for SIBA's applicability and compatibility with CRISPR-Cas system and its efficiency to specifically detect Bacillus anthracis Sterne. CRISPR-SIBA can be translated into developing cost-effective diagnostics for pathogens in resource constrained settings.
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Affiliation(s)
- Abhinandan Patnaik
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Sharad Kumar Rai
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India
| | - Ram Kumar Dhaked
- Biotechnology Division, Defence Research & Development Establishment, Jhansi Road, Gwalior 474002, MP, India.
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3
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Morimoto K, Juma KM, Yamagata M, Takita T, Kojima K, Suzuki K, Yanagihara I, Fujiwara S, Yasukawa K. Increase in the solubility of uvsY using a site saturation mutagenesis library for application in a lyophilized reagent for recombinase polymerase amplification. Mol Biol Rep 2024; 51:367. [PMID: 38411701 PMCID: PMC10899321 DOI: 10.1007/s11033-024-09367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Recombinase uvsY from bacteriophage T4, along with uvsX, is a key enzyme for recombinase polymerase amplification (RPA), which is used to amplify a target DNA sequence at a constant temperature. uvsY, though essential, poses solubility challenges, complicating the lyophilization of RPA reagents. This study aimed to enhance uvsY solubility. METHODS Our hypothesis centered on the C-terminal region of uvsY influencing solubility. To test this, we generated a site-saturation mutagenesis library for amino acid residues Lys91-Glu134 of the N-terminal (His)6-tagged uvsY. RESULTS Screening 480 clones identified A116H as the variant with superior solubility. Lyophilized RPA reagents featuring the uvsY variant A116H demonstrated enhanced performance compared to those with wild-type uvsY. CONCLUSIONS The uvsY variant A116H emerges as an appealing choice for RPA applications, offering improved solubility and heightened lyophilization feasibility.
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Affiliation(s)
- Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Masaya Yamagata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Kojima
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, 670-8524, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, 565-0871, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-Shi, Osaka, 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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4
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Kojima K, Morimoto K, Juma KM, Takita T, Saito K, Yanagihara I, Fujiwara S, Yasukawa K. Application of recombinant human pyruvate kinase in recombinase polymerase amplification. J Biosci Bioeng 2023; 136:341-346. [PMID: 37718149 DOI: 10.1016/j.jbiosc.2023.08.005] [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: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41°C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. In this study, we attempted to use pyruvate kinase instead of creatine kinase (CK) that has been consistently used as an ATP-regenerating enzyme in RPA. Human pyruvate kinase M1 (PKM) was expressed in Escherichia coli and purified from the cells. RPA with PKM was performed at 41°C with the in vitro synthesized urease subunit β (ureB) DNA from Ureaplasma parvum serovar 3 as a standard DNA. The optimal concentrations of PKM and phosphoenolpyruvate were 20 ng/μL and 10 mM, respectively. The RPA reaction with PKM was more sensitive than that with CK. PKM exhibited higher thermostability than CK, suggesting that the RPA reagents with PKM are preferable to those with CK for onsite use.
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Affiliation(s)
- Kenji Kojima
- Division of Bioanalytical Chemistry, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Saito
- Division of Bioanalytical Chemistry, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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5
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Juma KM, Inoue E, Asada K, Fukuda W, Morimoto K, Yamagata M, Takita T, Kojima K, Suzuki K, Nakura Y, Yanagihara I, Fujiwara S, Yasukawa K. Recombinase polymerase amplification using novel thermostable strand-displacing DNA polymerases from Aeribacillus pallidus and Geobacillus zalihae. J Biosci Bioeng 2023; 135:282-290. [PMID: 36806411 DOI: 10.1016/j.jbiosc.2023.01.009] [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: 10/20/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/19/2023]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), and strand-displacing DNA polymerase (Pol). Component instability and the need to store commercial kits in a deep freezer until use are some limitations of RPA. In a previous study, Bacillus stearothermophilus Pol (Bst-Pol) was used as a thermostable strand-displacing DNA polymerase in RPA. Here, we attempted to optimize the lyophilization conditions for RPA with newly isolated thermostable DNA polymerases for storage at room temperature. We isolated novel two thermostable strand-displacing DNA polymerases, one from a thermophilic bacterium Aeribacillus pallidus (H1) and the other from Geobacillus zalihae (C1), and evaluated their performances in RPA reaction. Urease subunit β (UreB) DNA from Ureaplasma parvum serovar 3 was used as a model target for evaluation. The RPA reaction with H1-Pol or C1-Pol was performed at 41 °C with the in vitro synthesized standard UreB DNA. The minimal initial copy numbers of standard DNA from which the amplified products were observed were 600, 600, and 6000 copies for RPA with H1-Pol, C1-Pol, and Bst-Pol, respectively. Optimization was carried out using RPA components, showing that the lyophilized RPA reagents containing H1-Pol exhibited the same performance as the corresponding liquid RPA reagents. In addition, lyophilized RPA reagents with H1-Pol showed almost the same activity after two weeks of storage at room temperature as the freshly prepared liquid RPA reagents. These results suggest that lyophilized RPA reagents with H1-Pol are preferable to liquid RPA reagents for onsite use.
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Eisuke Inoue
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kengo Asada
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masaya Yamagata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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6
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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7
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Cao G, Qiu Y, Long K, Ma Y, Luo H, Yang M, Hou J, Huo D, Hou C. Rapid and Ultrasensitive Approach for the Simultaneous Detection of Multilocus Mutations to Distinguish Rifampicin-Resistant Mycobacterium tuberculosis. Anal Chem 2022; 94:17653-17661. [PMID: 36473113 DOI: 10.1021/acs.analchem.2c04399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The untested empirical medications exacerbated the development of multidrug-resistant Mycobacterium tuberculosis (MDR-TB). Here, we develop a rapid and specific method based on loop-mediated isothermal amplification and duplex-specific nuclease for distinguishing rifampicin-resistant M. tuberculosis. Three probes were designed for the codons 516, 526, and 531 on the RNA polymerase β-subunit (rpoB) gene. These three sites accounted for more than 90% of the total mutations of the ropB gene in the rifampicin-resistant strain. The approach can perform simultaneous and sensitive detection of three mutant sites with the actual detection limit as 10 aM of DNA and 62.5 cfu·mL-1 of bacteria in 67 min under isothermal conditions. Moreover, the positive mode of the approach for MDR-TB can not only deal with the randomness and diversity of mutations but also provide an easier way for medical staff to read the results. Therefore, it is a particularly valuable method to handle major and urgent MDR-TB diagnostics.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Yue Qiu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Keyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Yi Ma
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| | - Huibo Luo
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Jingzhou Hou
- Postdoctoral Research Station, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China.,Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China.,Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
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8
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Mao Z, Chen R, Wang X, Zhou Z, Peng Y, Li S, Han D, Li S, Wang Y, Han T, Liang J, Ren S, Gao Z. CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety. Trends Food Sci Technol 2022; 122:211-222. [PMID: 35250172 PMCID: PMC8885088 DOI: 10.1016/j.tifs.2022.02.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND In the context of the current pandemic caused by the novel coronavirus, molecular detection is not limited to the clinical laboratory, but also faces the challenge of the complex and variable real-time detection fields. A series of novel coronavirus events were detected in the process of food cold chain packaging and transportation, making the application of molecular diagnosis in food processing, packaging, transportation, and other links urgent. There is an urgent need for a rapid detection technology that can adapt to the diversity and complexity of food safety. SCOPE AND APPROACH This review introduces a new molecular diagnostic technology-biosensor analysis technology based on CRISPR-Cas12a. Systematic clarification of its development process and detection principles. It summarizes and systematically organizes its applications in viruses, food-borne pathogenic bacteria, small molecule detection, etc. In the past four years, which provides a brand-new and comprehensive solution for food detection. Finally, this article puts forward the challenges and the prospects for food safety. KEY FINDINGS AND CONCLUSIONS The novel coronavirus hazards infiltrated every step of the food industry, from processing to packaging to transportation. The biosensor analytical technology based on CRISPR-Cas12a has great potential in the qualitative and quantitative analysis of infectious pathogens. CRISPR-Cas12a can effectively identify the presence of the specific nucleic acid targets and the small changes in sequences, which is particularly important for nucleic acid identification and pathogen detection. In addition, the CRISPR-Cas12a method can be adjusted and reconfigured within days to detect other viruses, providing equipment for nucleic acid diagnostics in the field of food safety. The future work will focus on the development of portable microfluidic devices for multiple detection. Shao et al. employed physical separation methods to separate Cas proteins in different microfluidic channels to achieve multiple detection, and each channel simultaneously detected different targets by adding crRNA with different spacer sequences. Although CRISPR-Cas12a technology has outstanding advantages in detection, there are several technical barriers in the transformation from emerging technologies to practical applications. The newly developed CRISPR-Cas12a-based applications and methods promote the development of numerous diagnostic and detection solutions, and have great potential in medical diagnosis, environmental monitoring, and especially food detection.
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Affiliation(s)
- Zefeng Mao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaojuan Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zixuan Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Sen Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Jun Liang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China,Corresponding author
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,Corresponding author
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,Corresponding author
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9
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Kubo S, Niimi H, Kitajima I. Rapid and direct detection of male DNA by recombinase polymerase amplification assay. Forensic Sci Int Genet 2022; 59:102704. [DOI: 10.1016/j.fsigen.2022.102704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/04/2022]
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10
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Juma KM, Takita T, Yamagata M, Ishitani M, Hayashi K, Kojima K, Suzuki K, Ando Y, Fukuda W, Fujiwara S, Nakura Y, Yanagihara I, Yasukawa K. Modified uvsY by N-terminal hexahistidine tag addition enhances efficiency of recombinase polymerase amplification to detect SARS-CoV-2 DNA. Mol Biol Rep 2022; 49:2847-2856. [PMID: 35098395 PMCID: PMC8801280 DOI: 10.1007/s11033-021-07098-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/16/2021] [Indexed: 11/28/2022]
Abstract
Background Methods Results Conclusions Supplementary Information
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Masaya Yamagata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Mika Ishitani
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kaichi Hayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, 670-8524, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuri Ando
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669‑1337, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669‑1337, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669‑1337, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka, 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka, 594-1101, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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11
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Biyani R, Sharma K, Kojima K, Biyani M, Sharma V, Kumawat T, Juma KM, Yanagihara I, Fujiwara S, Kodama E, Takamura Y, Takagi M, Yasukawa K, Biyani M. Development of robust isothermal RNA amplification assay for lab-free testing of RNA viruses. Sci Rep 2021; 11:15997. [PMID: 34362977 PMCID: PMC8346491 DOI: 10.1038/s41598-021-95411-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Simple tests of infectiousness that return results in minutes and directly from samples even with low viral loads could be a potential game-changer in the fight against COVID-19. Here, we describe an improved isothermal nucleic acid amplification assay, termed the RICCA (RNA Isothermal Co-assisted and Coupled Amplification) reaction, that consists of a simple one-pot format of ‘sample-in and result-out’ with a primary focus on the detection of low copy numbers of RNA virus directly from saliva without the need for laboratory processing. We demonstrate our assay by detecting 16S rRNA directly from E. coli cells with a sensitivity as low as 8 CFU/μL and RNA fragments from a synthetic template of SARS-CoV-2 with a sensitivity as low as 1740 copies/μL. We further demonstrate the applicability of our assay for real-time testing at the point of care by designing a closed format for paper-based lateral flow assay and detecting heat-inactivated SARS-COV-2 virus in human saliva at concentrations ranging from 28,000 to 2.8 copies/μL with a total assay time of 15–30 min.
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Affiliation(s)
- Radhika Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kirti Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Madhu Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan.,Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Vishnu Sharma
- Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Tarun Kumawat
- Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodocho, Izumi, Osaka, 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Eiichi Kodama
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryocho Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Masahiro Takagi
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan. .,BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan. .,Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India.
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12
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Optimization of reaction condition of recombinase polymerase amplification to detect SARS-CoV-2 DNA and RNA using a statistical method. Biochem Biophys Res Commun 2021; 567:195-200. [PMID: 34166918 PMCID: PMC8189764 DOI: 10.1016/j.bbrc.2021.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/31/2022]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal reaction that amplifies a target DNA sequence with a recombinase, a single-stranded DNA-binding protein (SSB), and a strand-displacing DNA polymerase. In this study, we optimized the reaction conditions of RPA to detect SARS-CoV-2 DNA and RNA using a statistical method to enhance the sensitivity. In vitro synthesized SARS-CoV-2 DNA and RNA were used as targets. After evaluating the concentration of each component, the uvsY, gp32, and ATP concentrations appeared to be rate-determining factors. In particular, the balance between the binding and dissociation of uvsX and DNA primer was precisely adjusted. Under the optimized condition, 60 copies of the target DNA were specifically detected. Detection of 60 copies of RNA was also achieved. Our results prove the fabrication flexibility of RPA reagents, leading to an expansion of the use of RPA in various fields.
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