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Rad MB, Mohebbi SR, Yadegar A, Ghourchian H. Porous GNPs assisted LAMP-CRISPR/Cas12a amperometric biosensor as a potential point of care testing system for SARS-CoV-2. Mikrochim Acta 2025; 192:280. [PMID: 40195165 DOI: 10.1007/s00604-025-07094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Accepted: 03/04/2025] [Indexed: 04/09/2025]
Abstract
A simple and ultrasensitive amperometric biosensor is introduced which has the potential to be applied as a point of care test for SARS-CoV-2 monitoring. It was prepared by integrating the reverse transcription loop-mediated isothermal amplification (RT‑LAMP) and CRISPR/Cas12a nuclease activity on a modified gold screen-printed electrode (GSPE). The GSPE is modified with double-end thiolated oligonucleotide reporters conjugated to porous gold nanoparticles (PGNPs) and inserted into a homemade poly-methyl methacrylate cartridge. This biosensor was integrated with a low-cost electronic kit to make a platform with the potential to be applied as a point-of-care testing system. The PGNPs on the reporters create a dense, negatively charged barrier that repels the redox couple of [Fe(CN)6]3-/4- from the GSPE surface. Upon the addition of a real sample, followed by LAMP amplification and Cas12a nuclease activity on disposable GSPE, in the presence of SARS-CoV-2, the single-guide RNA binds to the target sequence and activates Cas12a. The activated Cas12a then cleaves the reporters, releasing the PGNPs. This removal of electrostatic hindrance allows the redox couple of [Fe(CN)6]3-/4- to approach the positively charged GSPE, enhancing the amperometric signal. This biosensor offers an outstanding detection limit of 143 zM (~ 86 copies/mL) and a linear response from 4.7 to 7062 aM for SARS-CoV-2 real samples. By using double-end thiolated reporters and porous GNPs, this novel testing system makes it possible to minimize the required sample volume and reagent costs.
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Affiliation(s)
- Mohammad Behnam Rad
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hedayatollah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
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2
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Li Y, Zhao Y, Yi Z, Han S. A CRISPR/Cas13a-based and hybridization chain reaction coupled evanescent wave biosensor for SARS-CoV-2 gene detection. Analyst 2025; 150:1367-1376. [PMID: 40035496 DOI: 10.1039/d4an01584c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Timely and accurate diagnosis of RNA viruses, represented by the SARS-CoV-2, is the foundation for protecting people from health threats. Currently, direct detection of viral RNA genes remains the most accurate method. Herein, a rapid, ultrasensitive, and no heating equipment required CRISPR/Cas13a based evanescent wave fluorescence biosensing platform for quantitative detection of the SARS-CoV-2 gene is reported. The collateral effect of CRISPR/Cas13a for RNA is combined with a self-driven enzyme-free hybridization chain reaction (HCR) as a signal amplification step. When the initiator RNA strand is cleaved by Cas13a, the downstream signal amplification induced by HCR is blocked, and a multiple crRNA strategy is used to enhance the cleavage efficiency. The newly designed HCR assemblies are captured by the cDNA-modified optical fiber and generate a higher-intensity fluorescence signal induced by the evanescent field. The CRISPR/Cas13a-HCR evanescent wave fluorescence biosensing platform is capable of detection of SARS-CoV-2 with a LOD of 0.47 copies per μL and the detection time is within 35 min. The spike recovery tests in saliva and high specificity have demonstrated the potential of this method for point-of-care diagnosis. This method is also suitable for the detection of other RNA viruses, without the need to alter any design of the HCR component, and only the corresponding crRNA needs to be replaced.
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Affiliation(s)
- Yang Li
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Yikan Zhao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Zhihao Yi
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Shitong Han
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
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3
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Liu T, Politza AJ, Ahamed MA, Kshirsagar A, Zhu Y, Guan W. Compact multiplex PCR device for HIV-1 and HIV-2 viral load determination from finger-prick whole blood in resource-limited settings. Biosens Bioelectron 2025; 271:116997. [PMID: 39637742 DOI: 10.1016/j.bios.2024.116997] [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: 07/03/2024] [Revised: 11/20/2024] [Accepted: 11/25/2024] [Indexed: 12/07/2024]
Abstract
The human immunodeficiency virus (HIV) remains a major global health concern for which accurate viral load monitoring is essential for the management of HIV infection. The advent of antiretroviral therapy (ART) has transformed once-fatal HIV disease into a manageable chronic condition that now makes the need for VL testing which aims to satisfy international suppression targets 95-95-95 al l the more essential. Therefore, considering the complexity and diversity of HIV infection, it is essential to develop rapid diagnostic technologies suitable for different clinical situations. Here, we report on a multiplexed PCR device developed for simple and efficient quantification of HIV-1 or HIV-2 viral loads using finger-pricked whole blood from rural decentralized settings. This device is comprised of a previously developed RNA extraction module combined with an optimized real-time PCR amplification system. Together, these combine to simultaneously detect and differentiate HIV-1 & 2; as well are adopting a testing control of RNase P allowing for full diagnostic analysis from one sample. Our device also includes an intuitive user interface and is completely autonomous so it can serve individuals in remote areas who are unfamiliar with the field of medical testing. They get the results in a very short time of around 70 min and hence save on testing times without leaving accuracy behind. The efficiency and effectiveness of the device were validated through the analysis of 30 clinical samples, yielding a sensitivity of 100% for both HIV-1 and HIV-2. The specificity was found to be 100% for HIV-1 and 90.91% for HIV-2, demonstrating high diagnostic accuracy. One of the most attractive things about this device is that it comes in comparison to all other counterparts. Given that you can run the assay for less than $10, it could be an economically viable way to use this as a broadscale test in regions where healthcare budgets don't allow others. Hence it is quite a useful device to aid HIV management in resource-limited settings, where conventional laboratory facilities are out of reach due its simplicity and affordability with rapid output. The point-of-care test is an effective, low-cost, high quality diagnostic tool-promoting rapid testing for HIV-inexpensively overcoming the barriers to efficient control of and care in resource-limited settings.
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Affiliation(s)
- Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Md Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA
| | - Yusheng Zhu
- Department of Pathology and Laboratory Medicine, Pennsylvania State University, Hershey, 17033, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, 16802, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, 16802, USA.
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4
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Chen Y, Zhao R, Hu X, Wang X. The current status and future prospects of CRISPR-based detection of monkeypox virus: A review. Anal Chim Acta 2025; 1336:343295. [PMID: 39788645 DOI: 10.1016/j.aca.2024.343295] [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: 07/04/2024] [Revised: 09/29/2024] [Accepted: 09/30/2024] [Indexed: 01/12/2025]
Abstract
BACKGROUND The current pandemic of 2022 global mpox (formerly known as monkeypox), caused by infection with monkeypox virus (MPXV), has now reached over 120 countries. This constitutes a critical public health issue requiring effective disease management and surveillance. Rapid and reliable diagnosis is conducive to the control of infection, early intervention, and timely treatment. Clinical laboratories use various conventional diagnostic methods for detecting MPXV, including PCR, which can be regarded as a gold-standard diagnostic method. However, the application of PCR is limited by its requirements for high-cost equipment, skilled professionals, and a laboratory setting. RESULTS Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic systems have provided promising prospects for the rapid, sensitive, and specific detection of infectious diseases, especially in point-of-care settings. Over the past 2 years, an increasing number of researchers have concentrated on the application of the CRISPR method to mpox diagnosis. In the majority of cases, a two-step method was chosen, with CRISPR/Cas12a and recombinase polymerase amplification (RPA) as pre-amplification methods, followed by a fluorescence readout. Different strategies have been applied to overcome the encountered limitations of CRISPR detection, but no consensus on an integrated solution has been achieved. Thus, the application of the CRISPR/Cas system in mpox detection requires further exploration and improvement. SIGNIFICANCE This review discusses contemporary studies on MPXV CRISPR detection systems and the strategies proposed to address the challenges faced by CRISPR diagnosis with the hope of helping the development of CRISPR detection methods and improving pathogen detection technologies.
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Affiliation(s)
- Yingwei Chen
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, PR China; Department of Molecular Diagnostic Innovation Technology, Shanghai Academy of Experimental Medicine, Shanghai, PR China
| | - Ran Zhao
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, PR China; Department of Molecular Diagnostic Innovation Technology, Shanghai Academy of Experimental Medicine, Shanghai, PR China
| | - Xiaobo Hu
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, PR China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, PR China.
| | - Xueliang Wang
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, PR China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, PR China; Department of Molecular Diagnostic Innovation Technology, Shanghai Academy of Experimental Medicine, Shanghai, PR China.
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5
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Hassan YM, Mohamed AS, Hassan YM, El-Sayed WM. Recent developments and future directions in point-of-care next-generation CRISPR-based rapid diagnosis. Clin Exp Med 2025; 25:33. [PMID: 39789283 PMCID: PMC11717804 DOI: 10.1007/s10238-024-01540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 12/15/2024] [Indexed: 01/12/2025]
Abstract
The demand for sensitive, rapid, and affordable diagnostic techniques has surged, particularly following the COVID-19 pandemic, driving the development of CRISPR-based diagnostic tools that utilize Cas effector proteins (such as Cas9, Cas12, and Cas13) as viable alternatives to traditional nucleic acid-based detection methods. These CRISPR systems, often integrated with biosensing and amplification technologies, provide precise, rapid, and portable diagnostics, making on-site testing without the need for extensive infrastructure feasible, especially in underserved or rural areas. In contrast, traditional diagnostic methods, while still essential, are often limited by the need for costly equipment and skilled operators, restricting their accessibility. As a result, developing accessible, user-friendly solutions for at-home, field, and laboratory diagnostics has become a key focus in CRISPR diagnostic innovations. This review examines the current state of CRISPR-based diagnostics and their potential applications across a wide range of diseases, including cancers (e.g., colorectal and breast cancer), genetic disorders (e.g., sickle cell disease), and infectious diseases (e.g., tuberculosis, malaria, Zika virus, and human papillomavirus). Additionally, the integration of machine learning (ML) and artificial intelligence (AI) to enhance the accuracy, scalability, and efficiency of CRISPR diagnostics is discussed, alongside the challenges of incorporating CRISPR technologies into point-of-care settings. The review also explores the potential for these cutting-edge tools to revolutionize disease diagnosis and personalized treatment in the future, while identifying the challenges and future directions necessary to address existing gaps in CRISPR-based diagnostic research.
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Affiliation(s)
- Youssef M Hassan
- Department of Zoology, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Ahmed S Mohamed
- Biotechnology Program, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Yaser M Hassan
- Biotechnology Program, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Wael M El-Sayed
- Department of Zoology, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt.
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6
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Zhao J, Kong D, Zhang G, Zhang S, Wu Y, Dai C, Chen Y, Yang Y, Liu Y, Wei D. An Efficient CRISPR/Cas Cooperative Shearing Platform for Clinical Diagnostics Applications. Angew Chem Int Ed Engl 2024; 63:e202411705. [PMID: 39394860 DOI: 10.1002/anie.202411705] [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: 06/21/2024] [Revised: 10/05/2024] [Accepted: 10/07/2024] [Indexed: 10/14/2024]
Abstract
The CRISPR/Cas system is a powerful genome editing tool and possesses widespread applications in molecular diagnostics, therapeutics and genetic engineering. But easy folding of the target sequences causes remarkable deterioration of the recognition and shear efficiency in the case of single Cas-CRISPR RNA (crRNA) duplex. Here, we develop a CRISPR/Cas cooperative shearing (CRISPR-CS) system. Compared with traditional CRISPR/Cas system, two CRISPR/Cas-crRNA duplexes simultaneously recognize different sites in the target sequence, increasing recognition possibility and shearing efficiency. Cooperative shearing cuts more methylene blue-ssDNA reporters on the electrode, enabling unamplified nucleic acid electrochemical assay in less than 5 minutes with a detection limit of 9.5×10-20 M, 2 to 9 orders of magnitude lower than those of other electrochemical assays. The CRISPR-CS platform detects monkeypox, human papilloma virus and amyotrophic lateral sclerosis with an accuracy up to 98.1 %, demonstrating the potential application of the efficient cooperative shearing.
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Affiliation(s)
- Junhong Zhao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Guanghui Zhang
- Department of Laboratory Medicine, Shenzhen Hengsheng Hospital, Shenzhen, Guangdong, 518102, P. R. China
| | - Shen Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yuetong Yang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
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7
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Ahamed MA, Politza AJ, Liu T, Khalid MAU, Zhang H, Guan W. CRISPR-based strategies for sample-to-answer monkeypox detection: current status and emerging opportunities. NANOTECHNOLOGY 2024; 36:042001. [PMID: 39433062 PMCID: PMC11533882 DOI: 10.1088/1361-6528/ad892b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/06/2024] [Accepted: 10/21/2024] [Indexed: 10/23/2024]
Abstract
The global health threat posed by the Monkeypox virus (Mpox) requires swift, simple, and accurate detection methods for effective management, emphasizing the growing necessity for decentralized point-of-care (POC) diagnostic solutions. The clustered regularly interspaced short palindromic repeats (CRISPR), initially known for its effective nucleic acid detection abilities, presents itself as an attractive diagnostic strategy. CRISPR offers exceptional sensitivity, single-base specificity, and programmability. Here, we reviewed the latest developments in CRISPR-based POC devices and testing strategies for Mpox detection. We explored the crucial role of genetic sequencing in designing crRNA for CRISPR reaction and understanding Mpox transmission and mutations. Additionally, we showed the integration of CRISPR-Cas12 strategy with pre-amplification and amplification-free methods. Our study also focused on the significant role of Cas12 proteins and the effectiveness of Cas12 coupled with recombinase polymerase amplification (RPA) for Mpox detection. We envision the future prospects and challenges, positioning CRISPR-Cas12-based POC devices as a frontrunner in the next generation of molecular biosensing technologies.
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Affiliation(s)
- Md Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Muhammad Asad Ullah Khalid
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Huanshu Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
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8
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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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9
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Qian X, Xu Q, Lyon CJ, Hu TY. CRISPR for companion diagnostics in low-resource settings. LAB ON A CHIP 2024; 24:4717-4740. [PMID: 39268697 PMCID: PMC11393808 DOI: 10.1039/d4lc00340c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/15/2024] [Indexed: 09/17/2024]
Abstract
New point-of-care tests (POCTs), which are especially useful in low-resource settings, are needed to expand screening capacity for diseases that cause significant mortality: tuberculosis, multiple cancers, and emerging infectious diseases. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic (CRISPR-Dx) assays have emerged as powerful and versatile alternatives to traditional nucleic acid tests, revealing a strong potential to meet this need for new POCTs. In this review, we discuss CRISPR-Dx assay techniques that have been or could be applied to develop POCTs, including techniques for sample processing, target amplification, multiplex assay design, and signal readout. This review also describes current and potential applications for POCTs in disease diagnosis and includes future opportunities and challenges for such tests. These tests need to advance beyond initial assay development efforts to broadly meet criteria for use in low-resource settings.
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Affiliation(s)
- Xu Qian
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| | - Qiang Xu
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
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10
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Fu S, Li J, Chen J, Zhang L, Liu J, Liu H, Su X. Bacteriophage λ exonuclease and a 5'-phosphorylated DNA guide allow PAM-independent targeting of double-stranded nucleic acids. Nat Biotechnol 2024:10.1038/s41587-024-02388-9. [PMID: 39294394 DOI: 10.1038/s41587-024-02388-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 08/19/2024] [Indexed: 09/20/2024]
Abstract
Sequence-specific recognition of double-stranded nucleic acids is essential for molecular diagnostics and in situ imaging. Clustered regularly interspaced short palindromic repeats and Cas systems rely on protospacer-adjacent motif (PAM)-dependent double-stranded DNA (dsDNA) recognition, limiting the range of targetable sequences and leading to undesired off-target effects. Using single-molecule fluorescence resonance energy transfer analysis, we discover the enzymatic activity of bacteriophage λ exonuclease (λExo). We show binding of 5'-phosphorylated single-stranded DNA (pDNA) to complementary regions on dsDNA and DNA-RNA duplexes, without the need for a PAM-like motif. Upon binding, the λExo-pDNA system catalytically digests the pDNA into nucleotides in the presence of Mg2+. This process is sensitive to mismatches within a wide range of the pDNA-binding region, resulting in exceptional sequence specificity and reduced off-target effects in various applications. The absence of a requirement for a specific motif such as a PAM sequence greatly broadens the range of targets. We demonstrate that the λExo-pDNA system is a versatile tool for molecular diagnostics, DNA computing and gene imaging applications.
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Affiliation(s)
- Shengnan Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Linghao Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huiyu Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering and State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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11
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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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12
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Kaur R, Gupta S, Chauhan A, Mishra V, Sharma MK, Singh J. Harnessing the power of clustered regularly interspaced short palindromic repeats (CRISPR) based microfluidics for next-generation molecular diagnostics. Mol Biol Rep 2024; 51:896. [PMID: 39115550 DOI: 10.1007/s11033-024-09840-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/31/2024] [Indexed: 02/06/2025]
Abstract
CRISPR-based (Clustered regularly interspaced short palindromic repeats-based) technologies have revolutionized molecular biology and diagnostics, offering unprecedented precision and versatility. However, challenges remain, such as high costs, demanding technical expertise, and limited quantification capabilities. To overcome these limitations, innovative microfluidic platforms are emerging as powerful tools for enhancing CRISPR diagnostics. This review explores the exciting intersection of CRISPR and microfluidics, highlighting their potential to revolutionize healthcare diagnostics. By integrating CRISPR's specificity with microfluidics' miniaturization and automation, researchers are developing more sensitive and portable diagnostic tools for a range of diseases. These microfluidic devices streamline sample processing, improve diagnostic performance, and enable point-of-care applications, allowing for rapid and accurate detection of pathogens, genetic disorders, and other health conditions. The review discusses various CRISPR/Cas systems, including Cas9, Cas12, and Cas13, and their integration with microfluidic platforms. It also examines the advantages and limitations of these systems, highlighting their potential for detecting DNA and RNA biomarkers. The review also explores the key challenges in developing and implementing CRISPR-driven microfluidic diagnostics, such as ensuring robustness, minimizing cross-contamination, and achieving robust quantification. Finally, it highlights potential future directions for this rapidly evolving field, emphasizing the transformative potential of these technologies for personalized medicine and global health.
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Affiliation(s)
- Rasanpreet Kaur
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India
| | - Saurabh Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India.
| | - Arjun Chauhan
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India
| | - Vidhi Mishra
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India
| | - Manish Kumar Sharma
- Department of Biotechnology, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, Uttar Pradesh, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Saket Nagar, Bhopal, 462020, Madhya Pradesh, India
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13
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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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14
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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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15
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Song D, Xu W, Zhuo Y, Liu J, Zhu A, Long F. A CRISPR/Cas13a-powered catalytic hairpin assembly evanescent wave fluorescence biosensor for target amplification-free SARS-CoV-2 detection. SENSORS AND ACTUATORS B: CHEMICAL 2024; 405:135296. [DOI: 10.1016/j.snb.2024.135296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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16
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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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17
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Armani Khatibi E, Farshbaf Moghimi N, Rahimpour E. COVID-19: An overview on possible transmission ways, sampling matrices and diagnosis. BIOIMPACTS : BI 2024; 14:29968. [PMID: 39493896 PMCID: PMC11530968 DOI: 10.34172/bi.2024.29968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/17/2023] [Accepted: 10/25/2023] [Indexed: 11/05/2024]
Abstract
COVID-19 is an RNA virus belonging to the SARS family of viruses and includes a wide range of symptoms along with effects on other body organs in addition to the respiratory system. The high speed of transmission, severe complications, and high death rate caused scientists to focus on this disease. Today, many different investigation types are performed on COVID-19 from various points of view in the literature. This review summarizes most of them to provide a useful guideline for researchers in this field. After a general introduction, this review is divided into three parts. In the first one, various transmission ways COVID-19 are classified and explained in detail. The second part reviews the used biological samples for the detection of virus and the final section describes the various methods reported for the diagnosis of COVID-19 in various biological matrices.
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Affiliation(s)
- Elina Armani Khatibi
- Department of Pharmaceutics, School of Pharmacy, Ardabil University of Medical Science, Ardabil, Iran
| | - Nastaran Farshbaf Moghimi
- Department of Pharmaceutics, School of Pharmacy, Ardabil University of Medical Science, Ardabil, Iran
| | - Elaheh Rahimpour
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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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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19
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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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20
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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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21
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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: 42] [Impact Index Per Article: 21.0] [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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22
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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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23
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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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24
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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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25
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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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26
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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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27
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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: 27] [Impact Index Per Article: 13.5] [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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28
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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: 15] [Impact Index Per Article: 7.5] [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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29
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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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30
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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: 1.5] [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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31
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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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32
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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: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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33
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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: 13] [Impact Index Per Article: 6.5] [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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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: 1.5] [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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35
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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: 14] [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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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: 18] [Impact Index Per Article: 9.0] [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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37
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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: 16] [Impact Index Per Article: 8.0] [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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38
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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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39
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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: 2.5] [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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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: 27] [Impact Index Per Article: 13.5] [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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41
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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: 5] [Impact Index Per Article: 2.5] [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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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: 20] [Impact Index Per Article: 10.0] [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: 2.3] [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: 1] [Impact Index Per Article: 0.3] [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: 15] [Impact Index Per Article: 5.0] [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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48
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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: 0.3] [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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49
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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: 2.3] [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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50
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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: 20] [Impact Index Per Article: 6.7] [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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