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Lei X, Ding L, Yang X, Xu F, Wu Y, Yu S. PAIT effect: Padlock activator inhibits the trans-cleavage activity of CRISPR/Cas12a. Biosens Bioelectron 2024; 263:116607. [PMID: 39067412 DOI: 10.1016/j.bios.2024.116607] [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: 04/23/2024] [Revised: 07/09/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The CRISPR/Cas12a system is increasingly used in biosensor development. However, high background signal and low sensitivity for the non-nucleic acid targets detection is challenging. Here, a padlock activator which could inhibit the trans-cleavage activity of CRISPR/Cas12a system in the intact form by steric hindrance effect (PAIT effect) was designed for non-nucleic acid targets detection. The PAIT effect disappeared when padlock activator was separated into two split activators. To verify the feasibility of padlock activator, a Ca2+ sensor was developed based on PAIT effect with the assistance of DNAzyme, activity of which was Ca2+ dependent. In the presence of Ca2+, DNAzyme was activated to cleave its substrate, a padlock activator modified with adenine ribonucleotide, into split padlock activators which would trigger the trans-cleavage activity of Cas12a to generate fluorescence. There was a mathematical relationship between the fluorescence intensity and the logarithm of Ca2+ concentration ranging from 10 pM to 1 nM, with a limit of detection of 3.98 pM. The little interference of Mg2+, Mn2+, Cd2+, Cu2+, Na+, Al3+, K+, Fe2+, and Fe3+ indicated high selectivity. Recovery ranged from 93.32% to 103.28% with RSDs from 1.87% to 12.74% showed a good accuracy and reliability. Furthermore, the proposed sensor could be applied to detect Ca2+ in mineral water, milk powder and urine. The results were consistent with that of flame atomic absorption spectroscopy. Thus, PAIT effect is valuable for expanding the application boundary of CRISPR/Cas12a system.
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Affiliation(s)
- Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Xiaonan Yang
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Feng Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
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2
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Xiao H, Xu J, Liu Y, Feng W, Pang B, Tao J, Zhang H. Integration of a Cas12a-mediated DNAzyme actuator with efficient RNA extraction for ultrasensitive colorimetric detection of viral RNA. Biosens Bioelectron 2024; 260:116429. [PMID: 38838573 DOI: 10.1016/j.bios.2024.116429] [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: 03/01/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024]
Abstract
Developing highly sensitive and specific on-site tests is imperative to strengthen preparedness against future emerging infectious diseases. Here, we describe the construction of a Cas12a-mediated DNAzyme actuator capable of converting the recognition of a specific DNA sequence into an amplified colorimetric signal. To address viral RNA extraction challenges for on-site applications, we developed a rapid and efficient method capable of lysing the viral particles, preserving the released viral RNA, and concentrating the viral RNA. Integration of the DNAzyme actuator with the viral RNA extraction method and loop-mediated isothermal amplification enables a streamlined colorimetric assay for highly sensitive colorimetric detection of respiratory RNA viruses in gargle and saliva. This assay can detect as few as 83 viral particles/100 μL in gargle and 166 viral particles/100 μL in saliva. The entire assay, from sample processing to visual detection, was completed within 1 h at a single controlled temperature. We validated the assay by detecting SARS-CoV-2 in 207 gargle and saliva samples, achieving a clinical sensitivity of 96.3 % and specificity of 100%. The assay is adaptable for detecting specific nucleic acid sequences in other pathogens and is suitable for resource-limited settings.
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Affiliation(s)
- Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - JingYang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Bo Pang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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3
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Zeng Q, Zhou M, Deng W, Gao Q, Li Z, Wu L, Liang D. Sensitive and visual detection of SARS-CoV-2 using RPA-Cas12a one-step assay with ssDNA-modified crRNA. Anal Chim Acta 2024; 1309:342693. [PMID: 38772660 DOI: 10.1016/j.aca.2024.342693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND CRISPR-Cas12a based one-step assays are widely used for nucleic acid detection, particularly for pathogen detection. However, the detection capability of the one-step assay is reduced because the Cas12a protein competes with the isothermal amplification enzymes for the target DNA and cleaves it. Therefore, the key to improving the sensitivity of the one-step assay is to address the imbalance between isothermal amplification and CRISPR detection. In previous study, we developed a Cas12a one-step assay using single-stranded DNA (ssDNA)-modified crRNA (mD-crRNA) and applied this method for the detection of pathogenic DNA. RESULTS Here, we utilized mD-crRNA to establish a sensitive one-step assay that enables the visual detection of SARS-CoV-2 under ultraviolet light, achieving a detection limit of 5 aM without cross-reactivity. The sensitivity of mD-crRNA in the one-step assay was 100-fold higher than that of wild-type crRNA. Mechanistic studies revealed that the addition of ssDNA at the 3' end of mD-crRNA attenuates the binding affinity between the Cas12a-mD-crRNA complex and the target DNA. Consequently, this reduction in binding affinity decreases the cis-cleavage activity of Cas12a, mitigating its cleavage of the target DNA in the one-step assay. As a result, there is an augmentation in the amplification and accumulation of target DNA, thereby enhancing detection sensitivity. In the clinical testing of 40 SARS-CoV-2 RNA samples, the concordance between the results of the one-step assay and known qPCR results was 97.5 %. SIGNIFICANCE The one-step assay using mD-crRNA proves to be highly sensitive and specificity and visually effective for the detection of SARS-CoV-2. Our study delves into the application of the mD-crRNA-mediated one-step assay in nucleic acid detection and its associated reaction mechanism. This holds great significance in addressing the inherent incompatibility issues between isothermal amplification and CRISPR detection.
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Affiliation(s)
- Qinlong Zeng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Miaojin Zhou
- MOE Key Lab of Rare Pediatric Diseases, Department of Cell Biology and Genetics, School of Basic Medical Sciences, University of South China, Hengyang, 421200, China
| | - Weiheng Deng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Qian Gao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
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4
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Sen P, Zhang Z, Sakib S, Gu J, Li W, Adhikari BR, Motsenyat A, L'Heureux-Hache J, Ang JC, Panesar G, Salena BJ, Yamamura D, Miller MS, Li Y, Soleymani L. High-Precision Viral Detection Using Electrochemical Kinetic Profiling of Aptamer-Antigen Recognition in Clinical Samples and Machine Learning. Angew Chem Int Ed Engl 2024; 63:e202400413. [PMID: 38458987 DOI: 10.1002/anie.202400413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
High-precision viral detection at point of need with clinical samples plays a pivotal role in the diagnosis of infectious diseases and the control of a global pandemic. However, the complexity of clinical samples that often contain very low viral concentrations makes it a huge challenge to develop simple diagnostic devices that do not require any sample processing and yet are capable of meeting performance metrics such as very high sensitivity and specificity. Herein we describe a new single-pot and single-step electrochemical method that uses real-time kinetic profiling of the interaction between a high-affinity aptamer and an antigen on a viral surface. This method generates many data points per sample, which when combined with machine learning, can deliver highly accurate test results in a short testing time. We demonstrate this concept using both SARS-CoV-2 and Influenza A viruses as model viruses with specifically engineered high-affinity aptamers. Utilizing this technique to diagnose COVID-19 with 37 real human saliva samples results in a sensitivity and specificity of both 100 % (27 true negatives and 10 true positives, with 0 false negative and 0 false positive), which showcases the superb diagnostic precision of this method.
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Affiliation(s)
- Payel Sen
- Department of Engineering Physics, McMaster University, Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | - Sadman Sakib
- Department of Engineering Physics, McMaster University, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | - Wantong Li
- Department of Engineering Physics, McMaster University, Canada
| | | | - Ariel Motsenyat
- Department of Integrated Biomedical Engineering and Health Sciences, McMaster University, Canada
| | | | - Jann C Ang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- McMaster Immunology Research Centre, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Gurpreet Panesar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | | | - Debora Yamamura
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Canada
| | - Matthew S Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- McMaster Immunology Research Centre, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- School of Biomedical Engineering, McMaster University, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- School of Biomedical Engineering, McMaster University, Canada
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5
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Yu S, Lei X, Qu C. MicroRNA Sensors Based on CRISPR/Cas12a Technologies: Evolution From Indirect to Direct Detection. Crit Rev Anal Chem 2024:1-17. [PMID: 38489095 DOI: 10.1080/10408347.2024.2329229] [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: 03/17/2024]
Abstract
MicroRNA (miRNA) has emerged as a promising biomarker for disease diagnosis and a potential therapeutic targets for drug development. The detection of miRNA can serve as a noninvasive tool in diseases diagnosis and predicting diseases prognosis. CRISPR/Cas12a system has great potential in nucleic acid detection due to its high sensitivity and specificity, which has been developed to be a versatile tool for nucleic acid-based detection of targets in various fields. However, conversion from RNA to DNA with or without amplification operation is necessary for miRNA detection based on CRISPR/Cas12a system, because dsDNA containing PAM sequence or ssDNA is traditionally considered as the activator of Cas12a. Until recently, direct detection of miRNA by CRISPR/Cas12a system has been reported. In this review, we provide an overview of the evolution of biosensors based on CRISPR/Cas12a for miRNA detection from indirect to direct, which would be beneficial to the development of CRISPR/Cas12a-based sensors with better performance for direct detection of miRNA.
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Affiliation(s)
- Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chenling Qu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
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6
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Zhou J, Li Z, Seun Olajide J, Wang G. CRISPR/Cas-based nucleic acid detection strategies: Trends and challenges. Heliyon 2024; 10:e26179. [PMID: 38390187 PMCID: PMC10882038 DOI: 10.1016/j.heliyon.2024.e26179] [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: 12/13/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
CRISPR/Cas systems have become integral parts of nucleic acid detection apparatus and biosensors. Various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/Cas12, CRISPR/Cas13, CRISPR/Cas14 and CRISPR/Cas3 utilize different mechanisms to detect or differentiate biological activities and nucleotide sequences. Usually, CRISPR/Cas-based nucleic acid detection systems are combined with polymerase chain reaction, loop-mediated isothermal amplification, recombinase polymerase amplification and transcriptional technologies for effective diagnostics. Premised on these, many CRISPR/Cas-based nucleic acid biosensors have been developed to detect nucleic acids of viral and bacterial pathogens in clinical samples, as well as other applications in life sciences including biosecurity, food safety and environmental assessment. Additionally, CRISPR/Cas-based nucleic acid detection systems have showed better specificity compared with other molecular diagnostic methods. In this review, we give an overview of various CRISPR/Cas-based nucleic acid detection methods and highlight some advances in their development and components. We also discourse some operational challenges as well as advantages and disadvantages of various systems. Finally, important considerations are offered for the improvement of CRISPR/Cas-based nucleic acid testing.
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Affiliation(s)
- Jian Zhou
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510000, People's Republic of China
- Department of Laboratory Medicines, the First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, People's Republic of China
| | - Zhuo Li
- Department of Laboratory Medicines, the First Affiliated Hospital of Xi'an Medical University, Xi'an, 710077, People's Republic of China
| | - Joshua Seun Olajide
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510000, People's Republic of China
| | - Gang Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, 510000, People's Republic of China
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7
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Das D, Lin CW, Chuang HS. On-chip screening of SARS-CoV-2 cDNA by LAMP-integrated rotational diffusometry. Talanta 2024; 267:125253. [PMID: 37776805 DOI: 10.1016/j.talanta.2023.125253] [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: 07/11/2023] [Revised: 09/10/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023]
Abstract
The unprecedented pandemic has raised the demand for prompt, precise, and large-scale virus detection techniques to control the transmission of contagious illnesses. In this study, a loop-mediated isothermal amplification (LAMP) based on-chip platform was developed to address this challenge using rotational diffusometry and functionalized Janus particles. A recombinant plasmid containing a cDNA sequence of the SARS-CoV-2 non-structural protein 2 (nsp2) gene was employed here as a proof-of-concept for COVID-19 detection. Specifically, designed primers and the functionalized Janus particles were simultaneously loaded on a microfluidic chip to perform the LAMP reaction on a hot plate. The optimal Janus particle concentrations for diffusometric analysis were thoroughly validated, and the performance of the on-chip LAMP reaction was assessed using thermal image analysis. Utilization of the highly sensitive rotational diffusometry achieved a limit of detection of 1 pg/μL in just 10 min with a sample volume of 20 μL. Our method delivered a tenfold higher sensitivity than the conventional method by utilizing only half of its usual required time. Overall, this study proposes a potential nucleic acid (NA) amplification device to aid the rapid diagnosis of various diseases by modifying the primers for different target genes.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung, 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, 701, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, 701, Taiwan.
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8
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Chen J, Ren B, Wang Z, Wang Q, Bi J, Sun X. Multiple Isothermal Amplification Coupled with CRISPR-Cas14a for the Naked-eye and Colorimetric Detection of Aflatoxin B1. ACS APPLIED MATERIALS & INTERFACES 2023; 15:55423-55432. [PMID: 38014527 DOI: 10.1021/acsami.3c13331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Aflatoxin B1 (AFB1) is highly toxic and challenging to remove, posing significant risks to both human health and economic development. Therefore, there is an urgent need to develop rapid, simple, and sensitive detection technologies. In this study, we introduce a naked-eye and colorimetric method based on multiple isothermal amplifications coupled with CRISPR-Cas14a and investigate its biosensing properties. This technique utilizes composite nanoprobes (MAPs) comprising magnetic nanoparticles and gold nanoparticles. AFB1 is efficiently identified through an aptamer competition process facilitated by magnetic nanoparticles , which triggers multiple isothermal amplification. This converts trace amounts of the toxin into a large quantity of DNA signal. Upon specific activation of the CRISPR-Cas14a complex, the MAPs are cleaved, resulting in significant changes in both color and colorimetric signal. The method demonstrates acceptable sensitivity, with a detection limit of 31.90 pg mL-1 and a wide detection range from 0.05 to 10 ng mL-1. Furthermore, the assay exhibits satisfactory specificity and high accuracy when it is applied to practical samples. Our approach offers a universal sensing platform with potential applications in food safety, environmental monitoring, and clinical diagnostics.
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Affiliation(s)
- Jiaojiao Chen
- College of Acupuncture and Orthopedics, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Beizhuo Ren
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Zhigang Wang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Qian Wang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Jing Bi
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Xuan Sun
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China
- Hubei Shizhen Laboratory, Wuhan 430061, China
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9
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Moon J, Liu C. Asymmetric CRISPR enabling cascade signal amplification for nucleic acid detection by competitive crRNA. Nat Commun 2023; 14:7504. [PMID: 37980404 PMCID: PMC10657364 DOI: 10.1038/s41467-023-43389-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Abstract
Nucleic acid detection powered by CRISPR technology provides a rapid, sensitive, and deployable approach to molecular diagnostics. While exciting, there remain challenges limiting its practical applications, such as the need for pre-amplification and the lack of quantitative ability. Here, we develop an asymmetric CRISPR assay for cascade signal amplification detection of nucleic acids by leveraging the asymmetric trans-cleavage behavior of competitive crRNA. We discover that the competitive reaction between a full-sized crRNA and split crRNA for CRISPR-Cas12a can induce cascade signal amplification, significantly improving the target detection signal. In addition, we find that CRISPR-Cas12a can recognize fragmented RNA/DNA targets, enabling direct RNA detection by Cas12a. Based on these findings, we apply our asymmetric CRISPR assay to quantitatively detect microRNA without the need for pre-amplification, achieving a detection sensitivity of 856 aM. Moreover, using this method, we analyze and quantify miR-19a biomarker in plasma samples from bladder cancer patients. This asymmetric CRISPR assay has the potential to be widely applied for simple and sensitive nucleic acid detection in various diagnostic settings.
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Affiliation(s)
- Jeong Moon
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06032, US
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06032, US.
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10
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Sharma N, Chi CH, Dabur D, Tsai ACC, Wu HF. SnO 2-xN x based tpod nanostructure for SARS-CoV2 spike protein detection. ENVIRONMENTAL RESEARCH 2023; 234:116505. [PMID: 37406724 DOI: 10.1016/j.envres.2023.116505] [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: 05/11/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
The worldwide spreading of severe acute respiratory syndrome SARS-CoV2 pandemic, a massive setback to every human being. In response to strategies actions against Covid-19 spreading many detection, prevention, and post-measures are being studied in large capacities. Association of SARS-CoV2 with ACE2 is well acknowledged and used for developing point-of-care detection kits. Recently, cases and studies have surfaced showing relation of ACE I/D polymorphism with spreading of SARS-CoV2 and highlighted a slip section towards detection and these studies show specificity with older males, high diabetes, and hypertension. To address the raised concern, we report synthesis of unique SnO2-xNx tpod nanostructure, showing affirmative attachment to both ACE1 and ACE2 efficiently. The attachment is examined in different ratios and studied with μ-Raman spectroscopy. The tpod nanostructure has served with its signature raman signals and used as probe for detection of SARS-CoV2 spike protein (S1). The linearity response for tpod raman signal at 630.4 cm-1 shows R2 0.9705, comparatively peak 1219.13 cm-1 show R2 0.9865 and calculated limit of detection of 35 nM.
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Affiliation(s)
- Nallin Sharma
- Department of Chemistry, National Sun Yat-Sen University, 70, Lien-Hai Road, Kaohsiung, 80424, Taiwan; Jeenn Chwanq Enterprise Co. Ltd, No. 14, Dazhu Road, Kaohsiung, 833, Taiwan
| | - Chia-Hung Chi
- Department of Chemistry, National Sun Yat-Sen University, 70, Lien-Hai Road, Kaohsiung, 80424, Taiwan
| | - Deepak Dabur
- International PhD Program for Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | | | - Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, 70, Lien-Hai Road, Kaohsiung, 80424, Taiwan; Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan; International PhD Program for Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan; Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan.
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11
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Ke X, Hu Y, Chen C, Hu T. A one-tube dual-readout biosensor for detection of nucleic acids and non-nucleic acids using CRISPR-ALP tandem assay. Analyst 2023; 148:4356-4364. [PMID: 37555739 DOI: 10.1039/d3an00918a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have been considered a next-generation molecular diagnosis tool. Single-readout mode has been extensively employed in massive CRISPR/Cas12a-based biosensors. In this work, we propose a one-tube dual-readout biosensor (CRISAT) for the first time for the detection of ultrasensitive nucleic acids and non-nucleic acids developed by harnessing CRISPR-ALP tandem assay. In the presence of a target, Cas12a is activated to randomly cut the single-stranded hyDNA sequence of MB@hyDNA-cALP, thus releasing abundant alkaline phosphatase (ALP) in the supernatant solution. By using 4-aminophenol phosphate as the substrate of ALP, p-aminophenol is produced, which then reacts with N-[3-(trimethoxysilyl)propyl]ethylenediamine or diethylenetriamine to generate silicon-containing polymer carbon dots (Si PCDs) or polymer carbon dots (PCDs) in situ, which can be observed by the naked eye or detected using a fluorescent device in the same solution. Using this strategy, a fluorescence and colorimetry dual-readout nanoplatform for CRISPR-based biosensors can be rationally developed. We ascertain the applicability of CRISAT by detecting the SARS-CoV-2 pseudovirus, achieving superior sensitivity and specificity. With simple modification of crRNAs, the CRISAT platform can also be employed to detect monkeypox virus (MPXV) and non-nucleic acids of adenosine triphosphate (ATP). This work shows great potential for the detection of nucleic acids and non-nucleic acids.
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Affiliation(s)
- Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
| | - Yi Hu
- Hefei National Lab for Physical Sciences at the Microscale and the Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, China
| | - Chuanxia Chen
- School of Materials Science and Engineering, University of Jinan, Jinan, Shandong, 250022, China.
| | - Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
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12
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Wu Z, Yu L, Shi W, Ma J. Argonaute protein-based nucleic acid detection technology. Front Microbiol 2023; 14:1255716. [PMID: 37744931 PMCID: PMC10515653 DOI: 10.3389/fmicb.2023.1255716] [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: 07/09/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
It is vital to diagnose pathogens quickly and effectively in the research and treatment of disease. Argonaute (Ago) proteins are recently discovered nucleases with nucleic acid shearing activity that exhibit specific recognition properties beyond CRISPR-Cas nucleases, which are highly researched but restricted PAM sequence recognition. Therefore, research on Ago protein-mediated nucleic acid detection technology has attracted significant attention from researchers in recent years. Using Ago proteins in developing nucleic acid detection platforms can enable efficient, convenient, and rapid nucleic acid detection and pathogen diagnosis, which is of great importance for human life and health and technological development. In this article, we introduce the structure and function of Argonaute proteins and discuss the latest advances in their use in nucleic acid detection.
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Affiliation(s)
- Zhiyun Wu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Li Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Institute of Stem Cell, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Jinhong Ma
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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13
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Deng B, Xue J. HIV infection detection using CRISPR/Cas systems: Present and future prospects. Comput Struct Biotechnol J 2023; 21:4409-4423. [PMID: 37711183 PMCID: PMC10498128 DOI: 10.1016/j.csbj.2023.09.005] [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: 06/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection poses substantial medical risks to global public health. An essential strategy to combat the HIV epidemic is timely and effective virus testing. CRISPR-based assays combine the highly compatible CRISPR system with different elements, yielding portability, digitization capabilities, low economic burden and low operational thresholds. The application of CRISPR-based assays has demonstrated rapid, accurate, and accessible means of pathogen testing, suggesting great potential as point-of-care (POC) assays. This review outlines the different types of CRISPR/Cas systems based on Cas proteins and their applications for the detection of HIV. Additionally, we also offer an overview of future perspectives on CRISPR-based methods for HIV detection, including advances in nucleic acid amplification-free testing, improved personal testing, and refined testing for HIV genotypes and drug-resistant strains.
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Affiliation(s)
- Bingpeng Deng
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Jing Xue
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
- Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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14
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Annamalai A, Karuppaiya V, Ezhumalai D, Cheruparambath P, Balakrishnan K, Venkatesan A. Nano-based techniques: A revolutionary approach to prevent covid-19 and enhancing human awareness. J Drug Deliv Sci Technol 2023; 86:104567. [PMID: 37313114 PMCID: PMC10183109 DOI: 10.1016/j.jddst.2023.104567] [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: 01/25/2023] [Revised: 04/22/2023] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
In every century of history, there are many new diseases emerged, which are not even cured by many developed countries. Today, despite of scientific development, new deadly pandemic diseases are caused by microorganisms. Hygiene is considered to be one of the best methods of avoiding such communicable diseases, especially viral diseases. Illness caused by SARS-CoV-2 was termed COVID-19 by the WHO, the acronym derived from "coronavirus disease 2019. The globe is living in the worst epidemic era, with the highest infection and mortality rate owing to COVID-19 reaching 6.89% (data up to March 2023). In recent years, nano biotechnology has become a promising and visible field of nanotechnology. Interestingly, nanotechnology is being used to cure many ailments and it has revolutionized many aspects of our lives. Several COVID-19 diagnostic approaches based on nanomaterial have been developed. The various metal NPs, it is highly anticipated that could be viable and economical alternatives for treating drug resistant in many deadly pandemic diseases in near future. This review focuses on an overview of nanotechnology's increasing involvement in the diagnosis, prevention, and therapy of COVID-19, also this review provides readers with an awareness and knowledge of importance of hygiene.
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Affiliation(s)
- Asaikkutti Annamalai
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
| | - Vimala Karuppaiya
- Cancer Nanomedicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, 636 011, Tamil Nadu, India
| | - Dhineshkumar Ezhumalai
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | | | - Kaviarasu Balakrishnan
- Dr. Krishnamoorthi Foundation for Advanced Scientific Research, Vellore, 632 001, Tamil Nadu, India
- Manushyaa Blossom Private Limited, Chennai, 600 102, Tamil Nadu, India
| | - Arul Venkatesan
- Marine Biotechnology Laboratory, Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, 605 014, Puducherry, India
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15
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Xu J, Liu Z, Zhang Z, Wu T. Unlocking the Full Potential of Cas12a: Exploring the Effects of Substrate and Reaction Conditions on Trans-Cleavage Activity. Anal Chem 2023. [PMID: 37392174 DOI: 10.1021/acs.analchem.3c01307] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
The trans-cleavage activity of Cas12a has been widely used with various applications. Here, we report that the trans-cleavage activity of Cas12a can be significantly affected by the fluorescent probe length and reaction buffer. The optimal probe length for Cas12a is found to be 15 nucleotides, and the optimal buffer is NEBuffer 4. Compared to the popularly used reaction conditions, the activity of Cas12a is improved by about 50-fold. In addition, the detection limit of Cas12a for DNA targets has been reduced by nearly three orders of magnitude. Our method provides a powerful tool for Cas12a trans-cleavage activity applications.
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Affiliation(s)
- Jie Xu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhujun Liu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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16
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Nouri R, Jiang Y, Politza AJ, Liu T, Greene WH, Zhu Y, Nunez JJ, Lian X, Guan W. STAMP-Based Digital CRISPR-Cas13a for Amplification-Free Quantification of HIV-1 Plasma Viral Loads. ACS NANO 2023; 17:10701-10712. [PMID: 37252938 PMCID: PMC11240847 DOI: 10.1021/acsnano.3c01917] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Quantification of HIV RNA in plasma is critical for identifying the disease progression and monitoring the effectiveness of antiretroviral therapy. While RT-qPCR has been the gold standard for HIV viral load quantification, digital assays could provide an alternative calibration-free absolute quantification method. Here, we reported a Self-digitization Through Automated Membrane-based Partitioning (STAMP) method to digitalize the CRISPR-Cas13 assay (dCRISPR) for amplification-free and absolute quantification of HIV-1 viral RNAs. The HIV-1 Cas13 assay was designed, validated, and optimized. We evaluated the analytical performances with synthetic RNAs. With a membrane that partitions ∼100 nL of reaction mixture (effectively containing 10 nL of input RNA sample), we showed that RNA samples spanning 4 orders of dynamic range between 1 fM (∼6 RNAs) to 10 pM (∼60k RNAs) could be quantified as fast as 30 min. We also examined the end-to-end performance from RNA extraction to STAMP-dCRISPR quantification using 140 μL of both spiked and clinical plasma samples. We demonstrated that the device has a detection limit of approximately 2000 copies/mL and can resolve a viral load change of 3571 copies/mL (equivalent to 3 RNAs in a single membrane) with 90% confidence. Finally, we evaluated the device using 140 μL of 20 patient plasma samples (10 positives and 10 negatives) and benchmarked the performance with RT-PCR. The STAMP-dCRISPR results agree very well with RT-PCR for all negative and high positive samples with Ct < 32. However, the STAMP-dCRISPR is limited in detecting low positive samples with Ct > 32 due to the subsampling errors. Our results demonstrated a digital Cas13 platform that could offer an accessible amplification-free quantification of viral RNAs. By further addressing the subsampling issue with approaches such as preconcentration, this platform could be further exploited for quantitatively determining viral load for an array of infectious diseases.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Wallace H Greene
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Yusheng Zhu
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Jonathan J Nunez
- Department of Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, Pennsylvania 17033, United States
| | - Xiaojun Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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17
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Zhu Y, Odiwuor N, Sha Z, Chen Y, Shao N, Wu X, Chen J, Li Y, Guo S, Shi D, Liu P, Zhang Y, Wei H, Tao SC. Rapid and Accurate Detection of SARS-CoV-2 Using an iPad-Controlled, High-Throughput, Portable, and Multiplex Hive-Chip Platform ( HiCube). ACS Sens 2023; 8:1960-1970. [PMID: 37093957 PMCID: PMC10152401 DOI: 10.1021/acssensors.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
Rapid and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the most effective measures to control the coronavirus disease 2019 (COVID-19) pandemic. However, there is still lack of an ideal detection platform capable of high sample throughput, portability, and multiplicity. Herein, by combining Hive-Chip (capillary microarray) and reverse transcriptional loop-mediated isothermal amplification (RT-LAMP), we developed an iPad-controlled, high-throughput (48 samples at one run), portable (smaller than a backpack), multiplex (monitoring 8 gene fragments in one reaction), and real-time detection platform for SARS-CoV-2 detection. This platform is composed of a portable Hive-Chip device (HiCube; 32.7 × 29.7 × 20 cm, 5 kg), custom-designed software, and optimized Hive-Chips. RT-LAMP primers targeting seven SARS-CoV-2 genes (S, E, M, N, ORF1ab, ORF3a, and ORF7a) and one positive control (human RNase P) were designed and prefixed in the Hive-Chip. On-chip RT-LAMP showed that the limit of detection (LOD) of SARS-CoV-2 synthetic RNAs is 1 copy/μL, and there is no cross-reaction among different target genes. The platform was validated by 100 clinical samples of SARS-CoV-2, and the results were highly consistent with those of the traditional real-time PCR assay. In addition, on-chip detection of 6 other respiratory pathogens showed no cross-reactivity. Overall, our platform has great potential for fast, accurate, and on-site detection of SARS-CoV-2.
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Affiliation(s)
- Yuanshou Zhu
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
- School of Biomedical Engineering,
Shanghai Jiao Tong University, Shanghai 200240,
China
| | - Nelson Odiwuor
- CAS Key Laboratory of Special Pathogens and Biosafety,
Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese
Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of
Science, Beijing 100049, China
| | - Zigan Sha
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Yanjing Chen
- Sports & Medicine Integrative Innovation Center
(SMIC), Capital University of Physical Education and Sports,
Beijing 100191, China
| | - Ning Shao
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Xudong Wu
- Department of Biomedical Engineering, School of Medicine,
Tsinghua University, Beijing 100084,
China
| | - Jianwei Chen
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Shujuan Guo
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Dawei Shi
- National Institutes for Food and Drug
Control, Beijing 102629, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine,
Tsinghua University, Beijing 100084,
China
| | - Yan Zhang
- Sports & Medicine Integrative Innovation Center
(SMIC), Capital University of Physical Education and Sports,
Beijing 100191, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety,
Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese
Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of
Science, Beijing 100049, China
| | - Sheng-ce Tao
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
- School of Biomedical Engineering,
Shanghai Jiao Tong University, Shanghai 200240,
China
- Perfect Diagnosis Biotechnology (ZhenCe)
Co., Ltd., Shanghai 200240, China
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18
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Yang H, Ledesma-Amaro R, Gao H, Ren Y, Deng R. CRISPR-based biosensors for pathogenic biosafety. Biosens Bioelectron 2023; 228:115189. [PMID: 36893718 DOI: 10.1016/j.bios.2023.115189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Pathogenic biosafety is a worldwide concern. Tools for analyzing pathogenic biosafety, that are precise, rapid and field-deployable, are highly demanded. Recently developed biotechnological tools, especially those utilizing CRISPR/Cas systems which can couple with nanotechnologies, have enormous potential to achieve point-of-care (POC) testing for pathogen infection. In this review, we first introduce the working principle of class II CRISPR/Cas system for detecting nucleic acid and non-nucleic acid biomarkers, and highlight the molecular assays that leverage CRISPR technologies for POC detection. We summarize the application of CRISPR tools in detecting pathogens, including pathogenic bacteria, viruses, fungi and parasites and their variants, and highlight the profiling of pathogens' genotypes or phenotypes, such as the viability, and drug-resistance. In addition, we discuss the challenges and opportunities of CRISPR-based biosensors in pathogenic biosafety analysis.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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19
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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20
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Chen Z, Wu C, Yuan Y, Xie Z, Li T, Huang H, Li S, Deng J, Lin H, Shi Z, Li C, Hao Y, Tang Y, You Y, Al-Hartomy OA, Wageh S, Al-Sehemi AG, Lu R, Zhang L, Lin X, He Y, Zhao G, Li D, Zhang H. CRISPR-Cas13a-powered electrochemical biosensor for the detection of the L452R mutation in clinical samples of SARS-CoV-2 variants. J Nanobiotechnology 2023; 21:141. [PMID: 37120637 PMCID: PMC10148006 DOI: 10.1186/s12951-023-01903-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Since the end of 2019, a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has deprived numerous lives worldwide, called COVID-19. Up to date, omicron is the latest variant of concern, and BA.5 is replacing the BA.2 variant to become the main subtype rampaging worldwide. These subtypes harbor an L452R mutation, which increases their transmissibility among vaccinated people. Current methods for identifying SARS-CoV-2 variants are mainly based on polymerase chain reaction (PCR) followed by gene sequencing, making time-consuming processes and expensive instrumentation indispensable. In this study, we developed a rapid and ultrasensitive electrochemical biosensor to achieve the goals of high sensitivity, the ability of distinguishing the variants, and the direct detection of RNAs from viruses simultaneously. We used electrodes made of MXene-AuNP (gold nanoparticle) composites for improved sensitivity and the CRISPR/Cas13a system for high specificity in detecting the single-base L452R mutation in RNAs and clinical samples. Our biosensor will be an excellent supplement to the RT-qPCR method enabling the early diagnosis and quick distinguishment of SARS-CoV-2 Omicron BA.5 and BA.2 variants and more potential variants that might arise in the future.
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Affiliation(s)
- Zhi Chen
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong, 511518, People's Republic of China
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Chenshuo Wu
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, 313001, People's Republic of China
| | - Yuxuan Yuan
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Zhongjian Xie
- Institute of Pediatrics, Shenzhen Children's Hospital, Institute of Pediatrics, Shenzhen Children's Hospital, Clinical Medical College of Southern University of Science and Technology, Shenzhen, Guangdong, 518038, P. R. China
| | - Tianzhong Li
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Hao Huang
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong, 511518, People's Republic of China
| | - Shuang Li
- College of Pharmacy, Dali University, Dali, 671000, P. R. China
| | - Jiefeng Deng
- College of Pharmacy, Dali University, Dali, 671000, P. R. China
| | - Huiling Lin
- Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Zhe Shi
- School of Physics & New Energy, Xuzhou University of Technology, Xuzhou, Jiangsu, 221018, People's Republic of China
| | - Chaozhou Li
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yabin Hao
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yuxuan Tang
- Shenzhen Metasensing Tech Limited Company, Shenzhen, 518000, People's Republic of China
| | - Yuehua You
- Department of Stomatology, Longhua People's Hospital Affiliated to Southern Medical University, Shenzhen, 518109, People's Republic of China
- School of Stomatology, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Omar A Al-Hartomy
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Swelm Wageh
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Abdullah G Al-Sehemi
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Ruitao Lu
- Shenzhen International Institute for Biomedical Research, Shenzhen, 518110, China
| | - Ling Zhang
- Key Lab of Semiconductor Materials Science, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Xuechun Lin
- Laboratory of All-Solid-State Light Sources, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, 518055, P. R. China.
| | - Guojun Zhao
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, Guangdong, 511518, People's Republic of China.
| | - Defa Li
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong, 518038, People's Republic of China.
| | - Han Zhang
- International Collaborative Laboratory of 2D, Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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21
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Zhou C, Li W, Zhao Y, Gu K, Liao Z, Guo B, Huang Z, Yang M, Wei H, Ma P, Li C, Li H, Tang Y, Lei C, Wang H. Sensitive detection of viable salmonella bacteria based on tertiary cascade signal amplification via splintR ligase ligation-PCR amplification-CRISPR/Cas12a cleavage. Anal Chim Acta 2023; 1248:340885. [PMID: 36813454 DOI: 10.1016/j.aca.2023.340885] [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: 08/27/2022] [Revised: 01/04/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023]
Abstract
Several viable Salmonella bacteria are capable of causing severe human diseases and huge economic losses. In this regard, viable Salmonella bacteria detection techniques that can identify small numbers of microbial cells are highly valuable. Here, we present a detection method (referred to as SPC) based on the amplification of tertiary signals using splintR ligase ligation, PCR amplification and CRISPR/Cas12a cleavage. The detection limit of the SPC assay was 6 copies (HilA RNA) and 10 CFU (cell). Based on Intracellular HilA RNA detection, this assay can be used to distinguish between viable and dead Salmonella. In addition, it is able to detect multiple serotypes of Salmonella and has been successfully used to detect Salmonella in milk or isolated from farms. Overall, this assay is a promising test for viable pathogens detection and biosafety control.
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Affiliation(s)
- Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Wenjing Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ziwei Liao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zheren Huang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ming Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hongcheng Wei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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22
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Xiao H, Hu J, Huang C, Feng W, Liu Y, Kumblathan T, Tao J, Xu J, Le XC, Zhang H. CRISPR techniques and potential for the detection and discrimination of SARS-CoV-2 variants of concern. Trends Analyt Chem 2023; 161:117000. [PMID: 36937152 PMCID: PMC9977466 DOI: 10.1016/j.trac.2023.117000] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
The continuing evolution of the SARS-CoV-2 virus has led to the emergence of many variants, including variants of concern (VOCs). CRISPR-Cas systems have been used to develop techniques for the detection of variants. These techniques have focused on the detection of variant-specific mutations in the spike protein gene of SARS-CoV-2. These sequences mostly carry single-nucleotide mutations and are difficult to differentiate using a single CRISPR-based assay. Here we discuss the specificity of the Cas9, Cas12, and Cas13 systems, important considerations of mutation sites, design of guide RNA, and recent progress in CRISPR-based assays for SARS-CoV-2 variants. Strategies for discriminating single-nucleotide mutations include optimizing the position of mismatches, modifying nucleotides in the guide RNA, and using two guide RNAs to recognize the specific mutation sequence and a conservative sequence. Further research is needed to confront challenges in the detection and differentiation of variants and sublineages of SARS-CoV-2 in clinical diagnostic and point-of-care applications.
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Affiliation(s)
- Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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23
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Song J, Song Y, Jang H, Moon J, Kang H, Huh YM, Son HY, Rho HW, Park M, Lim EK, Jung J, Jung Y, Park HG, Lee KG, Im SG, Kang T. Elution-free DNA detection using CRISPR/Cas9-mediated light-up aptamer transcription: Toward all-in-one DNA purification and detection tube. Biosens Bioelectron 2023; 225:115085. [PMID: 36696850 DOI: 10.1016/j.bios.2023.115085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/31/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
Accurate and efficient detection of DNA is crucial for disease diagnosis and health monitoring. The traditional methods for DNA analysis involve multiple steps, including sample preparation, lysis, extraction, amplification, and detection. In this study, we present a one-step elution-free DNA analysis method based on the combination of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated light-up aptamer transcription (CLAT) assay and a DNA-capturing poly(2-dimethylaminomethyl styrene) (pDMAMS)-coated tube. The sample solution and lysis buffer are added to the pDMAMS-coated tube, and the DNA is efficiently captured on the surface via electrostatic interaction and directly detected by CLAT assay. The ability of the CRISPR/Cas9 system to specifically recognize DNA enables direct detection of DNA captured on the pDMAMS-coated tube. The combination of CLAT assay and pDMAMS-coated tube simplifies DNA detection in a single tube without the need for complicated extraction steps, improving sensitivity. Our platform demonstrated attomolar sensitivity in the detection of target DNA in cell lysate (0.92 aM), urine (7.7 aM), and plasma (94.6 aM) samples within 1 h. The practical applicability of this method was further demonstrated in experiments with tumor-bearing mice. We believe that this approach brings us closer to an all-in-one DNA purification and detection tube system and has potential applications in tissue and liquid biopsies, as well as various other DNA sensing applications.
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Affiliation(s)
- Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Younseong Song
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jeong Moon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyunju Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Department of Biochemistry & Molecular Biology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Severance Biomedical Science Institute, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; YUHS-KRIBB Medical Convergence Research Institute, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea; Severance Biomedical Science Institute, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyun Wook Rho
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Mirae Park
- Department of Radiology, College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Yongwon Jung
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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24
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Mei J, Wang D, Zhang Y, Wu D, Cui J, Gan M, Liu P. Portable Paper-Based Nucleic Acid Enrichment for Field Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205217. [PMID: 36797206 PMCID: PMC10104631 DOI: 10.1002/advs.202205217] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/15/2023] [Indexed: 05/22/2023]
Abstract
Point-of-care testing (POCT) can be the method of choice for detecting infectious pathogens; these pathogens are responsible for not only infectious diseases such as COVID-19, but also for certain types of cancers. For example, infections by human papillomavirus (HPV) or Helicobacter pylori (H. pylori) are the main cause of cervical and stomach cancers, respectively. COVID-19 and many cancers are treatable with early diagnoses using POCT. A variety of nucleic acid testing have been developed for use in resource-limited environments. However, questions like unintegrated nucleic acid extraction, open detection systems increase the risk of cross-contamination, and dependence on expensive equipment and alternating current (AC) power supply, significantly limit the application of POCT, especially for on-site testing. In this paper, a simple portable platform is reported capable of rapid sample-to-answer testing within 30 min based on recombinase polymerase amplification (RPA) at a lower temperature, to detect SARS-CoV-2 virus and H. pylori bacteria with a limit of detection as low as 4 × 102 copies mL-1 . The platform used a battery-powered portable reader for on-chip one-pot amplification and fluorescence detection, and can test for multiple (up to four) infectious pathogens simultaneously. This platform can provide an alternative method for fast and reliable on-site diagnostic testing.
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Affiliation(s)
- Junyang Mei
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
- Central LaboratoryRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Dandan Wang
- CAS Key Laboratory of Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
| | - Yiheng Zhang
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
- Central LaboratoryRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Dan Wu
- CAS Key Laboratory of Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
| | - Jinhui Cui
- CAS Key Laboratory of Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
| | - Mingzhe Gan
- CAS Key Laboratory of Nano‐Bio InterfaceSuzhou Institute of Nano‐Tech and Nano‐BionicsChinese Academy of SciencesSuzhou215123China
| | - Peifeng Liu
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
- Central LaboratoryRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
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25
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Liu FX, Cui JQ, Wu Z, Yao S. Recent progress in nucleic acid detection with CRISPR. LAB ON A CHIP 2023; 23:1467-1492. [PMID: 36723235 DOI: 10.1039/d2lc00928e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.
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Affiliation(s)
- Frank X Liu
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Johnson Q Cui
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Zhihao Wu
- IIP-Advanced Materials, Interdisciplinary Program Office (IPO), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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26
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CRISPR-Cas assisted diagnostics: A broad application biosensing approach. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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27
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Yang DM, Chang TJ, Hung KF, Wang ML, Cheng YF, Chiang SH, Chen MF, Liao YT, Lai WQ, Liang KH. Smart healthcare: A prospective future medical approach for COVID-19. J Chin Med Assoc 2023; 86:138-146. [PMID: 36227021 PMCID: PMC9847685 DOI: 10.1097/jcma.0000000000000824] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
COVID-19 has greatly affected human life for over 3 years. In this review, we focus on smart healthcare solutions that address major requirements for coping with the COVID-19 pandemic, including (1) the continuous monitoring of severe acute respiratory syndrome coronavirus 2, (2) patient stratification with distinct short-term outcomes (eg, mild or severe diseases) and long-term outcomes (eg, long COVID), and (3) adherence to medication and treatments for patients with COVID-19. Smart healthcare often utilizes medical artificial intelligence (AI) and cloud computing and integrates cutting-edge biological and optoelectronic techniques. These are valuable technologies for addressing the unmet needs in the management of COVID. By leveraging deep learning/machine learning capabilities and big data, medical AI can perform precise prognosis predictions and provide reliable suggestions for physicians' decision-making. Through the assistance of the Internet of Medical Things, which encompasses wearable devices, smartphone apps, internet-based drug delivery systems, and telemedicine technologies, the status of mild cases can be continuously monitored and medications provided at home without the need for hospital care. In cases that develop into severe cases, emergency feedback can be provided through the hospital for rapid treatment. Smart healthcare can possibly prevent the development of severe COVID-19 cases and therefore lower the burden on intensive care units.
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Affiliation(s)
- De-Ming Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Address correspondence. Dr. De-Ming Yang, Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, 201, Section 2, Shi-Pai Road, Taipei 112, Taiwan, ROC. E-mail address: (D.-M. Yang). and Dr. Kung-Hao Liang, Laboratory of Systems Biomedical Science, Department of Medical Research, Taipei Veterans General Hospital, 201, Section 2, Shi-Pai Road, Taipei 112, Taiwan, ROC. E-mail: (K.-H. Liang)
| | - Tai-Jay Chang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Su-Hua Chiang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Mei-Fang Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yi-Ting Liao
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Laboratory of Systems Biomedical Science, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Wei-Qun Lai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Kung-Hao Liang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Laboratory of Systems Biomedical Science, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Address correspondence. Dr. De-Ming Yang, Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, 201, Section 2, Shi-Pai Road, Taipei 112, Taiwan, ROC. E-mail address: (D.-M. Yang). and Dr. Kung-Hao Liang, Laboratory of Systems Biomedical Science, Department of Medical Research, Taipei Veterans General Hospital, 201, Section 2, Shi-Pai Road, Taipei 112, Taiwan, ROC. E-mail: (K.-H. Liang)
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28
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Kumaran A, Jude Serpes N, Gupta T, James A, Sharma A, Kumar D, Nagraik R, Kumar V, Pandey S. Advancements in CRISPR-Based Biosensing for Next-Gen Point of Care Diagnostic Application. BIOSENSORS 2023; 13:202. [PMID: 36831968 PMCID: PMC9953454 DOI: 10.3390/bios13020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 05/25/2023]
Abstract
With the move of molecular tests from diagnostic labs to on-site testing becoming more common, there is a sudden rise in demand for nucleic acid-based diagnostic tools that are selective, sensitive, flexible to terrain changes, and cost-effective to assist in point-of-care systems for large-scale screening and to be used in remote locations in cases of outbreaks and pandemics. CRISPR-based biosensors comprise a promising new approach to nucleic acid detection, which uses Cas effector proteins (Cas9, Cas12, and Cas13) as extremely specialized identification components that may be used in conjunction with a variety of readout approaches (such as fluorescence, colorimetry, potentiometry, lateral flow assay, etc.) for onsite analysis. In this review, we cover some technical aspects of integrating the CRISPR Cas system with traditional biosensing readout methods and amplification technologies such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) and continue to elaborate on the prospects of the developed biosensor in the detection of some major viral and bacterial diseases. Within the scope of this article, we also discuss the recent COVID pandemic and the numerous CRISPR biosensors that have undergone development since its advent. Finally, we discuss some challenges and future prospects of CRISPR Cas systems in point-of-care testing.
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Affiliation(s)
- Akash Kumaran
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Nathan Jude Serpes
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Tisha Gupta
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Abija James
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Avinash Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Rupak Nagraik
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Vaneet Kumar
- Department of Natural Science, CT University, Ludhiana 142024, Punjab, India
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
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29
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Figueiredo D, Cascalheira A, Goncalves J. Rapid, multiplex detection of SARS-CoV-2 using isothermal amplification coupled with CRISPR-Cas12a. Sci Rep 2023; 13:849. [PMID: 36646742 PMCID: PMC9842216 DOI: 10.1038/s41598-022-27133-7] [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: 06/06/2022] [Accepted: 12/26/2022] [Indexed: 01/18/2023] Open
Abstract
In December 2019 an outbreak erupted due to the beta coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 in Wuhan, China. The disease caused by this virus (COVID-19) rapidly spread to all parts of the globe leading to a global pandemic. Efforts to combat the pandemic rely on RT-qPCR diagnostic tests that have high turnaround times (~ 24 h), are easily contaminated, need specialized equipment, facilities, and personnel that end up increasing the overall costs of this method. Loop-mediated isothermal amplification (LAMP) coupled with a reverse transcription step (RT-LAMP) is an alternative diagnostic method that can easily overcome these obstacles, when coupled with CRISPR/Cas it can eliminate false positives. Here we report a fast (~ 40 min), highly sensitive, point-of-care multiplex RT-LAMP and CRISPR/Cas12a assay to detect SARS-CoV-2. This fluorescence-based test achieved 100% specificity and 93% sensitivity using 25 positives and 50 negative patient samples for Ct < 35. Our reported LoD of 3 copies/µL will enable the robust, fast detection of the virus in a dedicated equipment which is a major step towards population-wide accessible testing.
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Affiliation(s)
| | | | - Joao Goncalves
- iMed- Research Institute for Medicines, Faculdade Farmácia da Universidade Lisboa, Lisboa, Portugal.
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30
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Wang S, Wang S, Tang Y, Peng G, Hao T, Wu X, Wei J, Qiu X, Zhou D, Zhu S, Li Y, Wu S. Detection of Klebsiella pneumonia DNA and ESBL positive strains by PCR-based CRISPR-LbCas12a system. Front Microbiol 2023; 14:1128261. [PMID: 36846807 PMCID: PMC9948084 DOI: 10.3389/fmicb.2023.1128261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
INTRODUCTION Klebsiella pneumonia (K. pneumonia) is a Gram-negative bacterium that opportunistically causes nosocomial infections in the lung, bloodstream, and urinary tract. Extended-spectrum β-Lactamases (ESBLs)-expressed K. pneumonia strains are widely reported to cause antibiotic resistance and therapy failure. Therefore, early identification of K. pneumonia, especially ESBL-positive strains, is essential in preventing severe infections. However, clinical detection of K. pneumonia requires a time-consuming process in agar disk diffusion. Nucleic acid detection, like qPCR, is precise but requires expensive equipment. Recent research reveals that collateral cleavage activity of CRISPR-LbCas12a has been applied in nucleic acid detection, and the unique testing model can accommodate various testing models. METHODS This study established a system that combined PCR with CRISPR-LbCas12a targeting the K. pneumoniae system. Additionally, this study summarized the antibiotic-resistant information of the past five years' K. pneumoniae clinic cases in Luohu Hospital and found that the ESBL-positive strains were growing. This study then designs a crRNA that targets SHV to detect ESBL-resistant K. pneumoniae. This work is to detect K. pneumoniae and ESBL-positive strains' nucleic acid using CRISPR-Cas12 technology. We compared PCR-LbCas12 workflow with PCR and qPCR techniques. RESULTS AND DISCUSSION This system showed excellent detection specificity and sensitivity in both bench work and clinical samples. Due to its advantages, its application can meet different detection requirements in health centers where qPCR is not accessible. The antibiotic-resistant information is valuable for further research.
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Affiliation(s)
- Shang Wang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shan Wang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ying Tang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, China
| | - Guoyu Peng
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Tongyu Hao
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
| | - Xincheng Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jiehong Wei
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
| | - Xinying Qiu
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Dewang Zhou
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Shimao Zhu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- *Correspondence: Yuqing Li, ; Song Wu,
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Medical Laboratory of Shenzhen Luohu People’s Hospital, Shenzhen, China
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
- *Correspondence: Yuqing Li, ; Song Wu,
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Rong G, Zheng Y, Chen Y, Zhang Y, Zhu P, Sawan M. COVID-19 Diagnostic Methods and Detection Techniques. ENCYCLOPEDIA OF SENSORS AND BIOSENSORS 2023. [PMCID: PMC8409760 DOI: 10.1016/b978-0-12-822548-6.00080-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yu H, Zhang H, Li J, Zhao Z, Deng M, Ren Z, Li Z, Xue C, Li MG, Chen Z. Rapid and Unamplified Detection of SARS-CoV-2 RNA via CRISPR-Cas13a-Modified Solution-Gated Graphene Transistors. ACS Sens 2022; 7:3923-3932. [PMID: 36472865 PMCID: PMC9745736 DOI: 10.1021/acssensors.2c01990] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
The disease caused by severe acute respiratory syndrome coronavirus, SARS-CoV-2, is termed COVID-19. Even though COVID-19 has been out for more than two years, it is still causing a global pandemic. Due to the limitations of sample collection, transportation, and kit performance, the traditional reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method has a long detection period and high testing costs. An increased risk of infection is inevitable, since many patients may not be diagnosed in time. The CRISPR-Cas13a system can be designed for RNA identification and knockdown, as a promising platform for nucleic acid detection. Here, we designed a solution-gated graphene transistor (SGGT) biosensor based on the CRISPR-Cas13a system. Using the gene-targeting capacity of CRISPR-Cas13a and gate functionalization via multilayer modification, SARS-CoV-2 nucleic acid sequences can be quickly and precisely identified without the need for amplification or fluorescence tagging. The limit of detection (LOD) in both buffer and serum reached the aM level, and the reaction time was about 10 min. The results of the detection of COVID-19 clinical samples from throat swabs agree with RT-PCR. In addition, the interchangeable gates significantly minimize the cost and time of device fabrication. In a nutshell, our biosensor technology is broadly applicable and will be suitable for point-of-care (POC) testing.
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Affiliation(s)
- Haiyang Yu
- State Key Laboratory of Advanced Technology for
Materials Synthesis and Processing, Wuhan University of
Technology, Wuhan430070, China
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Huibin Zhang
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Jinhua Li
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Zheng Zhao
- State Key Laboratory of Advanced Technology for
Materials Synthesis and Processing, Wuhan University of
Technology, Wuhan430070, China
- Sanya Science and Education Innovation Park
of Wuhan University of Technology, Sanya572000,
China
| | - Minhua Deng
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Zhanpeng Ren
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Ziqin Li
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Chenglong Xue
- Collaborative Innovation Center for Advanced Organic
Chemical Materials Co-constructed by the Province and Ministry, Key Laboratory for the
Green Preparation and Application of Functional Materials, Ministry of Education, Hubei
Key Laboratory of Polymer Materials, School of Materials Science and Engineering,
Hubei University, Wuhan430062, China
| | - Mitch Guijun Li
- Division of Integrative Systems and Design,
The Hong Kong University of Science and Technology, Clear
Water Bay, Kowloon, Hong Kong SAR999077, China
| | - Zhaowei Chen
- Division of Nephrology, Renmin Hospital
of Wuhan University, Wuhan430060, China
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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Park J, Han H, Jeung JH, Jang H, Park C, Ahn JK. CRISPR/Cas13a-assisted AMP generation for SARS-CoV-2 RNA detection using a personal glucose meter. BIOSENSORS & BIOELECTRONICS: X 2022; 12:100283. [PMID: 36405495 PMCID: PMC9659363 DOI: 10.1016/j.biosx.2022.100283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Herein, we described a washing- and label-free clustered regularly interspaced short palindromic repeats (CRISPR)/LwaCas13a-based RNA detection method utilizing a personal glucose meter (PGM), which relies on the trans-cleavage activity of CRISPR/Cas13a and kinase reactions. In principle, the presence of target RNA activates the trans-cleavage of CRISPR/Cas13a, generating 2',3'-cyclic phosphate adenosine, which is converted to adenosine monophosphate (AMP) by the T4 polynucleotide kinase. Subsequently, the AMP is converted to adenosine diphosphate (ADP) through phosphorylation by a myokinase; ADP is then used as a substrate in the cascade enzymatic reaction promoted by pyruvate kinase and hexokinase. The overall reaction leads to the continuous conversion of glucose to glucose-6-phosphate, resulting in a reduction of glucose concentration proportional to the level of target RNA, which can therefore be indirectly measured with a PGM. By employing this novel strategy, severe acute respiratory syndrome coronavirus-2 RNA can be successfully detected with excellent specificity. In addition, we were able to overcome non-specific responses of CRISPR/Cas13a and distinguish single nucleotide polymorphisms by introducing a single-base mismatch in the complementary RNA. Our study provides an alternative coronavirus disease 2019 detection technology that is affordable, accessible, and portable with a fast turnaround time and excellent selectivity.
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Affiliation(s)
- Junhyun Park
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Hyogu Han
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea
- Department of Chemistry, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Jae Hoon Jeung
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Hyowon Jang
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon, 34141, South Korea
| | - Chihyun Park
- Daejeon District Office, National Forensic Service, Daejeon, 34054, South Korea
| | - Jun Ki Ahn
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea
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Liu X, Bai L, Cao X, Wu F, Yin T, Lu W. Rapid determination of SARS-CoV-2 nucleocapsid proteins based on 2D/2D MXene/P–BiOCl/Ru(bpy) 32+ heterojunction composites to enhance electrochemiluminescence performance. Anal Chim Acta 2022; 1234:340522. [PMID: 36328721 PMCID: PMC9575274 DOI: 10.1016/j.aca.2022.340522] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/29/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022]
Abstract
At the end of 2019, the novel coronavirus disease 2019 (COVID-19), a cluster of atypical pneumonia caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been known as a highly contagious disease. Herein, we report the MXene/P–BiOCl/Ru(bpy)32+ heterojunction composite to construct an electrochemiluminescence (ECL) immunosensor for SARS-CoV-2 nucleocapsid protein (CoVNP) determination. Two-dimensional (2D) material ultrathin phosphorus-doped bismuth oxychloride (P–BiOCl) is exploited and first applied in ECL. 2D architectures MXene not only act as “soft substrate” to improve the properties of P–BiOCl, but also synergistically work with P–BiOCl. Owing to the inimitable set of bulk and interfacial properties, intrinsic high electrochemical conductivity, hydrophilicity and good biocompatible of 2D/2D MXene/P–BiOCl/Ru(bpy)32+, this as-exploited heterojunction composite is an efficient signal amplifier and co-reaction accelerator in the presence of tri-n-propylamine (TPA) as a coreactant. The proposed MXene/P–BiOCl/Ru(bpy)32+-TPA system exhibits a high and stable ECL signal and achieves ECL emission quenching for “signal on-off” recognition of CoVNP. Fascinatingly, the constructed ECL biosensor towards CoVNP allows a wide linear concentration range from 1 fg/mL to 10 ng/mL and a low limit of detection (LOD) of 0.49 fg/mL (S/N = 3). Furthermore, this presented strategy sheds light on designing a highly efficient ECL nanostructure through the combination of 2D MXene architectures with 2D semiconductor materials in the field of nanomedicine. This ECL biosensor can successfully detect CoVNP in human serum, which can promote the prosperity and development of diagnostic methods of SARS-CoV-2.
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Affiliation(s)
- Xuebo Liu
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Liwei Bai
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, China
| | - Feng Wu
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tao Yin
- College of Medical Imaging, Shanxi Medical University, Taiyuan, 030001, China
| | - Wenbo Lu
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, 030031, China,Corresponding author
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36
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Akarapipad P, Bertelson E, Pessell A, Wang TH, Hsieh K. Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19. BIOSENSORS 2022; 12:bios12110978. [PMID: 36354487 PMCID: PMC9688249 DOI: 10.3390/bios12110978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 05/29/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.
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Affiliation(s)
- Patarajarin Akarapipad
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Bertelson
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander Pessell
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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37
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Rong G, Zheng Y, Li X, Guo M, Su Y, Bian S, Dang B, Chen Y, Zhang Y, Shen L, Jin H, Yan R, Wen L, Zhu P, Sawan M. A high-throughput fully automatic biosensing platform for efficient COVID-19 detection. Biosens Bioelectron 2022; 220:114861. [PMCID: PMC9630290 DOI: 10.1016/j.bios.2022.114861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 09/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
We propose a label-free biosensor based on a porous silicon resonant microcavity and localized surface plasmon resonance. The biosensor detects SARS-CoV-2 antigen based on engineered trimeric angiotensin converting enzyme-2 binding protein, which is conserved across different variants. Robotic arms run the detection process including sample loading, incubation, sensor surface rinsing, and optical measurements using a portable spectrometer. Both the biosensor and the optical measurement system are readily scalable to accommodate testing a wide range of sample numbers. The limit of detection is 100 TCID50/ml. The detection time is 5 min, and the throughput of one single robotic site is up to 384 specimens in 30 min. The measurement interface requires little training, has standard operation, and therefore is suitable for widespread use in rapid and onsite COVID-19 screening or surveillance.
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Affiliation(s)
- Guoguang Rong
- CenBRAIN Neurotech, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Yuqiao Zheng
- CenBRAIN Neurotech, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Xiangqing Li
- School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Mengzhun Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake, University, Hangzhou, Zhejiang, 310030, China,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310030, China,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310030, China
| | - Yi Su
- CenBRAIN Neurotech, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Sumin Bian
- CenBRAIN Neurotech, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Bobo Dang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake, University, Hangzhou, Zhejiang, 310030, China,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310030, China,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310030, China
| | - Yin Chen
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, Zhejiang, 310051, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, Zhejiang, 310051, China
| | - Linhai Shen
- Hangzhou Center for Disease Control and Prevention, 568 Mingshi Road, Jianggan District, Hangzhou, Zhejiang, 310021, China
| | - Hui Jin
- Hangzhou Center for Disease Control and Prevention, 568 Mingshi Road, Jianggan District, Hangzhou, Zhejiang, 310021, China
| | - Renhong Yan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake, University, Hangzhou, Zhejiang, 310030, China,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, 310030, China
| | - Liaoyong Wen
- School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
| | - Peixi Zhu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Mohamad Sawan
- CenBRAIN Neurotech, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China,Institute of Advanced Study, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China,Corresponding author. CenBRAIN Neurotech, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang, 310030, China
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Soh JH, Balleza E, Abdul Rahim MN, Chan HM, Mohd Ali S, Chuah JKC, Edris S, Atef A, Bahieldin A, Ying JY, Sabir JS. CRISPR-based systems for sensitive and rapid on-site COVID-19 diagnostics. Trends Biotechnol 2022; 40:1346-1360. [PMID: 35871983 PMCID: PMC9174145 DOI: 10.1016/j.tibtech.2022.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/15/2022] [Accepted: 06/02/2022] [Indexed: 01/21/2023]
Abstract
The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 diagnosis is crucial for effective medical intervention and transmission control. RT-PCR is the most sensitive/specific, but requires costly equipment and trained personnel in centralized laboratories, which are inaccessible to resource-limited areas. Antigen rapid tests enable point-of-care (POC) detection but are significantly less sensitive/specific. CRISPR-Cas systems are compatible with isothermal amplification and dipstick readout, enabling sensitive/specific on-site testing. However, improvements in sensitivity and workflow complexity are needed to spur clinical adoption. We outline the mechanisms/strategies of major CRISPR-Cas systems, evaluate their on-site diagnostic capabilities, and discuss future research directions.
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Affiliation(s)
- Jun Hui Soh
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | - Enrique Balleza
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | | | - Hsi-Min Chan
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | - Siswand Mohd Ali
- NanoBio Lab, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,A*STAR Infectious Diseases Labs, A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | | | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia,Al-Borg Medical Laboratories, Al Borg Diagnostics, Jeddah, Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jackie Y. Ying
- NanoBio Lab, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,A*STAR Infectious Diseases Labs, A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,Institute of Materials Research and Engineering (IMRE), A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,Correspondence:
| | - Jamal S.M. Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia,Correspondence:
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Blanluet C, Huyke DA, Ramachandran A, Avaro AS, Santiago JG. Detection and Discrimination of Single Nucleotide Polymorphisms by Quantification of CRISPR-Cas Catalytic Efficiency. Anal Chem 2022; 94:15117-15123. [PMID: 36251847 DOI: 10.1021/acs.analchem.2c03338] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The specificity of CRISPR-Cas12 assays is attractive for the detection of single nucleotide polymorphisms (SNPs) implicated in, e.g., cancer and SARS-CoV-2 variants. Such assays often employ endpoint measurements of SNP or wild type (WT) activated Cas12 trans-cleavage activity; however, the fundamental kinetic effects of SNP versus WT activation remain unknown. We here show that endpoint-based assays are limited by arbitrary experimental choices (like used reporter concentration and assay duration) and work best for known target concentrations. More importantly, we show that SNP (versus WT) activation results in measurable kinetic shifts in the Cas12 trans-cleavage substrate affinity (KM) and apparent catalytic efficiency (kcat*/KM). To address endpoint-based assay limitations, we then develop an assay based on the quantification of Michaelis-Menten parameters and apply this assay to a 20 base pair WT target of the SARS-CoV-2 E gene. We find that the kcat*/KM measured for WT is 130-fold greater than the lowest kcat*/KM among all 60 measured SNPs (compared to a 4.8-fold for endpoint fluorescence of the same SNP). KM also offers a strong ability to distinguish SNPs, varies 27-fold over all the cases, and, importantly, is insensitive to the target concentration. Last, we point out trends among kinetic rates and SNP base and location within the CRISPR-Cas12 targeted region.
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Affiliation(s)
- Charles Blanluet
- CentraleSupelec - Universite Paris-Saclay, 91190Gif-sur-Yvette, France.,Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Diego A Huyke
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Ashwin Ramachandran
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey08540, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey08540, United States
| | - Alexandre S Avaro
- CentraleSupelec - Universite Paris-Saclay, 91190Gif-sur-Yvette, France.,Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
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Zhang X, Yang Y, Cao J, Qi Z, Li G. Point-of-care CRISPR/Cas biosensing technology: A promising tool for preventing the possible COVID-19 resurgence caused by contaminated cold-chain food and packaging. FOOD FRONTIERS 2022; 4:FFT2176. [PMID: 36712576 PMCID: PMC9874772 DOI: 10.1002/fft2.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/1912] [Revised: 12/12/1912] [Accepted: 12/12/1912] [Indexed: 02/01/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused great public health concern and has been a global threat due to its high transmissibility and morbidity. Although the SARS-CoV-2 transmission mainly relies on the person-to-person route through the respiratory droplets, the possible transmission through the contaminated cold-chain food and packaging to humans has raised widespread concerns. This review discussed the possibility of SARS-CoV-2 transmission via the contaminated cold-chain food and packaging by tracing the occurrence, the survival of SARS-CoV-2 in the contaminated cold-chain food and packaging, as well as the transmission and outbreaks related to the contaminated cold-chain food and packaging. Rapid, accurate, and reliable diagnostics of SARS-CoV-2 is of great importance for preventing and controlling the COVID-19 resurgence. Therefore, we summarized the recent advances on the emerging clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system-based biosensing technology that is promising and powerful for preventing the possible COVID-19 resurgence caused by the contaminated cold-chain food and packaging during the COVID-19 pandemic, including CRISPR/Cas system-based biosensors and their integration with portable devices (e.g., smartphone, lateral flow assays, microfluidic chips, and nanopores). Impressively, this review not only provided an insight on the possibility of SARS-CoV-2 transmission through the food supply chain, but also proposed the future opportunities and challenges on the development of CRISPR/Cas system-based detection methods for the diagnosis of SARS-CoV-2.
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Affiliation(s)
- Xianlong Zhang
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Yan Yang
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Juanjuan Cao
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Zihe Qi
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Guoliang Li
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
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Zhang X, Shi Y, Chen G, Wu D, Wu Y, Li G. CRISPR/Cas Systems-Inspired Nano/Biosensors for Detecting Infectious Viruses and Pathogenic Bacteria. SMALL METHODS 2022; 6:e2200794. [PMID: 36114150 DOI: 10.1002/smtd.202200794] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Infectious pathogens cause severe human illnesses and great deaths per year worldwide. Rapid, sensitive, and accurate detection of pathogens is of great importance for preventing infectious diseases caused by pathogens and optimizing medical healthcare systems. Inspired by a microbial defense system (i.e., CRISPR/ CRISPR-associated proteins (Cas) system, an adaptive immune system for protecting microorganisms from being attacked by invading species), a great many new biosensors have been successfully developed and widely applied in the detection of infectious viruses and pathogenic bacteria. Moreover, advanced nanotechnologies have also been integrated into these biosensors to improve their detection stability, sensitivity, and accuracy. In this review, the recent advance in CRISPR/Cas systems-based nano/biosensors and their applications in the detection of infectious viruses and pathogenic bacteria are comprehensively reviewed. First of all, the categories and working principles of CRISPR/Cas systems for establishing the nano/biosensors are simply introduced. Then, the design and construction of CRISPR/Cas systems-based nano/biosensors are comprehensively discussed. In the end, attentions are focused on the applications of CRISPR/Cas systems-based nano/biosensors in the detection of infectious viruses and pathogenic bacteria. Impressively, the remaining opportunities and challenges for the further design and development of CRISPR/Cas system-based nano/biosensors and their promising applications are proposed.
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Affiliation(s)
- Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Yiheng Shi
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Guang Chen
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Di Wu
- Institute for Global Food Security, Queen's University Belfast, Belfast, BT95DL, UK
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
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Huang T, Zhang R, Li J. CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives. J Adv Res 2022:S2090-1232(22)00240-5. [PMID: 36367481 PMCID: PMC10403697 DOI: 10.1016/j.jare.2022.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements. AIM OF REVIEW This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation. KEY SCIENTIFIC CONCEPTS OF REVIEW Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.
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Wang J, Yang X, Wang X, Wang W. Recent Advances in CRISPR/Cas-Based Biosensors for Protein Detection. Bioengineering (Basel) 2022; 9:bioengineering9100512. [PMID: 36290480 PMCID: PMC9598526 DOI: 10.3390/bioengineering9100512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022] Open
Abstract
CRISPR is an acquired immune system found in prokaryotes that can accurately recognize and cleave foreign nucleic acids, and has been widely explored for gene editing and biosensing. In the past, CRISPR/Cas-based biosensors were mainly applied to detect nucleic acids in the field of biosensing, and their applications for the detection of other types of analytes were usually overlooked such as small molecules and disease-related proteins. The recent work shows that CRISPR/Cas biosensors not only provide a new tool for protein analysis, but also improve the sensitivity and specificity of protein detections. However, it lacks the latest review to summarize CRISPR/Cas-based biosensors for protein detection and elucidate their mechanisms of action, hindering the development of superior biosensors for proteins. In this review, we summarized CRISPR/Cas-based biosensors for protein detection based on their mechanism of action in three aspects: antibody-assisted CRISPR/Cas-based protein detection, aptamer-assisted CRISPR/Cas-based protein detection, and miscellaneous CRISPR/Cas-based methods for protein detection, respectively. Moreover, the prospects and challenges for CRISPR/Cas-based biosensors for protein detection are also discussed.
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Affiliation(s)
- Jing Wang
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
- Correspondence: (J.W.); (W.W.)
| | - Xifang Yang
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
| | - Xueliang Wang
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
| | - Wanhe Wang
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, China
- Correspondence: (J.W.); (W.W.)
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Nyaruaba R, Mwaliko C, Dobnik D, Neužil P, Amoth P, Mwau M, Yu J, Yang H, Wei H. Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks. Clin Microbiol Rev 2022; 35:e0016821. [PMID: 35258315 PMCID: PMC9491181 DOI: 10.1128/cmr.00168-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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Affiliation(s)
- Raphael Nyaruaba
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Caroline Mwaliko
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Pavel Neužil
- Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Matilu Mwau
- Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Junping Yu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
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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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Thapa S, Singh KRB, Verma R, Singh J, Singh RP. State-of-the-Art Smart and Intelligent Nanobiosensors for SARS-CoV-2 Diagnosis. BIOSENSORS 2022; 12:637. [PMID: 36005033 PMCID: PMC9405813 DOI: 10.3390/bios12080637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/16/2022]
Abstract
The novel coronavirus appeared to be a milder infection initially, but the unexpected outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), commonly called COVID-19, was transmitted all over the world in late 2019 and caused a pandemic. Human health has been disastrously affected by SARS-CoV-2, which is still evolving and causing more serious concerns, leading to the innumerable loss of lives. Thus, this review provides an outline of SARS-CoV-2, of the traditional tools to diagnose SARS-CoV-2, and of the role of emerging nanomaterials with unique properties for fabricating biosensor devices to diagnose SARS-CoV-2. Smart and intelligent nanomaterial-enabled biosensors (nanobiosensors) have already proven their utility for the diagnosis of several viral infections, as various detection strategies based on nanobiosensor devices are already present, and several other methods are also being investigated by researchers for the determination of SARS-CoV-2 disease; however, considerably more is undetermined and yet to be explored. Hence, this review highlights the utility of various nanobiosensor devices for SARS-CoV-2 determination. Further, it also emphasizes the future outlook of nanobiosensing technologies for SARS-CoV-2 diagnosis.
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Affiliation(s)
- Sushma Thapa
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Kshitij RB Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ranjana Verma
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak 484887, Madhya Pradesh, India
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Verma MK, Roychowdhury S, Sahu BD, Mishra A, Sethi KK. CRISPR-based point-of-care diagnostics incorporating Cas9, Cas12, and Cas13 enzymes advanced for SARS-CoV-2 detection. J Biochem Mol Toxicol 2022; 36:e23113. [PMID: 35642647 PMCID: PMC9347549 DOI: 10.1002/jbt.23113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
An outbreak of the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first came to light in December 2019, which has unfolded rapidly and turned out to be a global pandemic. Early prognosis of viral contamination involves speedy intervention, disorder control, and good-sized management of the spread of disease. Reverse transcription-polymerase chain reaction, considered the gold standard test for detecting nucleic acids and pathogen diagnosis, provides high sensitivity and specificity. However, reliance on high-priced equipped kits, associated reagents, and skilled personnel slow down sickness detection. Lately, the improvement of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated protein)-based diagnostic systems has reshaped molecular diagnosis due to their low cost, simplicity, speed, efficiency, high sensitivity, specificity, and versatility, which is vital for accomplishing point-of-care diagnostics. We reviewed and summarized CRISPR-Cas-based point-of-care diagnostic strategies and research in these paintings while highlighting their characteristics and challenges for identifying SARS-CoV-2.
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Affiliation(s)
- Monika K. Verma
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Sanjana Roychowdhury
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Bidya Dhar Sahu
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Awanish Mishra
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Kalyan K. Sethi
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
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Song J, Cha B, Moon J, Jang H, Kim S, Jang J, Yong D, Kwon HJ, Lee IC, Lim EK, Jung J, Park HG, Kang T. Smartphone-Based SARS-CoV-2 and Variants Detection System using Colorimetric DNAzyme Reaction Triggered by Loop-Mediated Isothermal Amplification (LAMP) with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). ACS NANO 2022; 16:11300-11314. [PMID: 35735410 PMCID: PMC9236205 DOI: 10.1021/acsnano.2c04840] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Coronavirus disease (COVID-19) has affected people for over two years. Moreover, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has raised concerns regarding its accurate diagnosis. Here, we report a colorimetric DNAzyme reaction triggered by loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPR), referred to as DAMPR assay for detecting SARS-CoV-2 and variants genes with attomolar sensitivity within an hour. The CRISPR-associated protein 9 (Cas9) system eliminated false-positive signals of LAMP products, improving the accuracy of DAMPR assay. Further, we fabricated a portable DAMPR assay system using a three-dimensional printing technique and developed a machine learning (ML)-based smartphone application to routinely check diagnostic results of SARS-CoV-2 and variants. Among blind tests of 136 clinical samples, the proposed system successfully diagnosed COVID-19 patients with a clinical sensitivity and specificity of 100% each. More importantly, the D614G (variant-common), T478K (delta-specific), and A67V (omicron-specific) mutations of the SARS-CoV-2 S gene were detected selectively, enabling the diagnosis of 70 SARS-CoV-2 delta or omicron variant patients. The DAMPR assay system is expected to be employed for on-site, rapid, accurate detection of SARS-CoV-2 and its variants gene and employed in the diagnosis of various infectious diseases.
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Affiliation(s)
- Jayeon Song
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic
of Korea
| | - Baekdong Cha
- School
of Integrated Technology, Gwangju Institute
of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu,
Gwangju 61005, Republic
of Korea
| | - Jeong Moon
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic
of Korea
- Department
of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic
of Korea
| | - Sunjoo Kim
- Department
of Laboratory Medicine, Gyeongsang National
University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do 52727, Republic of Korea
- Gyeongnam
Center for Disease Control and Prevention, 300 Jungang-daero, Uichang-gu,
Changwon-si, Gyeongsangnamdo 51154, Republic of Korea
| | - Jieun Jang
- Gyeongnam
Center for Disease Control and Prevention, 300 Jungang-daero, Uichang-gu,
Changwon-si, Gyeongsangnamdo 51154, Republic of Korea
| | - Dongeun Yong
- Department
of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hyung-Jun Kwon
- Functional
Biomaterial Research Center, KRIBB, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - In-Chul Lee
- Functional
Biomaterial Research Center, KRIBB, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic
of Korea
- Department
of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu,
Daejeon 34113, Republic
of Korea
| | - Juyeon Jung
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic
of Korea
| | - Hyun Gyu Park
- Department
of Chemical and Biomolecular Engineering (BK21+ Program), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic
of Korea
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A Review on Potential Electrochemical Point-of-Care Tests Targeting Pandemic Infectious Disease Detection: COVID-19 as a Reference. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070269] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fast and accurate point-of-care testing (POCT) of infectious diseases is crucial for diminishing the pandemic miseries. To fight the pandemic coronavirus disease 2019 (COVID-19), numerous interesting electrochemical point-of-care (POC) tests have been evolved to rapidly identify the causal organism SARS-CoV-2 virus, its nucleic acid and antigens, and antibodies of the patients. Many of those electrochemical biosensors are impressive in terms of miniaturization, mass production, ease of use, and speed of test, and they could be recommended for future applications in pandemic-like circumstances. On the other hand, self-diagnosis, sensitivity, specificity, surface chemistry, electrochemical components, device configuration, portability, small analyzers, and other features of the tests can yet be improved. Therefore, this report reviews the developmental trend of electrochemical POC tests (i.e., test platforms and features) reported for the rapid diagnosis of COVID-19 and correlates any significant advancements with relevant references. POCTs incorporating microfluidic/plastic chips, paper devices, nanomaterial-aided platforms, smartphone integration, self-diagnosis, and epidemiological reporting attributes are also surfed to help with future pandemic preparedness. This review especially screens the low-cost and easily affordable setups so that management of pandemic disease becomes faster and easier. Overall, the review is a wide-ranging package for finding appropriate strategies of electrochemical POCT targeting pandemic infectious disease detection.
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Wang Y, Xue T, Wang M, Ledesma-Amaro R, Lu Y, Hu X, Zhang T, Yang M, Li Y, Xiang J, Deng R, Ying B, Li W. CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. SENSORS AND ACTUATORS B-CHEMICAL 2022; 362:131765. [PMID: 35370361 PMCID: PMC8957482 DOI: 10.1016/j.snb.2022.131765] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is one of the greatest threats to global human health. Point-of-care diagnostic tools for SARS-CoV-2 could facilitate rapid therapeutic intervention and mitigate transmission. In this work, we report CRISPR-Cas13a cascade-based viral RNA (Cas13C) assay for label-free and isothermal determination of SARS-CoV-2 and its mutations in clinical samples. Cas13a/crRNA was utilized to directly recognize the target of SARS-CoV-2 RNA, and the recognition events sequentially initiate the transcription amplification to produce light-up RNA aptamers for output fluorescence signal. The recognition of viral RNA via Cas13a-guide RNA ensures a high specificity to distinguish SARS-CoV-2 from MERS-CoV and SARS-CoV, as well as viral mutations. A post transcription amplification strategy was triggered after CRISPR-Cas13a recognition contributes to an amplification cascade that achieves high sensitivity for detecting SARS-CoV-2 RNA, with a limit of detection of 0.216 fM. In addition, the Cas13C assay could be able to discriminate single-nucleotide mutation, which was proven with N501Y in SARS-Cov-2 variant. This method was validated by a 100% agreement with RT-qPCR results from 12 clinical throat swab specimens. The Cas13C assay has the potential to be used as a routine nucleic acid test of SARS-CoV-2 virus in resource-limited regions.
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Affiliation(s)
- Yuxi Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.,Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Xue
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Ying Lu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.,State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinyue Hu
- Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.,State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Ming Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin Xiang
- Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.,Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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