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Paenkaew S, Poommouang A, Pradit W, Chomdej S, Nganvongpanit K, Siengdee P, Buddhachat K. Feasibility of implementing RPA coupled with CRISPR-Cas12a (RPA-Cas12a) for Hepatozoon canis detection in dogs. Vet Parasitol 2024; 331:110298. [PMID: 39217761 DOI: 10.1016/j.vetpar.2024.110298] [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: 05/22/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Hepatozoonosis, caused by the protozoan Hepatozoon canis, is a prevalent blood disease affecting owned and stray dogs and cats. The prevalence of these parasites among companion animals in Thailand remains poorly understood. Diagnosing the old-world form of the disease is challenging due to the wide range of nonspecific clinical signs and the reliance on finding low levels of Hepatozoon gamonts in blood smears for conventional diagnosis. PCR demonstrates high specificity and sensitivity but it requires sophisticated instrumentation. Therefore, we established recombinase polymerase amplification (RPA) coupled with Cas12a for H. canis detection based on 18S rRNA. Our findings showed that RPA-Cas12a using gRNA_H was highly specific to H. canis, without yielding positives for other pathogen species including Babesia species. Even in cases of co-infection, RPA-Cas12a only detected positives in samples containing H. canis. This approach detected minimal amounts of H. canis18S rRNA-harboring plasmid at 10 copies per reaction, whereas plasmid-spiked canine blood enabled detection at a minimal amount of 100 copies per reaction. The performance of RPA-Cas12a was validated by comparing it with quantitative PCR-high resolution melting analysis (qPCR-HRM) and sequencing based on 35 canine blood samples. RPA-Cas12a demonstrated precision and accuracy values of 94 % and 90 %, respectively comparable to qPCR-HRM. Overall, these results indicate that RPA-Cas12a serves as a promising tool for H. canis detection as indicated by comparable performance to qPCR-HRM and is suitable for implementation in small animal hospitals or clinics due to its minimal resource requirements, thereby contributing to effective diagnosis and treatment for infected dogs.
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Affiliation(s)
- Suphaporn Paenkaew
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Anocha Poommouang
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, 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
- 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: Environmental Health, Chulabhorn Graduate Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Innovation and Technology for Detection and Advanced Materials (ITDAM), Naresuan University, Phitsanulok 65000, Thailand.
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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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Yang J, Zhao Y, Qian L, Yu Y, Zhang Y, Zhang J. Modularization of dual recognized CRISPR/Cas12a system for the detection of Staphylococcus aureus assisted by hydrazone chemistry. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134877. [PMID: 38901249 DOI: 10.1016/j.jhazmat.2024.134877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024]
Abstract
In this work, a dual recognized CRISPR/Cas12a system has been proposed, in which the activation chain is cleverly divided into two parts that can serve for precise dual target recognition, and hydrazone chemistry is introduced for the formation of a whole activation chain. It has been further explored to construct a new method for the specific and sensitive detection of Staphylococcus aureus (SA) as one of the most common pathogens in infectious diseases. In virtue of proximity effect contributed by complementary base pairing, hydrazone chemistry accelerates the formation of the whole activation strand and improves the specificity of the CRISPR/Cas12a system, serving for the accurate analysis of SA. Moreover, the temporary aggregation of CRISPR/Cas12a around SA enhances its catalytical efficiency so as to further amplify signal. With high sensitivity, stability, reproducibility and specificity, the established method has been successfully applied to detect SA in complex substrates. Meanwhile, our established method can well evaluate the inhibition effect of chlorogenic acid and congo red in comparison with flow cytometry. ENVIRONMENTAL IMPLICATION: Bacterial pathogens exist widely in the environment and seriously threaten the safety of human health. Staphylococcus aureus (SA) is the most common pathogen of human suppurative infection, which can cause local suppurative infection, pneumonia, and even systemic infections such as sepsis. In this work, a dual recognized CRISPR/Cas12a system mediated by hydrazone chemistry has been proposed. With high sensitivity and low detection limit, the established method can specifically detect SA and effectively evaluate the antibacterial effect of inhibitors. This method is expected to be further developed into a detection method in different scenarios such as environmental monitoring and clinical diagnosis.
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Affiliation(s)
- Jingyi Yang
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yining Zhao
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Lelin Qian
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Ying Yu
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China; Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yuan Zhang
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China.
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Wu Q, Xie L, Ma L, Long X, Liu L, Chen A, Cui Y, Zhang Y, He Y. A CRISPR/Cas12a-based fluorescence method for the amplified detection of total antioxidant capacity. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5564-5570. [PMID: 39072477 DOI: 10.1039/d4ay01150c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The CRISPR/Cas12a system is a powerful signal amplification tool that has been widely used in nucleic acid detection. It has also been applied to the assay of non-nucleic acid targets, mainly relying on strategies for converting target determination into nucleic acid detection. Herein, we describe a CRISPR/Cas12a-based fluorescence method for sensitive detection of the total antioxidant capacity (TAC) by utilizing a strategy of converting TAC determination into Mn2+ detection. Specifically, the reduction of MnO2 nanosheets by antioxidants produces plenty of Mn2+, which accelerates the trans-cleavage activity of CRISPR/Cas12a. Thus, a fluorescence enhanced detection method for TAC was established, with a detection limit as low as 0.04 mg L-1 for a typical antioxidant, ascorbic acid. More importantly, this method has been proven to successfully analyze TAC in beverages. The excellent analytical performance of this method demonstrates the great potential of the CRISPR/Cas12a system in simple and sensitive TAC analysis.
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Affiliation(s)
- Qi Wu
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Longyingzi Xie
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Lanrui Ma
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Xinqi Long
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Lei Liu
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Aihua Chen
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Yongliang Cui
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Yaohai Zhang
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
| | - Yue He
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, P. R. China.
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, P. R. China
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Zhang Y, Liu H, Nakagawa Y, Nagasaka Y, Ding T, Tang SY, Yalikun Y, Goda K, Li M. Enhanced CRISPR/Cas12a-based quantitative detection of nucleic acids using double emulsion droplets. Biosens Bioelectron 2024; 257:116339. [PMID: 38688231 DOI: 10.1016/j.bios.2024.116339] [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: 03/04/2024] [Revised: 04/05/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Pairing droplet microfluidics and CRISPR/Cas12a techniques creates a powerful solution for the detection and quantification of nucleic acids at the single-molecule level, due to its specificity, sensitivity, and simplicity. However, traditional water-in-oil (W/O) single emulsion (SE) droplets often present stability issues, affecting the accuracy and reproducibility of assay results. As an alternative, water-in-oil-in-water (W/O/W) double emulsion (DE) droplets offer superior stability and uniformity for droplet digital assays. Moreover, unlike SE droplets, DE droplets are compatible with commercially available flow cytometry instruments for high-throughput analysis. Despite these advantages, no study has demonstrated the use of DE droplets for CRISPR-based nucleic acid detection. In our study, we conducted a comparative analysis to assess the performance of SE and DE droplets in quantitative detection of human papillomavirus type 18 (HPV18) DNA based on CRISPR/Cas12a. We evaluated the stability of SEs and DEs by examining size variation, merging extent, and content interaction before and after incubation at different temperatures and time points. By integrating DE droplets with flow cytometry, we achieved high-throughput and high-accuracy CRISPR/Cas12a-based quantification of target HPV18 DNA. The DE platform, when paired with CRISPR/Cas12a and flow cytometry techniques, emerges as a reliable tool for absolute quantification of nucleic acid biomarkers.
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Affiliation(s)
- Yang Zhang
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Hangrui Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yuta Nakagawa
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuzuki Nagasaka
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tianben Ding
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shi-Yang Tang
- School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan; Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA; Institute of Technological Sciences, Wuhan University, Hubei, 430072, China
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
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Liu X, Yuan W, Xiao H. Recent progress on DNAzyme-based biosensors for pathogen detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4917-4937. [PMID: 38984495 DOI: 10.1039/d4ay00934g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Pathogens endanger food safety, agricultural productivity, and human health. Those pathogens are spread through direct/indirect contact, airborne transmission and food/waterborne transmission, and some cause severe health consequences. As the population grows and global connections intensify, the transmission of infectious diseases expands. Traditional detection methods for pathogens still have some shortcomings, such as time-consuming procedures and high operational costs. To fulfil the demands for simple and effective detection, numerous biosensors have been developed. DNAzyme, a unique DNA structure with catalytic activity, is gradually being applied in the field of pathogen detection owing to its ease of preparation and use. In this review, we concentrated on the two main types of DNAzyme, hemin/G-quadruplex DNAzyme (HGD) and RNA-cleaving DNAzyme (RCD), explaining their research progress in pathogen detection. Furthermore, we introduced two additional novel DNAzymes, CLICK 17 DNAzyme and Supernova DNAzyme, which showed promising potential in pathogen detection. Finally, we summarize the strengths and weaknesses of these four DNAzymes and offer feasible recommendations for the development of biosensors.
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Affiliation(s)
- Xingxing Liu
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Wenxu Yuan
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Heng Xiao
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
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Chen Y, Yan B, Chen W, Zhang X, Liu Z, Zhang Q, Li L, Hu M, Zhao X, Xu X, Lv Q, Luo Y, Cai Y, Liu Y. Development of the CRISPR-Cas12a system for editing of Pseudomonas aeruginosa phages. iScience 2024; 27:110210. [PMID: 39055914 PMCID: PMC11269290 DOI: 10.1016/j.isci.2024.110210] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
Pseudomonas aeruginosa is a common opportunistic pathogen. The potential efficacy of phage therapy has attracted the attention of researchers, but efficient gene-editing tools are lacking, limiting the study of their biological properties. Here, we designed a type V CRISPR-Cas12a system for the gene editing of P. aeruginosa phages. We first evaluated the active cutting function of the CRISPR-Cas12a system in vitro and discovered that it had a higher gene-cutting efficiency than the type II CRISPR-Cas9 system in three different P. aeruginosa phages. We also demonstrated the system's ability to precisely edit genes in Escherichia coli phages, Salmonella phages, and P. aeruginosa phages. Using the aforementioned strategies, non-essential P. aeruginosa phage genes can be efficiently deleted, resulting in a reduction of up to 5,215 bp (7.05%). Our study has provided a rapid, efficient, and time-saving tool that accelerates progress in phage engineering.
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Affiliation(s)
- Yibao Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- Shandong Vamph Animal Health Products Co., LTD, Jinan, China
| | - Bingjie Yan
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Weizhong Chen
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xue Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Zhengjie Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Qing Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Lulu Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Ming Hu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- Shandong Vamph Animal Health Products Co., LTD, Jinan, China
| | - Xiaonan Zhao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Xiaohui Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Qianghua Lv
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Yanbo Luo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Yumei Cai
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- Shandong Vamph Animal Health Products Co., LTD, Jinan, China
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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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Tang X, Chen Y, Wang B, Luo D, Wang J, He Y, Feng L, Xu Y, Xie S, Chen M, Chang K. Autonomous Feedback-Driven Engineered DNAzyme-Coated Trojan Horse-like Nanocapsules for On-Demand CRISPR/Cas9 Delivery. ACS NANO 2024; 18:13950-13965. [PMID: 38751197 PMCID: PMC11140835 DOI: 10.1021/acsnano.4c04147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Manipulating the expression of cellular genes through efficient CRISPR/Cas9 delivery is rapidly evolving into a desirable tumor therapeutics. The exposure of CRISPR/Cas9 to a complex external environment poses challenges for conventional delivery carriers in achieving responsive and accurate release. Here, we report a Trojan horse-like nanocapsule for the on-demand delivery of CRISPR/Cas9 in a microRNA-responsive manner, enabling precise tumor therapy. The nanocapsule comprises a nanoassembled, engineered DNAzyme shell encasing a Cas9/sgRNA complex core. The DNAzyme, functioning as a catalytic unit, undergoes a conformational change in the presence of tumor-associated microRNA, followed by activating a positive feedback-driven autonomous catabolic cycle of the nanocapsule shell. This catabolic cycle is accomplished through chain reactions of DNAzyme "cleavage-hybridization-cleavage", which ensures sensitivity in microRNA recognition and effective release of Cas9/sgRNA. Utilizing this Trojan horse-like nanocapsule, as low as 1.7 pM microRNA-21 can trigger the on-demand release of Cas9/sgRNA, enabling the specific editing of the protumorigenic microRNA coding gene. The resulting upregulation of tumor suppressor genes induces apoptosis in tumor cells, leading to significant inhibition of tumor growth by up to 75.94%. The Trojan horse-like nanocapsule, with superior programmability and biocompatibility, is anticipated to serve as a promising carrier for tailoring responsive gene editing systems, achieving enhanced antitumor specificity and efficacy.
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Affiliation(s)
- Xiaoqi Tang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Yihui Chen
- Department
of General Surgery, Xinqiao Hospital, Army
Medical University, Chongqing 400037, China
| | - Binpan Wang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Dan Luo
- Department
of Biological and Environmental Engineering, Cornell University, Ithaca New York 14853-5701, United States
| | - Jue Wang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Yuan He
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Liu Feng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Ying Xu
- Department
of Clinical Laboratory Medicine, School
of Clinical Medicine & The First Affiliated Hospital of Chengdu
Medical College, Chengdu 610500, China
| | - Shuang Xie
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Ming Chen
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
- College
of Pharmacy and Laboratory Medicine, Third
Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
| | - Kai Chang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba, Chongqing 400038, China
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10
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Ke X, Liang A, Chen C, Hu T. A one-pot CRISPR-RCA strategy for ultrasensitive and specific detection of circRNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3256-3262. [PMID: 38726809 DOI: 10.1039/d4ay00693c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Accurate and precise detection of circular RNA (circRNA) is imperative for its clinical use. However, the inherent challenges in circRNA detection, arising from its low abundance and potential interference from linear isomers, necessitate innovative solutions. In this study, we introduce, for the first time, the application of the CRISPR/Cas12a system to establish a one-pot, rapid (30 minutes to 2 hours), specific and ultrasensitive circRNA detection strategy, termed RETA-CRISPR (reverse transcription-rolling circle amplification (RT-RCA) with the CRISPR/Cas12a). This method comprises two steps: (1) the RT-RCA process of circRNA amplification, generating repeat units containing the back-splicing junction (BSJ) sequences; and (2) leveraging the protospacer adjacent motif (PAM)-independent Cas12a/crRNA complex to precisely recognize target sequences with BSJ, thereby initiating the collateral cleavage activity of Cas12a to generate a robust fluorescence signal. Remarkably, this approach exhibits the capability to detect circRNAs at a concentration as low as 300 aM. The sensor has been successfully employed for accurate detection of a potential hepatocellular carcinoma biomarker hsa_circ_0001445 (circRNA1445) in various cell lines. In conclusion, RETA-CRISPR seamlessly integrates the advantages of exponential amplification reaction and the robust collateral cleavage activity of Cas12a, positioning it as a compelling tool for practical CRISPR-based diagnostics.
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Affiliation(s)
- Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
| | - Ajuan Liang
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Obstetrics and Gynecology Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Chuanxia Chen
- School of Materials Science and Engineering, University of Jinan, Jinan 250022, China
| | - Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310000, China
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11
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Sun K, Pu L, Chen C, Chen M, Li K, Li X, Li H, Geng J. An autocatalytic CRISPR-Cas amplification effect propelled by the LNA-modified split activators for DNA sensing. Nucleic Acids Res 2024; 52:e39. [PMID: 38477342 DOI: 10.1093/nar/gkae176] [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: 08/10/2023] [Revised: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
CRISPR-Cas systems with dual functions offer precise sequence-based recognition and efficient catalytic cleavage of nucleic acids, making them highly promising in biosensing and diagnostic technologies. However, current methods encounter challenges of complexity, low turnover efficiency, and the necessity for sophisticated probe design. To better integrate the dual functions of Cas proteins, we proposed a novel approach called CRISPR-Cas Autocatalysis Amplification driven by LNA-modified Split Activators (CALSA) for the highly efficient detection of single-stranded DNA (ssDNA) and genomic DNA. By introducing split ssDNA activators and the site-directed trans-cleavage mediated by LNA modifications, an autocatalysis-driven positive feedback loop of nucleic acids based on the LbCas12a system was constructed. Consequently, CALSA enabled one-pot and real-time detection of genomic DNA and cell-free DNA (cfDNA) from different tumor cell lines. Notably, CALSA achieved high sensitivity, single-base specificity, and remarkably short reaction times. Due to the high programmability of nucleic acid circuits, these results highlighted the immense potential of CALSA as a powerful tool for cascade signal amplification. Moreover, the sensitivity and specificity further emphasized the value of CALSA in biosensing and diagnostics, opening avenues for future clinical applications.
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Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China
| | - Lei Pu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
- School of Pharmacy, North Sichuan Medical College, 637000 Nanchong, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Huanqing Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China
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12
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Kim MJ, Haizan I, Ahn MJ, Park DH, Choi JH. Recent Advances in Lateral Flow Assays for Viral Protein Detection with Nanomaterial-Based Optical Sensors. BIOSENSORS 2024; 14:197. [PMID: 38667190 PMCID: PMC11048458 DOI: 10.3390/bios14040197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Controlling the progression of contagious diseases is crucial for public health management, emphasizing the importance of early viral infection diagnosis. In response, lateral flow assays (LFAs) have been successfully utilized in point-of-care (POC) testing, emerging as a viable alternative to more traditional diagnostic methods. Recent advancements in virus detection have primarily leveraged methods such as reverse transcription-polymerase chain reaction (RT-PCR), reverse transcription-loop-mediated isothermal amplification (RT-LAMP), and the enzyme-linked immunosorbent assay (ELISA). Despite their proven effectiveness, these conventional techniques are often expensive, require specialized expertise, and consume a significant amount of time. In contrast, LFAs utilize nanomaterial-based optical sensing technologies, including colorimetric, fluorescence, and surface-enhanced Raman scattering (SERS), offering quick, straightforward analyses with minimal training and infrastructure requirements for detecting viral proteins in biological samples. This review describes the composition and mechanism of and recent advancements in LFAs for viral protein detection, categorizing them into colorimetric, fluorescent, and SERS-based techniques. Despite significant progress, developing a simple, stable, highly sensitive, and selective LFA system remains a formidable challenge. Nevertheless, an advanced LFA system promises not only to enhance clinical diagnostics but also to extend its utility to environmental monitoring and beyond, demonstrating its potential to revolutionize both healthcare and environmental safety.
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Affiliation(s)
- Min Jung Kim
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (M.J.K.); (D.-H.P.)
| | - Izzati Haizan
- Department of Bioprocess Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea;
| | - Min Ju Ahn
- Department of Biotechnology, Jeonbuk National University, 79 Gobongro, Iksan-si 54596, Jeollabuk-do, Republic of Korea;
| | - Dong-Hyeok Park
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (M.J.K.); (D.-H.P.)
| | - Jin-Ha Choi
- School of Chemical Engineering, Clean Energy Research Center, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea; (M.J.K.); (D.-H.P.)
- Department of Bioprocess Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si 54896, Jeollabuk-do, Republic of Korea;
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13
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Wang L, Li X, Li L, Cao L, Zhao Z, Huang T, Li J, Zhang X, Cao S, Zhang N, Wang X, Gong P. Establishment of an ultrasensitive and visual detection platform for Neospora caninum based-on the RPA-CRISPR/Cas12a system. Talanta 2024; 269:125413. [PMID: 38042139 DOI: 10.1016/j.talanta.2023.125413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023]
Abstract
Neospora caninum is a protozoan parasite that causes neosporosis in cattle, and leads to a high rate of abortion and severe financial losses. Rapid and accurate detection is particularly important for preventing and controlling neosporosis. In our research, a highly effective diagnostic technique based on the RPA-CRISPR/Cas system was created to successfully identify N. caninum against the Nc5 gene, fluorescent reporter system and the lateral flow strip (LFS) biosensor were exploited to display results. The specificity and sensitivity of the PRA-CRISPR/Cas12a assay were evaluated. We discovered that it was highly specific and did not react with any other pathogens. The limit of detection (LOD) for this technology was as low as one parasite per milliliter when employing the fluorescent reporter system, and was approximately ten parasites per milliliter based on the LFS biosensor and under blue or UV light. Meanwhile, the placental tissue samples were detected by our RPA-CRISPR/Cas12a detection platform were completely consistent with that of the nested PCR assay (59.4 %, 19/32). The canine feces were detected by our RPA-CRISPR/Cas12a detection platform were completely consistent with that of the nested PCR assay (8.6 %, 6/70). The RPA-CRISPR/Cas12a detection procedure was successfully finished in within 90 min and offers advantages of high sensitivity and specificity, speed and low cost. The technique was better suitable for extensive neosporosis screening in non-laboratory and resource-constrained locations. This study provided a new strategy for more rapid and portable identification of N. caninum.
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Affiliation(s)
- Li Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Xin Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Lu Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Lili Cao
- Jilin Academy of Animal Husbandry and Veterinary Medicine, Changchun, 130062, China.
| | - Zhiteng Zhao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Taojun Huang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Jianhua Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Songgao Cao
- Pingdu People's Hospital, Qingdao, 266700, China.
| | - Nan Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Xiaocen Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Pengtao Gong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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14
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Kasputis T, He Y, Ci Q, Chen J. On-Site Fluorescent Detection of Sepsis-Inducing Bacteria using a Graphene-Oxide CRISPR-Cas12a (GO-CRISPR) System. Anal Chem 2024; 96:2676-2683. [PMID: 38290431 PMCID: PMC10867801 DOI: 10.1021/acs.analchem.3c05459] [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: 11/30/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Sepsis is an extremely dangerous medical condition that emanates from the body's response to a pre-existing infection. Early detection of sepsis-inducing bacterial infections can greatly enhance the treatment process and potentially prevent the onset of sepsis. However, current point-of-care (POC) sensors are often complex and costly or lack the ideal sensitivity for effective bacterial detection. Therefore, it is crucial to develop rapid and sensitive biosensors for the on-site detection of sepsis-inducing bacteria. Herein, we developed a graphene oxide CRISPR-Cas12a (GO-CRISPR) biosensor for the detection of sepsis-inducing bacteria in human serum. In this strategy, single-stranded (ssDNA) FAM probes were quenched with single-layer graphene oxide (GO). Target-activated Cas12a trans-cleavage was utilized for the degradation of the ssDNA probes, detaching the short ssDNA probes from GO and recovering the fluorescent signals. Under optimal conditions, we employed our GO-CRISPR system for the detection of Salmonella Typhimurium (S. Typhimurium) with a detection sensitivity of as low as 3 × 103 CFU/mL in human serum, as well as a good detection specificity toward other competing bacteria. In addition, the GO-CRISPR biosensor exhibited excellent sensitivity to the detection of S. Typhimurium in spiked human serum. The GO-CRISPR system offers superior rapidity for the detection of sepsis-inducing bacteria and has the potential to enhance the early detection of bacterial infections in resource-limited settings, expediting the response for patients at risk of sepsis.
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Affiliation(s)
- Tom Kasputis
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Yawen He
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Qiaoqiao Ci
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Juhong Chen
- Department
of Biological Systems Engineering, Virginia
Tech, Blacksburg, Virginia 24061, United States
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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15
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Wen J, Deng H, He D, Yuan Y. Dual-functional DNAzyme powered CRISPR-Cas12a sensor for ultrasensitive and high-throughput detection of Pb 2+ in freshwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168708. [PMID: 37992834 DOI: 10.1016/j.scitotenv.2023.168708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Freshwater lead pollution has posed severe threat to the environment and human health, underscoring the urgent necessity for accurate and user-friendly detection methods. Herein, we introduce a novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) sensor for highly sensitive Pb2+ detection. To accomplish this, we designed a dual-functional deoxyribozyme (df-DNAzyme) probe that functions as an activator for the CRISPR-Cas12a system while also recognizing Pb2+. The df-DNAzyme probe was subsequently combined with gold nanoparticles (AuNPs) to fabricate a DNAzyme/AuNP nanoprobe, facilitating the activation of CRISPR-Cas12a in a one-to-multiple manner. Upon exposure to Pb2+, the df-DNAzyme is cleaved, causing disintegration of the DNAzyme/AuNP nanoprobe from magnetic beads. The degraded DNAzyme/AuNP containing multiple double-stranded DNA activators efficiently triggers CRISPR-Cas12a activity, initiating cleavage of fluorescence-quenched reporter DNA and generating amplified signals accordingly. The amplified fluorescence signal is accurately quantified using a quantitative polymerase chain reaction (qPCR) instrument capable of measuring 96 or 384 samples simultaneously at the microliter scale. This technique demonstrates ultra-sensitive detection capability for Pb2+ at concentrations as low as 1 pg/L within a range from 1 pg/L to 10 μg/L, surpassing limits set by World Health Organization (WHO) and United States Environmental Protection Agency (US EPA) guidelines. This study offers an ultrasensitive and high-throughput method for the detection of Pb2+ in freshwater, thereby advancing a novel approach towards the development of precise and convenient techniques for detecting harmful contaminants.
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Affiliation(s)
- Junlin Wen
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Hongjie Deng
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Daigui He
- Guangdong Mechanical & Electrical Polytechnic, Guangzhou 510550, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
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16
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Qu H, Zhang W, Li J, Fu Q, Li X, Wang M, Fu G, Cui J. A rapid and sensitive CRISPR-Cas12a for the detection of Fusobacterium nucleatum. Microbiol Spectr 2024; 12:e0362923. [PMID: 38197659 PMCID: PMC10845955 DOI: 10.1128/spectrum.03629-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024] Open
Abstract
Fusobacterium nucleatum (Fn), as a conditional pathogen, can cause a range of oral and gastrointestinal diseases. However, existing clinical detection methods require expensive equipment and complex procedures, which are inconvenient for large-scale screening in epidemiological research. The purpose of this study was to establish a reliable, rapid, and inexpensive detection method based on CRISPR/Cas12a technology for the detection of Fn. Specific recombinase polymerase amplification (RPA) primer sequences and crRNA sequences were designed based on the nusG gene of Fn. Subsequently, a fluorescence assay and a lateral flow immunoassay were established using the RPA and CRISPR-Cas12a system (RPA-CRISPR-Cas12a). Sensitivity validation revealed a limit of detection of 5 copies/µL. This method could distinguish Fn from other pathogens with excellent specificity. Furthermore, the RPA-CRISPR-Cas12a assay was highly consistent with the classical quantitative real-time PCR method when testing periodontal pocket samples. This makes it a promising method for the detection of Fn and has the potential to play an increasingly important role in infectious disease testing.IMPORTANCEFusobacterium nucleatum (Fn) naturally exists in the microbial communities of the oral and gastrointestinal tracts of healthy individuals and can cause inflammatory diseases in the oral and gastrointestinal tracts. Recent studies have shown that Fn is closely associated with the occurrence and development of gastrointestinal cancer. Therefore, the detection of Fn is very important. Unlike the existing clinical detection methods, this study established a fluorescence-based assay and lateral flow immunoassay based on the RPA and CRISPR-Cas12a system (RPA-CRISPR-Cas12a), which is fast, reliable, and inexpensive and can complete the detection within 30-40 minutes. This makes it a promising method for the detection of Fn and has the potential to play an increasingly important role in infectious disease testing.
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Affiliation(s)
- Hai Qu
- Department of Pathogens, Medical College, Zhengzhou University, Zhengzhou, China
| | - Wenjing Zhang
- Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Jianghao Li
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | - Qingshan Fu
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | - Xiaoxia Li
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | | | - Guangyu Fu
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | - Jing Cui
- Department of Pathogens, Medical College, Zhengzhou University, Zhengzhou, China
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17
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Wang J, Duan Z, Luo D. Fiber Optic SPR POCT: A Novel Nucleic Acid Detection Biosensor for Environmental Viruses. RESEARCH (WASHINGTON, D.C.) 2024; 7:0296. [PMID: 38288060 PMCID: PMC10823875 DOI: 10.34133/research.0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024]
Abstract
In the post-COVID-19 pandemic era, the long-term surveillance of pathogens is still important. The rapid detection of pathogens facilitates the accurate and convenient real-time monitoring of microbial contamination and improves the management of diseases. Here, a novel surface plasmon resonance (SPR)-based point of care testing (POCT) approach of microorganism nucleic acids with the guidance of CRISPR enzyme is described, including the application of optical fiber-based detection of trace SARS-CoV2 virus in sewage water on SPR and validation of the plasmonic biosensor for the detection of single-nucleotide mutations in natural water samples.
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Affiliation(s)
- Jing Wang
- Department of Laboratory Medicine,
Shenzhen Hospital of Integrated Traditional and Western Medicine, Shenzhen, China
| | - Zhaojun Duan
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China
| | - Dixian Luo
- Department of Laboratory Medicine,
Shenzhen Hospital of Integrated Traditional and Western Medicine, Shenzhen, China
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18
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Li Y, Zhou S, Wu Q, Gong C. CRISPR/Cas gene editing and delivery systems for cancer therapy. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1938. [PMID: 38456346 DOI: 10.1002/wnan.1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 03/09/2024]
Abstract
CRISPR/Cas systems stand out because of simplicity, efficiency, and other superiorities, thus becoming attractive and brilliant gene-editing tools in biomedical field including cancer therapy. CRISPR/Cas systems bring promises for cancer therapy through manipulating and engineering on tumor cells or immune cells. However, there have been concerns about how to overcome the numerous physiological barriers and deliver CRISPR components to target cells efficiently and accurately. In this review, we introduced the mechanisms of CRISPR/Cas systems, summarized the current delivery strategies of CRISPR/Cas systems by physical methods, viral vectors, and nonviral vectors, and presented the current application of CRISPR/Cas systems in cancer clinical treatment. Furthermore, we discussed prospects related to delivery approaches of CRISPR/Cas systems. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Yingjie Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shiyao Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qinjie Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Changyang Gong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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19
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Wu X, Zhao Y, Guo C, Liu C, Zhang Q, Chen Y, Liu Y, Zhang X. RatioCRISPR: A ratiometric biochip based on CRISPR/Cas12a for automated and multiplexed detection of heteroplasmic SNPs in mitochondrial DNA. Biosens Bioelectron 2023; 241:115676. [PMID: 37714059 DOI: 10.1016/j.bios.2023.115676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Mitochondrial genetic diseases are often characterized by heteroplasmic single nucleotide polymorphisms (SNPs) where both wild-type (WT) and mutant-type (MT) coexist, making detection of accurate SNP abundance critical for diagnosis. Here, we present RatioCRISPR, an automated ratiometric biochip sensor based on the CRISPR/Cas12a system for detecting multiple heteroplasmic SNPs in mitochondrial DNA (mtDNA). The ratiometric sensor output is only influenced by the relative abundance of WT and MT, with minimal impact from sample concentration. Biochips allow the simultaneous detection of multiple SNP sites for more accurate disease diagnosis. RatioCRISPR can accurately detect 8 samples simultaneously within 25 min with a limit of detection (LOD) of 15.7 aM. We successfully detected 13 simulated samples of three mtDNA point mutations (m.3460G>A, m.11778G>A, and m.14484T>C), which lead to Leber's hereditary optic neuropathy (LHON) and set a threshold (60%) of heteroplasmy to evaluate disease risk. This automated and accurate biosensor has broad applications in diagnosing multiple SNPs, especially those with heteroplasmic variations, making it an advanced and convenient tool for mtDNA disease diagnosis.
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Affiliation(s)
- Xiaolong Wu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Yi Zhao
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Chuanghao Guo
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Conghui Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Qianling Zhang
- Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Yong Chen
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China; Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China.
| | - Yizhen Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China; Shenzhen Key Laboratory of Nano-Biosensing Technology, Shenzhen, 518060, Guangdong, PR China.
| | - Xueji Zhang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
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20
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Ding Y, Huang Z, Li X, Tang M, Li W, Feng S, Zhao L, Zhang J, Yuan S, Shan F, Jiao P. Development of a reverse transcription loop-mediated isothermal amplification based clustered regularly interspaced short palindromic repeats Cas12a assay for duck Tembusu virus. Front Microbiol 2023; 14:1301653. [PMID: 38098674 PMCID: PMC10720249 DOI: 10.3389/fmicb.2023.1301653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Duck Tembusu virus (DTMUV) is an emerging pathogen that poses a serious threat to the duck industry in China. Currently, polymerase chain reaction (PCR), quantitative PCR (qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) are commonly used for DTMUV detection. However, these methods require complex steps and special equipment and easily cause false-positive results. Therefore, we urgently need to establish a simple, sensitive and specific method for the clinical field detection of DTMUV. In this study, we developed an RT-LAMP-based CRISPR-Cas12a assay targeting the C gene to detect DTMUV with a limited detection of 3 copies/μL. This assay was specific for DTMUV without cross-reaction with other common avian viruses and only required some simple pieces of equipment, such as a thermostat water bath and blue/UV light transilluminator. Furthermore, this assay showed 100% positive predictive agreement (PPA) and negative predictive agreement (NPA) relative to SYBR Green qPCR for DTMUV detection in 32 cloacal swabs and 22 tissue samples, supporting its application for clinical field detection.
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Affiliation(s)
- Yangbao Ding
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
| | - Zhanhong Huang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Xinbo Li
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Mei Tang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Weiqiang Li
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Siyu Feng
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Luxiang Zhao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Junsheng Zhang
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Shichao Yuan
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Fen Shan
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou Zoo, Guangzhou, China
| | - Peirong Jiao
- College of Veterinary Medicine, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, China
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21
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Jia Z, Zhang Y, Zhang C, Wei X, Zhang M. Biosensing Intestinal Alkaline Phosphatase by Pregnancy Test Strips Based on Target-Triggered CRISPR-Cas12a Activity to Monitor Intestinal Inflammation. Anal Chem 2023; 95:14111-14118. [PMID: 37668549 DOI: 10.1021/acs.analchem.3c03099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
With an increasing incidence worldwide, inflammatory bowel disease (IBD) is a chronic inflammatory disease affecting the gastrointestinal tract, which impairs the life quality of patients. Therefore, it is of great significance to construct a sensitive, simple, and convenient biosensor to analyze IBD-associated biomarkers for an auxiliary diagnosis of IBD. Intestinal alkaline phosphatase (IAP), expressed by the intestinal epithelium, is an endogenous protein that is thought to play a vital role in maintaining intestinal homeostasis and is considered a potential biomarker for IBD. Here, an IAP detection method was developed using pregnancy test strips by dephosphorylation. Initially, a double-stranded DNA (dsDNA) was designed to respond to IAP and acted as an activator of Cas12a. In the presence of IAP, the designed dsDNA was not digested by lambda exonuclease (λ exo), which hybridized to the Cas12a-crRNA duplex and resulted in the activation of the trans-cleavage of Cas12a. Further, the activated Cas12a cleaved the single-strand DNA (ssDNA) linker in the MBs-ssDNA-hCG probe, triggering the release of hCG. With magnetic separation, the released hCG could be quantitatively detected by pregnancy test strips. IAP levels were analyzed in feces from colitis and healthy mice by pregnancy test strips. The results showed that the IAP level of colitis mice (3.89 ± 1.92 U/L) was much lower than that of healthy mice (39.64 ± 24.93 U/L), indicating the correlation between IAP and intestinal inflammation. Taken together, a sensitive, user-friendly detection assay based on pregnancy test strips was constructed to monitor IAP and used as an auxiliary diagnostic approach for IBD in a clinical scene.
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Affiliation(s)
- Zhenzhen Jia
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Yujie Zhang
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Chuanyu Zhang
- School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Xueyong Wei
- School of Instrument Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049, P. R. China
| | - Mingzhen Zhang
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
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22
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Wu J, Huang Y, Ding X, Kang L, Wang X, Li D, Cheng W, Liu G, Xue J, Ding S. CPA-Cas12a-based lateral flow strip for portable assay of Methicillin-resistant Staphylococcus aureus in clinical sample. J Nanobiotechnology 2023; 21:234. [PMID: 37481551 PMCID: PMC10362775 DOI: 10.1186/s12951-023-02002-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/13/2023] [Indexed: 07/24/2023] Open
Abstract
The rapid and accurate identification of methicillin-resistant Staphylococcus aureus at an early antibiotic therapy stage would be benefit to disease diagnosis and antibiotic selection. Herein, we integrated cross-priming amplification (CPA) and CRISPR/Cas 12a (designated as CPA-Cas 12a) systems to establish a sensitive and efficient lateral flow assay to detect methicillin-resistant Staphylococcus aureus. This assay relies on the CPA isothermal nucleic acid amplification strategy which can amplify the DNA extracted from Staphylococcus aureus and accompanying the indiscriminately trans-cleavage process of Cas 12a/CrRNA duplex after recognizing specific sequence. Taking the advantage of reporter and high turnover Cas 12a activity, a dramatic change in response was achieved to produce a significant increase in the analytical sensitivity. The signal conversion and output were realized using a lateral flow strip to achieve field-deployable detection. Furthermore, this bioassay was accommodated with a microfluidic device to realize automatically portable detection. This proposed assay completed within 30 min with the detection limit of 5 CFU mL-1, was verified by testing bacterial suspension and 202 clinical samples. Given the high sensitivity, specificity and efficiency, this colorimetric readout assay through strip could be further promoted to the clinical diagnosis, clinical medication of multidrug-resistant bacteria.
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Affiliation(s)
- Jiangling Wu
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Yu Huang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Xiaojuan Ding
- Department of Clinical Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Lina Kang
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Xiaoliang Wang
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Dandan Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Gang Liu
- Department of Critical Care Medicine, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China.
| | - Jianjiang Xue
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), college of laboratory medicine, Chongqing Medical University, Chongqing, 400016, China
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23
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Hu Y, Qiao Y, Li XQ, Xiang Z, Wan Y, Wang P, Yang Z. Development of an inducible Cas9 nickase and PAM-free Cas12a platform for bacterial diagnostics. Talanta 2023; 265:124931. [PMID: 37451121 DOI: 10.1016/j.talanta.2023.124931] [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: 03/20/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Rapid, efficient, specific and sensitive diagnostic techniques are critical for selecting appropriate treatments for drug-resistant bacterial infections. To address this challenge, we have developed a novel diagnostic method, called the Dual-Cas Tandem Diagnostic Platform (DTDP), which combines the use of Cas9 nickase (Cas9n) and Cas12a. DTDP works by utilizing the Cas9n-sgRNA complex to create a nick in the target strand's double-stranded DNA (dsDNA). This prompts DNA polymerase to displace the single-stranded DNA (ssDNA) and leads to cycles of DNA replication through nicking, displacement, and extension. The ssDNA is then detected by the Cas12a-crRNA complex (which is PAM-free), activating trans-cleavage and generating a fluorescent signal from the fluorescent reporter. DTDP exhibits a high sensitivity (1 CFU/mL or 100 ag/μL), high specificity (specifically to MRSA in nine pathogenic species), and excellent accuracy (100%). The dual RNA recognition process in our method improves diagnostic specificity by decreasing the limitations of Cas12a in detecting dsDNA protospacer adjacent motifs (PAMs) and leverages multiple advantages of multi-Cas enzymes in diagnostics. This novel approach to pathogenic microorganism detection has also great potential for clinical diagnosis.
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Affiliation(s)
- Yuanzhao Hu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Yuefeng Qiao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Xiu-Qing Li
- Agriculture and Agri-Food Canada, Fredericton, New Brunswick, E3B 4Z7, Canada; Nutra Health Products and Technologies Inc., Fredericton NB E3B 6J5, Canada
| | - Zhenbo Xiang
- Rizhao Science and Technology Innovation Service Center, 369 Jining Road, Rizhao, Shandong, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Peng Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Zhiqing Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China; Rizhao Science and Technology Innovation Service Center, 369 Jining Road, Rizhao, Shandong, China.
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24
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Deng F, Pan J, Chen M, Liu Z, Chen J, Liu C. Integrating CRISPR-Cas12a with catalytic hairpin assembly as a logic gate biosensing platform for the detection of polychlorinated biphenyls in water samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163465. [PMID: 37068691 DOI: 10.1016/j.scitotenv.2023.163465] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/23/2023] [Accepted: 04/08/2023] [Indexed: 06/01/2023]
Abstract
Polychlorinated biphenyls (PCBs) are ubiquitous persistent organic pollutants that cause harmful effects on environmental safety and human health. There is an urgent need to develop an intelligent method for PCBs sensing. In this work, we proposed a logic gate biosensing platform for simultaneous detection of multiple PCBs. 2,3',5,5'-tetrachlorobiphenyl (PCB72) and 3,3',4,4'-tetrachlorobiphenyl (PCB77) were used as the two inputs to construct biocomputing logic gates. We used 0 and 1 to encode the inputs and outputs. The aptamer was used to recognize the inputs and release the trigger DNA. A catalytic hairpin assembly (CHA) module is designed to convert and amplify each trigger DNA into multiple programmable DNA duplexes, which initiate the trans-cleavage activity of CRISPR/Cas12a for the signal output. The activated Cas12 cleaves the BHQ-Cy5 modified single-stranded DNA (ssDNA) to yield the fluorescence reporting signals. In the YES logic gate, PCB72 was used as the only input to carry out the logic operation. In the OR, AND, and INHIBIT logic gates, PCB72 and PCB77 were used as the two inputs. The output signals can be visualized by the naked eye under UV light transilluminators or quantified by a microplate reader. Our constructed biosensing platform possesses the merits of multiple combinations of inputs, intuitive digital output, and high flexibility and scalability, which holds great promise for the intelligent detection of different PCBs.
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Affiliation(s)
- Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Manjia Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Chengshuai Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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25
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Șoldănescu I, Lobiuc A, Covașă M, Dimian M. Detection of Biological Molecules Using Nanopore Sensing Techniques. Biomedicines 2023; 11:1625. [PMID: 37371721 PMCID: PMC10295350 DOI: 10.3390/biomedicines11061625] [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: 05/16/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed and that can be tailored to be highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount to treating serious diseases. Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest in medicine, for advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis. This review offers a new perspective on current biomolecule sensing techniques, based on various types of nanopores, challenges, and approaches toward implementation in clinical settings.
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Affiliation(s)
- Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covașă
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
- Department of Computer, Electronics and Automation, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
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26
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Chen J, Shi G, Yan C. Portable biosensor for on-site detection of kanamycin in water samples based on CRISPR-Cas12a and an off-the-shelf glucometer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162279. [PMID: 36801336 DOI: 10.1016/j.scitotenv.2023.162279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
On-site and cost-effective monitoring of antibiotic residue in water samples using a ubiquitous device that is readily available to the general public is a big challenge. Herein, we developed a portable biosensor for kanamycin (KAN) detection based on a glucometer and CRISPR-Cas12a. The aptamer-KAN interactions liberate the trigger C strand, which can initiate the hairpin assembly to produce numerous double-stranded DNA. After recognition by CRISPR-Cas12a, Cas12a can cleave the magnetic bead and invertase-modified single-stranded DNA. After magnetic separation, the invertase can convert sucrose into glucose, which can be quantified by a glucometer. The linear range of the glucometer biosensor is from 1 pM to 100 nM and the detection limit is 1 pM. The biosensor also exhibited high selectivity and the nontarget antibiotics had no significant interference with KAN detection. The sensing system is robust and can work in complex samples with excellent accuracy and reliability. The recovery values were in the range of 89-107.2 % for water samples and 86-106.5 % for milk samples. The relative standard deviation (RSD) was below 5 %. With the advantages of simple operation, low cost, and easy accessibility to the public, this portable pocket-sized sensor can realize the on-site detection of antibiotic residue in resource-limited settings.
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Affiliation(s)
- Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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27
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Xiang X, Song M, Xu X, Lu J, Chen Y, Chen S, He Y, Shang Y. Microfluidic Biosensor Integrated with Signal Transduction and Enhancement Mechanism for Ultrasensitive Noncompetitive Assay of Multiple Mycotoxins. Anal Chem 2023; 95:7993-8001. [PMID: 37156096 DOI: 10.1021/acs.analchem.3c00813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
To achieve high-throughput ultrasensitive detection of mycotoxins in food, a functional DNA-guided transition-state CRISPR/Cas12a microfluidic biosensor (named FTMB) was successfully constructed. The signal transduction CRISPR/Cas12a strategy in FTMB has utilized DNA sequences with a specific recognition function and activators to form trigger switches. Meanwhile, the transition-state CRISPR/Cas12a system was constructed by adjusting the composition ratio of crRNA and activator to achieve a high response for low concentrations of target mycotoxins. On the other hand, the signal enhancement of FTMB has efficiently integrated the signal output of quantum dots (QDs) with the fluorescence enhancement effect of photonic crystals (PCs). The construction of universal QDs for the CRISPR/Cas12a system and PC films matching the photonic bandgap produced a significant signal enhancement by a factor of 45.6. Overall, FTMB exhibited a wide analytic range (10-5-101 ng·mL-1), low detection of limit (fg·mL-1), short detection period (∼40 min), high specificity, good precision (coefficients of variation <5%), and satisfactory practical sample analysis capacity (the consistency with HPLC at 88.76%-109.99%). It would provide a new and reliable solution for the rapid detection of multiple small molecules in the fields of clinical diagnosis and food safety.
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Affiliation(s)
- Xinran Xiang
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Minghui Song
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Xiaowei Xu
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Jiaran Lu
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuanyuan Chen
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Shuhan Chen
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yinglong He
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuting Shang
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
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28
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Kang Y, Zhang J, Zhao L, Yan H. Colorimetric miRNA detection based on self-primer-initiated CRISPR-Cas12a-assisted amplification. Biotechniques 2023; 74:172-178. [PMID: 37128982 DOI: 10.2144/btn-2023-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
miRNAs alter significantly throughout pregnancy to support the development of the fetus. However, sensitive detection of miRNA remains a challenge. Herein, a reliable miRNA detection approach integrating self-assembly-triggered signal amplification and CRISPR-Cas12a-system cleavage-based color generation is described. The colorimetric approach contains three signal amplification processes. The first signal amplification is formed by the released miRNA in a chain extension process. The produced sequence that is similar to the target miRNA initiates the second signal recycle. Finally, CRISPR-Cas12a-based transcleavage on linker sequences induces the third signal amplification. The method exhibits high sensitivity and a low limit of detection of 254 aM, showing promising prospects in disease diagnosis.
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Affiliation(s)
- Ying Kang
- Obstetrics Department I, Northwest Women & Children's Hospital, Xi'an, Shaanxi Province, 710061, China
| | - Jingjing Zhang
- Obstetrics Department I, Northwest Women & Children's Hospital, Xi'an, Shaanxi Province, 710061, China
| | - Lijuan Zhao
- Obstetrics Department I, Northwest Women & Children's Hospital, Xi'an, Shaanxi Province, 710061, China
| | - Hongli Yan
- Department of Obstetrics & Gynecology, Northwest Women & Children's Hospital, Xi'an, Shaanxi Province, 710061, China
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29
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Niu C, Liu J, Xing X, Zhang C. Exploring the Trans-Cleavage Activity with Rolling Circle Amplification for Fast Detection of miRNA. BIODESIGN RESEARCH 2023; 5:0010. [PMID: 37849464 PMCID: PMC10085249 DOI: 10.34133/bdr.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/28/2023] [Indexed: 10/19/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous short noncoding RNA. They regulate gene expression and function, essential to biological processes. It is necessary to develop an efficient detection method to determine these valuable biomarkers for the diagnosis of cancers. In this paper, we proposed a general and rapid method for sensitive and quantitative detection of miRNA by combining CRISPR-Cas12a and rolling circle amplification (RCA) with the precircularized probe. Eventually, the detection of miRNA-21 could be completed in 70 min with a limit of detection of 8.1 pM with high specificity. The reaction time was reduced by almost 4 h from more than 5 h to 70 min, which makes detection more efficient. This design improves the efficiency of CRISPR-Cas and RCA-based sensing strategy and shows great potential in lab-based detection and point-of-care test.
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Affiliation(s)
- Chenqi Niu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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30
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Politza AJ, Nouri R, Guan W. Digital CRISPR Systems for the Next Generation of Nucleic Acid Quantification. Trends Analyt Chem 2023; 159:116917. [PMID: 36744100 PMCID: PMC9894100 DOI: 10.1016/j.trac.2023.116917] [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] [Indexed: 01/09/2023]
Abstract
Digital CRISPR (dCRISPR) assays are an emerging platform of molecular diagnostics. Digital platforms introduce absolute quantification and increased sensitivity to bulk CRISPR assays. With ultra-specific targeting, isothermal operation, and rapid detection, dCRISPR systems are well-prepared to lead the field of molecular diagnostics. Here we summarized the common Cas proteins used in CRISPR detection assays. The methods of digital detection and critical performance factors are examined. We formed three strategies to frame the landscape of dCRISPR systems: (1) amplification free, (2) in-partition amplification, and (3) two-stage amplification. We also compared the performance of all systems through the limit of detection (LOD), testing time, and figure of merit (FOM). This work summarizes the details of digital CRISPR platforms to guide future development. We envision that improvements to LOD and dynamic range will position dCRISPR as the leading platform for the next generation of molecular biosensing.
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Affiliation(s)
- Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
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31
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Park DH, Choi MY, Choi JH. Recent Development in Plasmonic Nanobiosensors for Viral DNA/RNA Biomarkers. BIOSENSORS 2022; 12:bios12121121. [PMID: 36551088 PMCID: PMC9776357 DOI: 10.3390/bios12121121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 05/28/2023]
Abstract
Recently, due to the coronavirus pandemic, the need for early diagnosis of infectious diseases, including viruses, is emerging. Though early diagnosis is essential to prevent infection and progression to severe illness, there are few technologies that accurately measure low concentrations of biomarkers. Plasmonic nanomaterials are attracting materials that can effectively amplify various signals, including fluorescence, Raman, and other optical and electromagnetic output. In this review, we introduce recently developed plasmonic nanobiosensors for measuring viral DNA/RNA as potential biomarkers of viral diseases. In addition, we discuss the future perspective of plasmonic nanobiosensors for DNA/RNA detection. This review is expected to help the early diagnosis and pathological interpretation of viruses and other diseases.
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Kumar M, Maiti S, Chakraborty D. Capturing nucleic acid variants with precision using CRISPR diagnostics. Biosens Bioelectron 2022; 217:114712. [PMID: 36155952 DOI: 10.1016/j.bios.2022.114712] [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: 11/09/2021] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022]
Abstract
CRISPR/Cas systems have the ability to precisely target nucleotide sequences and enable their rapid identification and modification. While nucleotide modification has enabled the therapeutic correction of diseases, the process of identifying the target DNA or RNA has greatly expanded the field of molecular diagnostics in recent times. CRISPR-based DNA/RNA detection through programmable nucleic acid binding or cleavage has been demonstrated for a large number of pathogenic and non-pathogenic targets. Combining CRISPR detection with nucleic acid amplification and a terminal signal readout step allowed the development of numerous rapid and robust nucleic acid platforms. Wherever the Cas effector can faithfully distinguish nucleobase variants in the target, the platform can also be extended for sequencing-free rapid variant detection. Some initial PAM disruption-based SNV detection reports were limited to finding or integrating mutated/mismatched nucleotides within the PAM sequences. In this review, we try to summarize the developments made in CRISPR diagnostics (CRISPRDx) to date emphasizing CRISPR-based SNV detection. We also discuss the applications where such diagnostic modalities can be put to use, covering various fields of clinical research, SNV screens, disease genotyping, primary surveillance during microbial infections, agriculture, food safety, and industrial biotechnology. The ease of rapid design and implementation of such multiplexable assays can potentially expand the applications of CRISPRDx in the domain of affinity-based target sequencing, with immense possibilities for low-cost, quick, and widespread usage. In the end, in combination with proximity assays and a suicidal gene approach, CRISPR-based in vivo SNV detection and cancer cell targeting can be formulated as personalized gene therapy.
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Affiliation(s)
- Manoj Kumar
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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33
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Zhang B, Li M, Wei Y, Wang J, Wang Y, Shi P, Tang H, Song Z. Detection of target DNA with a visual CRISPR-associated hyperbranched rolling circle amplification technique. Anal Biochem 2022; 658:114940. [DOI: 10.1016/j.ab.2022.114940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/01/2022]
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Song Y, Gao K, Cai X, Cheng W, Ding S, Zhang D, Deng S. Controllable crRNA Self-Transcription Aided Dual-Amplified CRISPR-Cas12a Strategy for Highly Sensitive Biosensing of FEN1 Activity. ACS Synth Biol 2022; 11:3847-3854. [PMID: 36240131 DOI: 10.1021/acssynbio.2c00420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A controllable crRNA self-transcription aided dual-amplified CRISPR-Cas12a strategy (termed CST-Cas12a) was developed for highly sensitive and specific biosensing of flap endonuclease 1 (FEN1), a structure-selective nuclease in eukaryotic cells. In this strategy, a branched DNA probe with a 5' overhanging flap was designed to serve as a hydrolysis substrate of FEN1. The flap cut by FEN1 was annealed with a template probe and functioned as a primer for an extension reaction to produce a double-stranded DNA (dsDNA) containing a T7 promoter and crRNA transcription template. Assisting the T7 RNA polymerase, abundant crRNA was generated and assembled with Cas12a to form a Cas12a/crRNA complex, which can be activated by a dsDNA trigger and unlock the indiscriminate fluorophore-quencher reporter cleavage. The highly efficient dual signal amplification and near-zero background enabled CST-Cas12a with extraordinarily high sensitivity. Under optimized conditions, this method allowed highly sensitive biosensing of FEN1 activity in the range of 1 × 10-5 U μL-1 to 5 × 10-2 U μL-1 with a detection limit of 5.2 × 10-6 U μL-1 and achieved excellent specificity for FEN1 in the presence of other interfering enzymes. The inhibitory capabilities of chemicals on FEN1 were also investigated. Further, the newly established CST-Cas12a strategy was successfully applied to FEN1 biosensing in complex biological samples, which might be a reliable biosensing platform for highly sensitive and specific detection of FEN1 activity in clinical applications.
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Affiliation(s)
- Yang Song
- Laboratory of Forensic Medicine and Biomedical Informatics, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.,Cancer Center, Institute of Surgery Research, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, P. R. China
| | - Ke Gao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Xiaoying Cai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Decai Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, P. R. China
| | - Shixiong Deng
- Laboratory of Forensic Medicine and Biomedical Informatics, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
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35
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Ding S, Wei Y, Chen G, Du F, Cui X, Huang X, Yuan Y, Dong J, Tang Z. Detection of Cancer Marker Flap Endonuclease 1 Using One-Pot Transcription-Powered Clustered Regularly Interspaced Short Palindromic Repeat/Cas12a Signal Expansion. Anal Chem 2022; 94:13549-13555. [PMID: 36121799 DOI: 10.1021/acs.analchem.2c03054] [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: 11/29/2022]
Abstract
As a critical functional protein in DNA replication and genome stability, flap endonuclease 1 (FEN1) has been considered a promising biomarker and druggable target for multiple cancers. We report here a transcription-powered clustered regularly interspaced short palindromic repeat (CRISPR)/Cas12a signal expansion platform for rapid and sensitive detection of FEN1. In this method, the probe cleavage by FEN1 generated a free 5' flap single-stranded DNA which could hybridize with the single-stranded T7 promoter-bearing template and trigger the extension. Then, the CRISPR guide RNA (crRNA) transcribed from the extended template activated the collateral DNase activity of Cas12a, releasing the fluorophore from the quenched DNA signal probe to report the FEN1 detection result. The high specificity for FEN1 was validated by comparing with other repair-relevant proteins. The limit of detection (LOD) could be as low as 0.03 mU, which is sensitive enough to detect the FEN1 activity in biological samples. In addition, the inhibition assay of FEN1 was also successfully achieved with this platform, proving its potential in inhibitor screening. In summary, this study provides a novel biosensor for FEN1 activity analysis and provides new insights into the development of CRISPR-based biosensors for non-nucleic acid targets.
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Affiliation(s)
- Sheng Ding
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yinghua Wei
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
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36
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Li X, Chen X, Mao M, Peng C, Wang Z. Accelerated CRISPR/Cas12a-based small molecule detection using bivalent aptamer. Biosens Bioelectron 2022; 217:114725. [PMID: 36179433 DOI: 10.1016/j.bios.2022.114725] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
CRISPR/Cas holds great promise for biosensing applications, however, restricted to nucleic acid targets. Here, we broaden the sensing target of CRISPR/Cas to small molecules via integrating a bivalent aptamer as a recognition component. Using adenosine 5'-triphosphate (ATP) as a model molecule, we found that a bivalent aptamer we selected could shorten the binding time between the aptamer and ATP from 30 min to 3 min, thus dramatically accelerating the detection of ATP. The accelerated bivalent aptamer binding to ATP was mainly ascribed to the extended conformation of the aptamer, which was stabilized through linking with a 5 T bases connector on specific loops of the monovalent aptamer. To facilitate on-site detection, we integrated lateral flow assay (LFA) with the CRISPR/Cas sensing strategy (termed BA-CASLFA) to serve as a visual readout of the presence of ATP. In addition, in the CASLFA platform, due to the unique characteristics of LFA, the thermal step of Cas12a inactivation can be omitted. The BA-CASLFA could output a colorimetric "TURN ON" signal for ATP within 26 min, which could be easily discriminated by the naked eye and sensitively quantified by the portable reader. Furthermore, we showed the versatility of BA-CASLFA for detecting kanamycin using a kanamycin bivalent aptamer obtained through the same design as the ATP bivalent aptamer. Therefore, this strategy is amenable to serve as a general sensing strategy for small molecular targets. The above work opened a new way in developing CRISPR-based on-site sensors for clinic diagnosis, food safety, and environmental analysis.
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Affiliation(s)
- Xiuping Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China
| | - Xiujin Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471000, PR China
| | - Minxin Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China
| | - Chifang Peng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China.
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Lihu Road 1800, Wuxi, 214122, PR China
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37
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CRISPR-Cas12a-activated palindrome-catalytic hairpin assembly for ultrasensitive fluorescence detection of HIV-1 DNA. Anal Chim Acta 2022; 1227:340303. [DOI: 10.1016/j.aca.2022.340303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/20/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022]
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38
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Ke X, Ou Y, Lin Y, Hu T. Enhanced chemiluminescence imaging sensor for ultrasensitive detection of nucleic acids based on HCR-CRISPR/Cas12a. Biosens Bioelectron 2022; 212:114428. [DOI: 10.1016/j.bios.2022.114428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 12/13/2022]
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39
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Huang J, Liang Z, Liu Y, Zhou J, He F. Development of an MSPQC Nucleic Acid Sensor Based on CRISPR/Cas9 for the Detection of Mycobacterium tuberculosis. Anal Chem 2022; 94:11409-11415. [PMID: 35930710 DOI: 10.1021/acs.analchem.2c02538] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Accurate and rapid detection of nucleic acid plays a vital role in the clinical treatment of tuberculosis caused by Mycobacterium tuberculosis (M.TB). However, false-negative and false-positive results caused by base mismatches could affect the detection accuracy. Inspired by the unique property of CRISPR/Cas9, we proposed a new MSPQC M.TB sensor based on the CRISPR/Cas9 system, which can distinguish single-base mismatches in 10 bases from the protospacer adjacent motif (PAM) region. In the proposed sensor, single-stranded DNA on Au interdigital electrodes was used as a capture probe for the target and an initiator for hybridization chain reaction (HCR). HCR was used to generate long double-stranded DNA (dsDNA), which could span the Au interdigital electrodes. CRISPR/Cas9 was used as recognition components to recognize capture/target dsDNA. When the target existed, the capture probe hybridized with the target to form dsDNA, which could be recognized and cut by CRISPR/Cas9. Thus, the DNA connection between electrodes was cut off and resulted in the MSPQC response. When no target existed, the capture probe remained single-stranded and could not be recognized and cut by CRISPR/Cas9. Therefore, DNA connection between electrodes was reserved. Moreover, silver staining technology was utilized to improve the sensitivity of detection. M.TB was detected by the proposed sensor using specific sequence fragments of 16S rRNA of M.TB as the target. The detection time was down to 2.3 h. The limit of detection (LOD) was 30 CFU/mL.
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Affiliation(s)
- Ji Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zi Liang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jiandang Zhou
- Department of Clinical Laboratory, The Third Xiangya Hospital, Xiangya Medical College of Central South University, Changsha 410208, P. R. China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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40
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Huang YY, Zhang XY, Zhu P, Ji L. Development of clustered regularly interspaced short palindromic repeats/CRISPR-associated technology for potential clinical applications. World J Clin Cases 2022; 10:5934-5945. [PMID: 35949837 PMCID: PMC9254185 DOI: 10.12998/wjcc.v10.i18.5934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 04/24/2022] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) proteins constitute the innate adaptive immune system in several bacteria and archaea. This immune system helps them in resisting the invasion of phages and foreign DNA by providing sequence-specific acquired immunity. Owing to the numerous advantages such as ease of use, low cost, high efficiency, good accuracy, and a diverse range of applications, the CRISPR-Cas system has become the most widely used genome editing technology. Hence, the advent of the CRISPR/Cas technology highlights a tremendous potential in clinical diagnosis and could become a powerful asset for modern medicine. This study reviews the recently reported application platforms for screening, diagnosis, and treatment of different diseases based on CRISPR/Cas systems. The limitations, current challenges, and future prospectus are summarized; this article would be a valuable reference for future genome-editing practices.
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Affiliation(s)
- Yue-Ying Huang
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Xiao-Yu Zhang
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Ping Zhu
- School of Medical Laboratory, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Ling Ji
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen 518035, Guangdong Province, China
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41
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Drobysh M, Liustrovaite V, Baradoke A, Rucinskiene A, Ramanaviciene A, Ratautaite V, Viter R, Chen CF, Plikusiene I, Samukaite-Bubniene U, Slibinskas R, Ciplys E, Simanavicius M, Zvirbliene A, Kucinskaite-Kodze I, Ramanavicius A. Electrochemical Determination of Interaction between SARS-CoV-2 Spike Protein and Specific Antibodies. Int J Mol Sci 2022; 23:ijms23126768. [PMID: 35743208 PMCID: PMC9223850 DOI: 10.3390/ijms23126768] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 12/27/2022] Open
Abstract
The serologic diagnosis of coronavirus disease 2019 (COVID-19) and the evaluation of vaccination effectiveness are identified by the presence of antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this paper, we present the electrochemical-based biosensing technique for the detection of antibodies specific to the SARS-CoV-2 proteins. Recombinant SARS-CoV-2 spike proteins (rSpike) were immobilised on the surface of a gold electrode modified by a self-assembled monolayer (SAM). This modified electrode was used as a sensitive element for the detection of polyclonal mouse antibodies against the rSpike (anti-rSpike). Electrochemical impedance spectroscopy (EIS) was used to observe the formation of immunocomplexes while cyclic voltammetry (CV) was used for additional analysis of the surface modifications. It was revealed that the impedimetric method and the elaborate experimental conditions are appropriate for the further development of electrochemical biosensors for the serological diagnosis of COVID-19 and/or the confirmation of successful vaccination against SARS-CoV-2.
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Affiliation(s)
- Maryia Drobysh
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania;
| | - Viktorija Liustrovaite
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
| | - Ausra Baradoke
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania;
| | - Alma Rucinskiene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania;
| | - Almira Ramanaviciene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
- State Research Institute Center of Innovative Medicine, LT-08406 Vilnius, Lithuania
| | - Vilma Ratautaite
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania;
| | - Roman Viter
- Institute of Atomic Physics and Spectroscopy, University of Latvia, LV-1004 Riga, Latvia;
- Center for Collective Use of Research Equipment, Sumy State University, 40000 Sumy, Ukraine
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei City 106, Taiwan;
| | - Ieva Plikusiene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
| | - Urte Samukaite-Bubniene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
| | - Rimantas Slibinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (R.S.); (E.C.); (M.S.); (A.Z.); (I.K.-K.)
| | - Evaldas Ciplys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (R.S.); (E.C.); (M.S.); (A.Z.); (I.K.-K.)
| | - Martynas Simanavicius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (R.S.); (E.C.); (M.S.); (A.Z.); (I.K.-K.)
| | - Aurelija Zvirbliene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (R.S.); (E.C.); (M.S.); (A.Z.); (I.K.-K.)
| | - Indre Kucinskaite-Kodze
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (R.S.); (E.C.); (M.S.); (A.Z.); (I.K.-K.)
| | - Arunas Ramanavicius
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania; (M.D.); (V.L.); (A.R.); (A.R.); (V.R.); (I.P.); (U.S.-B.)
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +37-060-032-332
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42
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Drobysh M, Liustrovaite V, Baradoke A, Rucinskiene A, Ramanaviciene A, Ratautaite V, Viter R, Chen CF, Plikusiene I, Samukaite-Bubniene U, Slibinskas R, Ciplys E, Simanavicius M, Zvirbliene A, Kucinskaite-Kodze I, Ramanavicius A. Electrochemical Determination of Interaction between SARS-CoV-2 Spike Protein and Specific Antibodies. Int J Mol Sci 2022. [PMID: 35743208 DOI: 10.1149/1945-7111/ac5d91] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
The serologic diagnosis of coronavirus disease 2019 (COVID-19) and the evaluation of vaccination effectiveness are identified by the presence of antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this paper, we present the electrochemical-based biosensing technique for the detection of antibodies specific to the SARS-CoV-2 proteins. Recombinant SARS-CoV-2 spike proteins (rSpike) were immobilised on the surface of a gold electrode modified by a self-assembled monolayer (SAM). This modified electrode was used as a sensitive element for the detection of polyclonal mouse antibodies against the rSpike (anti-rSpike). Electrochemical impedance spectroscopy (EIS) was used to observe the formation of immunocomplexes while cyclic voltammetry (CV) was used for additional analysis of the surface modifications. It was revealed that the impedimetric method and the elaborate experimental conditions are appropriate for the further development of electrochemical biosensors for the serological diagnosis of COVID-19 and/or the confirmation of successful vaccination against SARS-CoV-2.
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Affiliation(s)
- Maryia Drobysh
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania
| | - Viktorija Liustrovaite
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
| | - Ausra Baradoke
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania
| | - Alma Rucinskiene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania
| | - Almira Ramanaviciene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
- State Research Institute Center of Innovative Medicine, LT-08406 Vilnius, Lithuania
| | - Vilma Ratautaite
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania
| | - Roman Viter
- Institute of Atomic Physics and Spectroscopy, University of Latvia, LV-1004 Riga, Latvia
- Center for Collective Use of Research Equipment, Sumy State University, 40000 Sumy, Ukraine
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei City 106, Taiwan
| | - Ieva Plikusiene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
| | - Rimantas Slibinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Evaldas Ciplys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Martynas Simanavicius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Aurelija Zvirbliene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Indre Kucinskaite-Kodze
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Arunas Ramanavicius
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, 03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, LT-10257 Vilnius, Lithuania
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Ravina, Gill PS, Narang J, Kumar A, Mohan H. Development of amperometric biosensor based on cloned hemagglutinin gene of H1N1 (swine flu) virus. 3 Biotech 2022; 12:141. [PMID: 35664651 PMCID: PMC9156826 DOI: 10.1007/s13205-022-03200-8] [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: 03/04/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
The recent emergence of respiratory viruses especially COVID-19 and swine flu has underscored the need for robust and bedside detection methods. Swine flu virus is a very infectious virus of the respiratory system. Timely detection of this virus with high specificity and sensitivity is crucial for reducing morbidity as well as mortality. Cloning of gene segments into a non-infectious agent helps in the development of detection methods, vaccine development, and other studies. In this study, cloning was used to develop a biosensor for H1N1 pdm09 detection. A segment of the hemaglutinin gene was cloned in a vector and characterized with the help of colony touch PCR and blue–white screening. The recombinant plasmid was extracted, and the gene segment was confirmed with the help of HA-specific primers. A 5′ amine group-attached hemagglutinin (HA) gene-specific DNA probe was immobilized on the working gold electrode surface to make a quick, specific, reliable, and sensitive detection method for H1N1pdm09 virus in human nasal swab samples. The HA probe was immobilized on the cysteine applied gold electrode of the screen-printed electrode through 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS). Differential pulse voltammetry was performed with the help of methylene blue, which is a redox indicator for the detection of single-stranded cloned HA gene segment. The developed sensor depicted high sensitivity for the H1N1 influenza virus with a detection limit of 0.6 ng ssDNA/6 µl of the cloned HA sample. Specificity was also checked using H3N2 virus, N. meningitides, influenza A and positive H1N1pdm09 samples.
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Hu T, Ke X, Ou Y, Lin Y. CRISPR/Cas12a-Triggered Chemiluminescence Enhancement Biosensor for Sensitive Detection of Nucleic Acids by Introducing a Tyramide Signal Amplification Strategy. Anal Chem 2022; 94:8506-8513. [PMID: 35635022 DOI: 10.1021/acs.analchem.2c01507] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-based biosensors have attracted increasing attention in accurate and sensitive nucleic acid detection. In this work, we report a CRISPR/Cas12a-triggered chemiluminescence enhancement biosensor for the ultrasensitive detection of nucleic acids by introducing tyramide signal amplification for the first time (termed CRICED). The hybrid chain DNA (crDNA) formed by NH2-capture DNA (capDNA) and biotin-recognition DNA (recDNA) was preferentially attached to the magnetic beads (MBs), and the streptavidin-HRP was subsequently introduced to obtain MB@HRP-crDNA. In the presence of the DNA target, the activated CRISPR/Cas12a is capable of randomly cutting initiator DNA (intDNA) into vast short products, and thus the fractured intDNA could not trigger the toehold-mediated DNA-strand displacement reaction (TSDR) event with MB@HRP-crDNA. After the addition of tyramine-AP and H2O2, abundant HRP-tyramine-AP emerges through the covalent attachment of HRP-tyramine, exhibiting enhanced chemiluminescence (CL) signals or visual image readouts. By virtue of this biosensor, we achieved high sensitivity of synthetic DNA target and amplified DNA plasmid using recombinase polymerase amplification (RPA) as low as 17 pM and single-copy detection, respectively. Our proposed CRICED was further evaluated to test 20 HPV clinical samples, showing a superior sensitivity of 87.50% and specificity of 100.00%. Consequently, the CRICED platform could be an attractive means for ultrasensitive and imaging detection of nucleic acids and holds a promising strategy for the practical application of CRISPR-based diagnostics.
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Affiliation(s)
- Tao Hu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Xinxin Ke
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Yangjing Ou
- International Peace Maternity & Child Health Hospital, Shanghai Municipal Key Clinical Specialty, Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yu Lin
- International Peace Maternity & Child Health Hospital, Shanghai Municipal Key Clinical Specialty, Institute of Embryo-Fetal Original Adult Disease, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
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Białkowska K, Komorowski P, Gomez-Ramirez R, de la Mata FJ, Bryszewska M, Miłowska K. Interaction of Cationic Carbosilane Dendrimers and Their siRNA Complexes with MCF-7 Cells Cultured in 3D Spheroids. Cells 2022; 11:cells11101697. [PMID: 35626734 PMCID: PMC9140188 DOI: 10.3390/cells11101697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
Cationic dendrimers are effective carriers for the delivery of siRNA into cells; they can penetrate cell membranes and protect nucleic acids against RNase degradation. Two types of dendrimers (CBD-1 and CBD-2) and their complexes with pro-apoptotic siRNA (Mcl-1 and Bcl-2) were tested on MCF-7 cells cultured as spheroids. Cytotoxicity of dendrimers and dendriplexes was measured using the live–dead test and Annexin V-FITC Apoptosis Detection Kit (flow cytometry). Uptake of dendriplexes was examined using flow cytometry and confocal microscopy. The live–dead test showed that for cells in 3D, CBD-2 is more toxic than CBD-1, contrasting with the data for 2D cultures. Attaching siRNA to a dendrimer molecule did not lead to increased cytotoxic effect in cells, either after 24 or 48 h. Measurements of apoptosis did not show a high increase in the level of the apoptosis marker after 24 h exposure of spheroids to CBD-2 and its dendriplexes. Measurements of the internalization of dendriplexes and microscopy images confirmed that the dendriplexes were transported into cells of the spheroids. Flow cytometry analysis of internalization indicated that CBD-2 transported siRNAs more effectively than CBD-1. Cytotoxic effects were visible after incubation with 3 doses of complexes for CBD-1 and both siRNAs.
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Affiliation(s)
- Kamila Białkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (M.B.); (K.M.)
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland;
- Correspondence:
| | - Piotr Komorowski
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland;
- Department of Biophysics, Institute of Materials Science, Lodz University of Technology, 1/15 Stefanowskiego St., 90-924 Lodz, Poland
| | - Rafael Gomez-Ramirez
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - Francisco Javier de la Mata
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - Maria Bryszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (M.B.); (K.M.)
| | - Katarzyna Miłowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (M.B.); (K.M.)
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CRISPR/Cas12a-based electrochemical biosensor for highly sensitive detection of cTnI. Bioelectrochemistry 2022; 146:108167. [DOI: 10.1016/j.bioelechem.2022.108167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/23/2022] [Accepted: 05/16/2022] [Indexed: 12/16/2022]
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Liu F, Su H, Li M, Xie W, Yan Y, Shuai Q. Zwitterionic Modification of Polyethyleneimine for Efficient In Vitro siRNA Delivery. Int J Mol Sci 2022; 23:ijms23095014. [PMID: 35563405 PMCID: PMC9100541 DOI: 10.3390/ijms23095014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Polyethylenimine (PEI) has been widely used in gene delivery. However, its high cytotoxicity and undesired non-specific protein adsorption hinder the overall delivery efficacy and the practical applications of PEI-based gene delivery systems. In this study, we prepared hydrophobically modified PEIs (H-PEIs) via the reaction of octanal with 40% of primary amines in PEI25k and PEI10k, respectively. Two common zwitterionic molecules, 1,3-propanesultone and β-propiolactone, were then used for the modification of the resulting H-PEIs to construct polycationic gene carriers with zwitterionic properties (H-zPEIs). The siRNA delivery efficiency and cytotoxicity of these materials were evaluated in Hela-Luc and A549-Luc cell lines. Compared with their respective parental H-PEIs, different degrees of zwitterionic modification showed different effects in reducing cytotoxicity and delivery efficiency. All zwitterion-modified PEIs showed excellent siRNA binding capacity, reduced nonspecific protein adsorption, and enhanced stability upon nuclease degradation. It is concluded that zwitterionic molecular modification is an effective method to construct efficient vectors by preventing undesired interactions between polycationic carriers and biomacromolecules. It may offer insights into the modification of other cationic carriers of nucleic acid drugs.
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Affiliation(s)
- Fengfan Liu
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (F.L.); (H.S.); (M.L.); (W.X.)
| | - Huahui Su
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (F.L.); (H.S.); (M.L.); (W.X.)
| | - Mengqian Li
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (F.L.); (H.S.); (M.L.); (W.X.)
| | - Wanxuan Xie
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (F.L.); (H.S.); (M.L.); (W.X.)
| | - Yunfeng Yan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
- Correspondence: (Y.Y.); (Q.S.)
| | - Qi Shuai
- National Engineering Research Center for Process Development of Active Pharmaceutical Ingredients, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (F.L.); (H.S.); (M.L.); (W.X.)
- Correspondence: (Y.Y.); (Q.S.)
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Luo T, Li J, He Y, Liu H, Deng Z, Long X, Wan Q, Ding J, Gong Z, Yang Y, Zhong S. Designing a CRISPR/Cas12a- and Au-Nanobeacon-Based Diagnostic Biosensor Enabling Direct, Rapid, and Sensitive miRNA Detection. Anal Chem 2022; 94:6566-6573. [PMID: 35451838 DOI: 10.1021/acs.analchem.2c00401] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Direct, rapid, sensitive, and selective detection of nucleic acids in complex biological fluids is crucial for medical early diagnosis. We herein combine the trans-cleavage ability of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a with Au-nanobeacon to establish a CRISPR-based biosensor, providing rapid miRNA detection with high speed and attomolar sensitivity. In this strategy, we first report that the trans-cleavage activity of CRISPR/cas12a, which was previously reported to be triggered only by target ssDNA or dsDNA, can be activated by the target miRNA directly. Therefore, this method is direct, i.e., does not need the conversion of miRNA into its complementary DNA (cDNA). Meanwhile, as compared to the traditional ssDNA reporters and molecular beacon (MB) reporters, the Au-nanobeacon reporters exhibit improved reaction kinetics and sensitivity. In this assay, the miRNA-21 could be detected with very high sensitivity in only 5 min. Finally, the proposed strategy enables rapid, sensitive, and selective miRNA determination in complex biological samples, providing a potential tool for medical early diagnosis.
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Affiliation(s)
- Tong Luo
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yao He
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Hui Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhiwei Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Xi Long
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Qingqing Wan
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiacheng Ding
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zan Gong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Shian Zhong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
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Liu X, Qiu X, Xu S, Che Y, Han L, Kang Y, Yue Y, Chen S, Li F, Li Z. A CRISPR-Cas12a-Assisted Fluorescence Platform for Rapid and Accurate Detection of Nocardia cyriacigeorgica. Front Cell Infect Microbiol 2022; 12:835213. [PMID: 35310854 PMCID: PMC8924655 DOI: 10.3389/fcimb.2022.835213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/15/2022] [Indexed: 12/26/2022] Open
Abstract
Nocardia cyriacigeorgica has gradually become a common pathogen in clinical microbial infections. Identification of Nocardia at the species level is essential to assess the susceptibility and pathogenicity of antimicrobials. However, there is no suitable method for rapid and accurate laboratory detection of N. cyriacigeorgica. In this study, we combined PCR amplification with the CRISPR-Cas12a system to establish a novel detection platform, named CRISPR-PCR, and applied it to the detection of N. cyriacigeorgica in clinical samples. The Cas12a protein exhibited collateral cleavage activity following CRISPR RNA binding to specific targets, then indiscriminately cleaved nearby single-stranded DNA, and this was evaluated for diagnostic nucleic acid detection by measuring the fluorescence signal using a fluorescence reader. The assay takes only 2 h, including DNA extraction for 20 min, nucleic acid pre-amplification for 70 min, and fluorescence detection for 20 min. The limit of detection for N. cyriacigeorgica was 10-3 ng and the specificity was 100%. Thus, the N. cyriacigeorgica CRISPR-PCR assay is a rapid and specific method for detecting N. cyriacigeorgica, and the CRISPR-PCR fluorescence detection platform has great potential for detection of other pathogens.
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Affiliation(s)
- Xueping Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaotong Qiu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuai Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Che
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lichao Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yutong Kang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Yue
- Key Laboratory of the Ministry of Education for the Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, China
| | - Shenglin Chen
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Fang Li
- Department of Medicine, Tibet University, Lhasa, China
| | - Zhenjun Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- *Correspondence: Zhenjun Li,
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50
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Safdar S, Driesen S, Leirs K, De Sutter D, Eyckerman S, Lammertyn J, Spasic D. Engineered tracrRNA for enabling versatile CRISPR-dCas9-based biosensing concepts. Biosens Bioelectron 2022; 206:114140. [PMID: 35247858 DOI: 10.1016/j.bios.2022.114140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 12/26/2022]
Abstract
In recent years, CRISPR-Cas (stands for: clustered regularly interspaced short palindromic repeats - CRISPR associated protein) based technologies have gained increasing attention in the biosensing field. Thanks to excellent sequence specificity, their use is of particular interest for detecting nucleic acid (NA) targets. In this context, signal generation and amplification can be realized by employing the cis-cleavage activity of the Cas9 protein, although other options involving the catalytically inactive dead Cas9 (dCas9) are increasingly explored. The latter are however mostly based on complex protein engineering processes and often lack efficient signal amplification. Here we showed for the first time that flexible signal generation and amplification properties can be integrated into the CRISPR-dCas9 complex based on a straightforward incorporation of a DNA sequence into the trans-activating CRISPR RNA (tracrRNA). The intrinsic nuclease activity of the engineered complex remained conserved, while the incorporated DNA stretch enabled two modes of amplified fluorescent signal generation: (1) as an RNA-cleaving DNA-based enzyme (DNAzyme) or (2) as hybridization site for biotinylated DNA probes, allowing subsequent enzyme labeling. Both signal generation strategies were demonstrated in solution as well as while coupled to a solid surface. Finally, in a proof of concept bioassay, we demonstrated the successful detection of single stranded DNA on magnetic microbeads using the engineered CRISPR-dCas9 complex. Thanks to the flexibility of incorporating different NA-based signal generation and amplification strategies, this novel NA engineering approach holds enormous promise for many new CRISPR-based biosensing applications.
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Affiliation(s)
- Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Seppe Driesen
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Karen Leirs
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, UGent Department of Biomolecular Medicine, Technologiepark 75, Zwijnaarde, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, UGent Department of Biomolecular Medicine, Technologiepark 75, Zwijnaarde, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
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