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Pian H, Wang H, Wang H, Li Z. Dual CRISPR/Cas13a Cascade Strand Displacement-Triggered Transcription for Point-of-Care Detection of Plasmodium in Asymptomatic Malaria. Anal Chem 2024; 96:7524-7531. [PMID: 38695755 DOI: 10.1021/acs.analchem.4c00230] [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: 05/15/2024]
Abstract
Asymptomatic infections of Plasmodium parasites are major obstacles to malaria control and elimination. A sensitive, specific, and user-friendly method is urgently needed for point-of-care (POC) Plasmodium diagnostics in asymptomatic malaria, especially in resource-limited settings. In this work, we present a POC method (termed Cas13a-SDT) based on the cascade sequence recognition and signal amplification of dual Cas13a trans-cleavage and strand displacement-triggered transcription (SDT). Cas13a-SDT not only achieves exceptional specificity in discriminating the target RNA from nontarget RNAs with any cross-interaction but also meets the sensitivity criterion set by the World Health Organization (WHO) for effective malaria detection. Remarkably, this novel method was successfully applied to screen malaria in asymptomatic infections from clinical samples. The proposed method provides a user-friendly and visually interpretable output mode while maintaining high accuracy and reliability comparable to RT-PCR. These excellent features demonstrate the significant potential of Cas13a-SDT for POC diagnosis of Plasmodium infections, laying a vital foundation for advancing malaria control and elimination efforts.
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Affiliation(s)
- Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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2
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Gu X, Tang Q, Kang X, Ji H, Shi X, Shi L, Pan A, Zhu Y, Jiang W, Zhang J, Liu J, Wu M, Wu L, Qin Y. A portable CRISPR-Cas12a triggered photothermal biosensor for sensitive and visual detection of Staphylococcus aureus and Listeria monocytogenes. Talanta 2024; 271:125678. [PMID: 38277968 DOI: 10.1016/j.talanta.2024.125678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
The detection of foodborne pathogens is crucial for ensuring the maintenance of food safety. In the present study, a portable CRISPR-Cas12a triggered photothermal biosensor integrating branch hybrid chain reaction (bHCR) and DNA metallization strategy for sensitive and visual detection of foodborne pathogens was proposed. The sheared probes were utilized to block the locker probes, which enabled preventing the assembly of bHCR in the absence of target bacteria, while target bacteria can activate the cleavage of sheared probes through CRISPR-Cas12a. Therefore, the locker probes functioned as initiating chains, triggering the formation of the branching double-stranded DNA consisting of H1, H2, and H3. The silver particles, which were in situ deposited on the DNA structure, functioned as a signal factor for conducting photothermal detection. Staphylococcus aureus and Listeria monocytogenes were selected as the foodborne pathogens to verify the analytical performance of this CRISPR-Cas12a triggered photothermal sensor platform. The sensor exhibited a sensitive detection with a low detection limit of 1 CFU/mL, while the concentration ranged from 100 to 108 CFU/mL. Furthermore, this method could efficiently detect target bacteria in multiple food samples. The findings demonstrate that this strategy can serve as a valuable reference for the development of a portable platform enabling quantitative analysis, visualization, and highly sensitive detection of foodborne bacteria.
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Affiliation(s)
- Xijuan Gu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, China
| | - Qu Tang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Xiaoxia Kang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Huoyan Ji
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Xiuying Shi
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Linyi Shi
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Anli Pan
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, China
| | - Wenjun Jiang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jing Zhang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jinxia Liu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Mingmin Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China.
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China.
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3
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Altattan B, Ullrich J, Mattig E, Poppe A, Martins R, Bier FF. Direct TAMRA-dUTP labeling of M. tuberculosis genes using loop-mediated isothermal amplification (LAMP). Sci Rep 2024; 14:5611. [PMID: 38454089 PMCID: PMC10920756 DOI: 10.1038/s41598-024-55289-x] [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: 10/09/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Fluorescent molecule-based direct labeling of amplified DNA is a sensitive method employed across diverse DNA detection and diagnostics systems. However, using pre-labeled primers only allows for the attachment of a single fluorophore to each DNA strand and any modifications of the system are less flexible, requiring new sets of primers. As an alternative, direct labeling of amplified products with modified nucleotides is available, but still poorly characterized. To address these limitations, we sought a direct and adaptable approach to label amplicons produced through Loop-mediated isothermal amplification (LAMP), using labeled nucleotides (dUTPs) rather than primers. The focus of this study was the development and examination of a direct labeling technique of specific genes, including those associated with drug resistance in Mycobacterium tuberculosis. We used 5-(3-Aminoallyl)-2'-deoxyuridine-5'triphosphate, tagged with 5/6-TAMRA (TAMRA-dUTP) for labeling LAMP amplicons during the amplification process and characterized amplification and incorporation efficiency. The optimal TAMRA-dUTP concentration was first determined based on amplification efficiency (0.5% to total dNTPs). Higher concentrations of modified nucleotides reduced or completely inhibited the amplification yield. Target size also showed to be determinant to the success of amplification, as longer sequences showed lower amplification rates, thus less TAMRA incorporated amplicons. Finally, we were able to successfully amplify all four M. tuberculosis target genes using LAMP and TAMRA-modified dUTPs.
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Affiliation(s)
- Basma Altattan
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Jasmin Ullrich
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
| | - Emily Mattig
- Fraunhofer Institute for Cell Therapy and Immunology-Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
| | - Aline Poppe
- Fraunhofer Institute for Cell Therapy and Immunology-Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
| | - Renata Martins
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
| | - Frank F Bier
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
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4
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Liu T, Politza AJ, Kshirsagar A, Zhu Y, Guan W. Compact Point-of-Care Device for Self-Administered HIV Viral Load Tests from Whole Blood. ACS Sens 2023; 8:4716-4727. [PMID: 38011515 PMCID: PMC11222019 DOI: 10.1021/acssensors.3c01819] [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] [Indexed: 11/29/2023]
Abstract
Human immunodeficiency virus (HIV) is a significant problem to consider as it can lead to acquired immune deficiency syndrome (AIDS). Fortunately, AIDS is manageable through antiretroviral therapy (ART). However, frequent viral load monitoring is needed to monitor the effectiveness of the therapy. The current reverse transcription-polymerase chain reaction (RT-PCR) viral load monitoring is highly effective, but is challenged by being resource-intensive and inaccessible, and its turnaround time does not meet demand. An unmet need exists for an affordable, rapid, and user-friendly point-of-care device that could revolutionize and ensure therapeutic effectiveness, particularly in resource-limited settings. In this work, we explored a point-of-care HIV viral load device to address this need. This device can perform streamlined plasma separation, viral RNA extraction, and real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) semiquantitative testing in an ultracompact device. We developed an absorption-based membrane plasma separation method suitable for finger-prick blood samples, achieving an efficiency of 80%. We also designed a syringe-based RNA extraction method for on-site plasma processing with a viral recovery efficiency of 86%. We created a portable device with a smartphone interface for real-time semiquantitative RT-LAMP, which is useful for monitoring viral load. The device uses lyophilized reagents, processed with our lyophilization method, which remain stable for 16 weeks. The device can accurately categorize viral load into low, medium, and high categories with 95% accuracy. We believe this point-of-care HIV self-test device, offering convenience and long-term storage, could aid patients in home-based ART treatment monitoring.
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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
| | - 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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5
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Gulinaizhaer A, Yang C, Zou M, Ma S, Fan X, Wu G. Detection of monkeypox virus using helicase dependent amplification and recombinase polymerase amplification combined with lateral flow test. Virol J 2023; 20:274. [PMID: 37996921 PMCID: PMC10668421 DOI: 10.1186/s12985-023-02223-8] [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: 06/20/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
The monkeypox virus (MPXV) is a zoonotic DNA virus that belongs to the poxvirus family. Conventional laboratory methods for detecting MPXV are complex and expensive, making them unsuitable for detecting the virus in regions with limited resources. In this study, we using the Helicase dependent amplification (HDA) method and the Recombinase polymerase amplification (RPA) technique in combination with the lateral flow test (LFT), together with a self-designed qPCR technique for the detection of the MPXV specific conserved fragment F3L, to compare the sensitivity and specificity of the three assays. By analyzing the sensitivity detection results using Probit, it can be seen that the limit of detection (LOD) of the HDA-LFT detection target is 9.86 copies/µL (95% confidence interval, CI 7.52 copies/µL lower bound), the RPA-LFT detection target is 6.97 copies/µL (95% CI 3.90 copies/µL lower bound), and the qPCR detection target is 479.24 copies/mL (95% CI 273.81 copies/mL lower bound). The specificity test results showed that the specificity of the three methods mentioned above was higher than 90% in detecting pseudoviruses of the same genus of MPXV. The simple, highly sensitive, and specific MPXV assay developed in this study is anticipated to provide a solid foundation for future applications in the early screening, diagnosis, and evaluation of the efficacy of MPXV. This is the first time the HDA-LFT assay has been utilized to detect MPXV infection.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Chuankun Yang
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Mingyuan Zou
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Shuo Ma
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China
| | - Xiaobo Fan
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China.
- Diagnostics Department, Medical School of Southeast University, Nanjing, 210009, People's Republic of China.
| | - Guoqiu Wu
- Zhongda Hospital, Center of Clinical Laboratory Medicine, Medical School, Southeast University, Nanjing, 210009, People's Republic of China.
- Diagnostics Department, Medical School of Southeast University, Nanjing, 210009, People's Republic of China.
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, People's Republic of China.
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6
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Yaren O, McCarter J, Morris AR, Bradley KM, Karalkar NB, McLendon DC, Kim D, Eastmond BH, Burkett-Cadena ND, Alto BW, Benner SA. Multiplex Surveillance Kit Using Sweetened Solid Support to Detect Arboviruses Isothermally in Mosquito Saliva from the Field. Anal Chem 2023; 95:10736-10743. [PMID: 37390024 DOI: 10.1021/acs.analchem.3c01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Recently reported "displaceable probe" loop amplification (DP-LAMP) architecture has shown to amplify viral RNA from SARS-CoV-2 with little sample processing. The architecture allows signals indicating the presence of target nucleic acids to be spatially separated, and independent in sequence, from the complicated concatemer that LAMP processes create as part of their amplification process. This makes DP-LAMP an attractive molecular strategy to integrate with trap and sampling innovations to detect RNA from arboviruses carried by mosquitoes in the field. These innovations include (a) development of organically produced carbon dioxide with ethylene carbonate as a bait deployable in mosquito trap, avoiding the need for dry ice, propane tanks, or inorganic carbonates and (b) a process that induces mosquitoes to lay virus-infected saliva on a quaternary ammonium-functionalized paper (Q-paper) matrix, where (c) the matrix (i) inactivates the deposited viruses, (ii) releases their RNA, and (iii) captures viral RNA in a form that keeps it stable for days at ambient temperatures. We report this integration here, with a surprisingly simple workflow. DP-LAMP with a reverse transcriptase was found to amplify arboviral RNA directly from Q-paper, without requiring a separate elution step. This capture-amplification-detection architecture can be multiplexed, with the entire system integrated into a device that can support a campaign of surveillance, in the wild outdoors, that reports the prevalence of arboviruses from field-captured mosquitoes.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Jacquelyn McCarter
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Andrew R Morris
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- College of Medicine, University of Florida, Gainesville, Florida 32611,, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Nilesh B Karalkar
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Daniel C McLendon
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Dongmin Kim
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Bradley H Eastmond
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
- Thermo Fisher Scientific, Frederick, Maryland 02451, USA
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Barry W Alto
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
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7
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Peng W, Tan Y, Shen C, Tang Y, Li F. Enabling a universal lateral flow readout for DNA strand displacement via disassembling chemical labels. Chem Commun (Camb) 2023. [PMID: 37366312 DOI: 10.1039/d3cc01743e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Herein, we describe a novel strategy that enables lateral flow readout for DNA strand displacement via disassembling chemical labels (DCL). Comparing it to a classic fluorogenic assay, we demonstrate that our DCL-based lateral flow assay is highly sensitive and specific, capable of discriminating single nucleotide variants in buccal swab samples.
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Affiliation(s)
- Wanting Peng
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan 610064, P. R. China.
| | - Yun Tan
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan 610064, P. R. China.
| | - Chenlan Shen
- Department of Laboratory Medicine, Med + X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Yanan Tang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan 610064, P. R. China.
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan 610064, P. R. China.
- Department of Laboratory Medicine, Med + X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
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8
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Maltzeva YI, Gorbenko DA, Nikitina EV, Rubel MS, Kolpashchikov DM. Visual Detection of Stem-Loop Primer Amplification (SPA) Products without Denaturation Using Peroxidase-like DNA Machines (PxDM). Int J Mol Sci 2023; 24:7812. [PMID: 37175522 PMCID: PMC10177805 DOI: 10.3390/ijms24097812] [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: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Rapid, inexpensive, and accurate determination of nucleic acids is a decisive factor in evaluating population's health and monitoring treatment at point-of-care (POC) settings. Testing systems with visual outputs can provide instrument-free signal detection. Isothermal amplification technologies can substitute conventional polymerase chain reaction (PCR) testing due to compatibility with the POC diagnostic. Here, we have visually detected DNA fragments obtained by stem-loop-primer-assisted isothermal amplification (SPA), but not those obtained by PCR or LAMP amplification using DNA nanomachines with peroxidase-like activity (PxDM) with sensitivity to a single nucleotide substitution. Compared to the diagnostics with conventional loop-mediated isothermal amplification (LAMP), the PxDM method produces no false positive signals with the non-specific amplification products. The study suggests that PxDM, in conjunction with SPA isothermal amplification, can become a valid platform for POC testing systems.
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Affiliation(s)
- Yulia I. Maltzeva
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Daria A. Gorbenko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Ekaterina V. Nikitina
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St Petersburg, Russia
| | - Maria S. Rubel
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA;
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32826, USA
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9
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Gou H, Lin Q, Shen H, Jia K, Liang Y, Peng J, Zhang C, Qu X, Li Y, Lin J, Zhang J, Liao M. A novel linear displacement isothermal amplification with strand displacement probes (LDIA-SD) in a pocket-size device for point-of-care testing of infectious diseases. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 379:133244. [PMID: 36589905 PMCID: PMC9789534 DOI: 10.1016/j.snb.2022.133244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Nucleic acid amplification is crucial for disease diagnosis, especially lethal infectious diseases such as COVID-19. Compared with PCR, isothermal amplification methods are advantageous for point-of-care testing (POCT). However, complicated primer design limits their application in detecting some short targets or sequences with abnormal GC content. Herein, we developed a novel linear displacement isothermal amplification (LDIA) method using two pairs of conventional primers and Bacillus stearothermophilus (Bst) DNA polymerase, and reactions could be accelerated by adding an extra primer. Pseudorabies virus gE (high GC content) and Salmonella fimW (low GC content) genes were used to evaluate the LDIA assay. Using strand displacement (SD) probes, a LDIA-SD method was developed to realize probe-based specific detection. Additionally, we incorporated a nucleic acid-free extraction step and a pocket-sized device to realize POCT applications of the LDIA-SD method. The LDIA-SD method has advantages including facile primer design, high sensitivity and specificity, and applicability for POCT, especially for amplification of complex sequences and detection of infectious diseases.
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Affiliation(s)
- Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Qijie Lin
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Haiyan Shen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kaiyuan Jia
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yucen Liang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Junhao Peng
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Chunhong Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Xiaoyun Qu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
- Key Laboratory of Zoonoses, Ministry of Agriculture, Guangzhou 510642, China
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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10
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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11
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A novel fluorescence method based on loop-mediated isothermal amplification and universal molecular beacon in Mycobacterium tuberculosis detection. Talanta 2023. [DOI: 10.1016/j.talanta.2022.123996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Cao H, Xie J, Cheng J, Xu Y, Lu X, Tang J, Zhang X, Wang H. CRISPR Cas12a-Powered Silicon Surface-Enhanced Raman Spectroscopy Ratiometric Chip for Sensitive and Reliable Quantification. Anal Chem 2023; 95:2303-2311. [PMID: 36655772 DOI: 10.1021/acs.analchem.2c03990] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sensitive and reliable clustered regularly interspaced short palindromic repeats (CRISPR) quantification without preamplification of the sample remains a challenge. Herein, we report a CRISPR Cas12a-powered silicon surface-enhanced Raman spectroscopy (SERS) ratiometric chip for sensitive and reliable quantification. As a proof-of-concept application, we select the platelet-derived growth factor-BB (PDGF-BB) as the target. We first develop a microfluidic synthetic strategy to prepare homogeneous silicon SERS substrates, in which uniform silver nanoparticles (AgNPs) are in situ grown on a silicon wafer (AgNPs@Si) by microfluidic galvanic deposition reactions. Next, one 5'-SH-3'-ROX-labeled single-stranded DNA (ssDNA) is modified on AgNPs via Ag-S bonds. In our design, such ssDNA has two fragments: one fragment hybridizes to its complementary DNA (5'-Cy3-labeled ssDNA) to form double-stranded DNA (dsDNA) and the other fragment labeled with 6'-carboxy-X-rhodmine (ROX) extends out as a substrate for Cas12a. The cleavage of the ROX-tagged fragment by Cas12a is controlled by the presence or not of PDGF-BB. Meanwhile, Cy3 molecules serving as internal standard molecules still stay at the end of the rigid dsDNA, and their signals remain constant. Thereby, the ratio of ROX signal intensity to Cy3 intensity can be employed for the reliable quantification of PDGF-BB concentration. The developed chip features an ultrahigh sensitivity (e.g., the limit of detection is as low as 3.2 pM, approximately 50 times more sensitive than the fluorescence counterpart) and good reproducibility (e.g., the relative standard deviation is less than 5%) in the detection of PDGF-BB.
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Affiliation(s)
- Haiting Cao
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Jingxuan Xie
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Jiayi Cheng
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Yanan Xu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Xing Lu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Jie Tang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiaojie Zhang
- Department of Experimental Center, Medical College of Soochow University, Suzhou, Jiangsu 215123, China
| | - Houyu Wang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
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13
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Shin JS, Li S. DNA-Immobilized Fluorescent Polystyrene Nanoparticles as Probes with Tunable Detection Limits. ACS OMEGA 2022; 7:48310-48319. [PMID: 36591202 PMCID: PMC9798753 DOI: 10.1021/acsomega.2c06498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
DNA-immobilized nanoparticle probes show high target specificity; thus, they are employed in various bioengineering and biomedicine applications. When the nanoparticles employed are dye-loaded polymer particles, the resulting probes have the additional benefit of biocompatibility and versatile surface properties. In this study, we construct DNA-immobilized fluorescent polystyrene (PS) nanoparticles through controlled surface reactions. PS nanoparticles with surface carboxyl groups are utilized, and amine-functionalized dye molecules and capture DNAs are covalently immobilized via a one-pot reaction. We show that the surface chemistry employed allows for quantitative control over the number of fluorescent dyes and DNA strands immobilized on the PS nanoparticle surfaces. The nanoparticles thus prepared are then used for DNA detection. The off state of the nanoprobe is achieved by hybridizing quencher-functionalized DNAs (Q-DNAs) to the capture DNAs immobilized on nanoparticle surfaces. Target-DNAs (T-DNAs) are detected by the displacement of the prehybridized Q-DNAs. The nanoprobes show successful detection of T-DNAs with high sequence specificity and long-term stability. They also show excellent detection sensitivity, and the detection limit can be tuned by adjusting the capture DNA-to-dye ratio.
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14
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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15
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Ghouneimy A, Mahas A, Marsic T, Aman R, Mahfouz M. CRISPR-Based Diagnostics: Challenges and Potential Solutions toward Point-of-Care Applications. ACS Synth Biol 2022; 12:1-16. [PMID: 36508352 PMCID: PMC9872163 DOI: 10.1021/acssynbio.2c00496] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has challenged the conventional diagnostic field and revealed the need for decentralized Point of Care (POC) solutions. Although nucleic acid testing is considered to be the most sensitive and specific disease detection method, conventional testing platforms are expensive, confined to central laboratories, and are not deployable in low-resource settings. CRISPR-based diagnostics have emerged as promising tools capable of revolutionizing the field of molecular diagnostics. These platforms are inexpensive, simple, and do not require the use of special instrumentation, suggesting they could democratize access to disease diagnostics. However, there are several obstacles to the use of the current platforms for POC applications, including difficulties in sample processing and stability. In this review, we discuss key advancements in the field, with an emphasis on the challenges of sample processing, stability, multiplexing, amplification-free detection, signal interpretation, and process automation. We also discuss potential solutions for revolutionizing CRISPR-based diagnostics toward sample-to-answer diagnostic solutions for POC and home use.
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Affiliation(s)
- Ahmed Ghouneimy
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory
for Genome Engineering and Synthetic Biology, Division of Biological
Sciences, 4700 King Abdullah University
of Science and Technology, Thuwal 23955-6900, Saudi Arabia,
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16
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Kumar M, Maiti S, Chakraborty D. Capturing nucleic acid variants with precision using CRISPR diagnostics. Biosens Bioelectron 2022; 217:114712. [PMID: 36155952 DOI: 10.1016/j.bios.2022.114712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/02/2022]
Abstract
CRISPR/Cas systems have the ability to precisely target nucleotide sequences and enable their rapid identification and modification. While nucleotide modification has enabled the therapeutic correction of diseases, the process of identifying the target DNA or RNA has greatly expanded the field of molecular diagnostics in recent times. CRISPR-based DNA/RNA detection through programmable nucleic acid binding or cleavage has been demonstrated for a large number of pathogenic and non-pathogenic targets. Combining CRISPR detection with nucleic acid amplification and a terminal signal readout step allowed the development of numerous rapid and robust nucleic acid platforms. Wherever the Cas effector can faithfully distinguish nucleobase variants in the target, the platform can also be extended for sequencing-free rapid variant detection. Some initial PAM disruption-based SNV detection reports were limited to finding or integrating mutated/mismatched nucleotides within the PAM sequences. In this review, we try to summarize the developments made in CRISPR diagnostics (CRISPRDx) to date emphasizing CRISPR-based SNV detection. We also discuss the applications where such diagnostic modalities can be put to use, covering various fields of clinical research, SNV screens, disease genotyping, primary surveillance during microbial infections, agriculture, food safety, and industrial biotechnology. The ease of rapid design and implementation of such multiplexable assays can potentially expand the applications of CRISPRDx in the domain of affinity-based target sequencing, with immense possibilities for low-cost, quick, and widespread usage. In the end, in combination with proximity assays and a suicidal gene approach, CRISPR-based in vivo SNV detection and cancer cell targeting can be formulated as personalized gene therapy.
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Affiliation(s)
- Manoj Kumar
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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17
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Soh JH, Balleza E, Abdul Rahim MN, Chan HM, Mohd Ali S, Chuah JKC, Edris S, Atef A, Bahieldin A, Ying JY, Sabir JS. CRISPR-based systems for sensitive and rapid on-site COVID-19 diagnostics. Trends Biotechnol 2022; 40:1346-1360. [PMID: 35871983 PMCID: PMC9174145 DOI: 10.1016/j.tibtech.2022.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/15/2022] [Accepted: 06/02/2022] [Indexed: 01/21/2023]
Abstract
The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 diagnosis is crucial for effective medical intervention and transmission control. RT-PCR is the most sensitive/specific, but requires costly equipment and trained personnel in centralized laboratories, which are inaccessible to resource-limited areas. Antigen rapid tests enable point-of-care (POC) detection but are significantly less sensitive/specific. CRISPR-Cas systems are compatible with isothermal amplification and dipstick readout, enabling sensitive/specific on-site testing. However, improvements in sensitivity and workflow complexity are needed to spur clinical adoption. We outline the mechanisms/strategies of major CRISPR-Cas systems, evaluate their on-site diagnostic capabilities, and discuss future research directions.
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Affiliation(s)
- Jun Hui Soh
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | - Enrique Balleza
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | | | - Hsi-Min Chan
- Cellbae Pte Ltd, 61 Science Park Road, The Galen, #03-07/08, Singapore 117525, Singapore
| | - Siswand Mohd Ali
- NanoBio Lab, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,A*STAR Infectious Diseases Labs, A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | | | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia,Al-Borg Medical Laboratories, Al Borg Diagnostics, Jeddah, Saudi Arabia
| | - Ahmed Atef
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jackie Y. Ying
- NanoBio Lab, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,A*STAR Infectious Diseases Labs, A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,Institute of Materials Research and Engineering (IMRE), A*STAR, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore,Correspondence:
| | - Jamal S.M. Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, PO Box 80141, Jeddah 21589, Saudi Arabia,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia,Correspondence:
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18
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Sun Y, Xu YX, Wang N, Wang F, Hui CC, Cheng YW, Cui MJ, Huang QY, Xu JG, Kong XM. Time-resolved strand displacement amplification enables G-quadruplex-amplified detection of type 2 diabetes mellitus-related circulating microRNA-146a. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Li R, Wang Q, She K, Lu F, Yang Y. CRISPR/Cas systems usher in a new era of disease treatment and diagnosis. MOLECULAR BIOMEDICINE 2022; 3:31. [PMID: 36239875 PMCID: PMC9560888 DOI: 10.1186/s43556-022-00095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
The discovery and development of the CRISPR/Cas system is a milestone in precise medicine. CRISPR/Cas nucleases, base-editing (BE) and prime-editing (PE) are three genome editing technologies derived from CRISPR/Cas. In recent years, CRISPR-based genome editing technologies have created immense therapeutic potential with safe and efficient viral or non-viral delivery systems. Significant progress has been made in applying genome editing strategies to modify T cells and hematopoietic stem cells (HSCs) ex vivo and to treat a wide variety of diseases and disorders in vivo. Nevertheless, the clinical translation of this unique technology still faces many challenges, especially targeting, safety and delivery issues, which require further improvement and optimization. In addition, with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), CRISPR-based molecular diagnosis has attracted extensive attention. Growing from the specific set of molecular biological discoveries to several active clinical trials, CRISPR/Cas systems offer the opportunity to create a cost-effective, portable and point-of-care diagnosis through nucleic acid screening of diseases. In this review, we describe the development, mechanisms and delivery systems of CRISPR-based genome editing and focus on clinical and preclinical studies of therapeutic CRISPR genome editing in disease treatment as well as its application prospects in therapeutics and molecular detection.
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Affiliation(s)
- Ruiting Li
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China
| | - Qin Wang
- grid.412723.10000 0004 0604 889XSchool of Pharmacy, Southwest Minzu University, Chengdu, 610225 Sichuan China
| | - Kaiqin She
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Fang Lu
- grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yang Yang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
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20
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Zhang J, Hui H, Xu W, Hua K, Cui Y, Liu X. A label-free strategy for visual genotyping based on phosphate induced coloration reaction. RSC Adv 2022; 12:22091-22096. [PMID: 36043069 PMCID: PMC9364437 DOI: 10.1039/d2ra03989c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic variation plays a crucial role in disease occurrence and development. However, current genotyping strategies not only require a long turnaround time for DNA purification, but also depend on sophisticated apparatus and complex data interpretation, which seriously limits their application in point of care diagnostic test scenarios. In this study, by integrating phosphate induced coloration reaction and loop-mediated isothermal amplification, a rapid and portable strategy for straightforward genotyping has been established to cater to the demand of precision medicine. By employing phosphate ions produced during the amplification as a signal generator, not only can the genotyping result be interpreted with only naked eye from a low-cost label-free strip, but also the amplification efficiency is increased to facilitate genotyping with a robust biological specimen ignoring DNA polymerase inhibitors. Moreover, the introduction of alkaline lysis for DNA release allows whole blood to be identified accurately avoiding DNA purification. As a proof of concept, the insertion/deletion polymorphisms of the angiotensin-converting enzyme, a crucial factor associated with cardiovascular and cerebrovascular diseases, has been selected as a model to evaluate the performance of this method. Accurate results can be obtained from as low as 1 ng genomic DNA within 30 min. For clinical specimen detection, a concordance rate up to 100% has been found compared with PCR-based electrophoresis. Thus, this novel strategy may serve as a promising tool for straightforward genotyping to provide timely diagnostic information, especially in resource-poor medical institutions. Phosphate induced coloration reaction facilitates visual genotyping and the target variant can be accurately identified within 30 min from blood directly.![]()
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Affiliation(s)
- Jiaxing Zhang
- College of Life Sciences, Northwest University Xi'an 710069 China .,Department of Immunology, The Fourth Military Medical University Xi'an 710032 China
| | - Hui Hui
- Shannxi Provincial Cancer Hospital Xi'an 710061 China
| | - Wei Xu
- College of Life Sciences, Northwest University Xi'an 710069 China
| | - Kai Hua
- College of Life Sciences, Northwest University Xi'an 710069 China
| | - Yali Cui
- College of Life Sciences, Northwest University Xi'an 710069 China
| | - Xiaonan Liu
- College of Life Sciences, Northwest University Xi'an 710069 China
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21
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Liu T, Choi G, Tang Z, Kshirsagar A, Politza AJ, Guan W. Fingerpick Blood-Based Nucleic Acid Testing on A USB Interfaced Device towards HIV self-testing. Biosens Bioelectron 2022; 209:114255. [PMID: 35429770 PMCID: PMC9110109 DOI: 10.1016/j.bios.2022.114255] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/25/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
HIV self-testing is an emerging innovative approach that allows individuals who want to know their HIV status to collect their own specimen, perform a test, and interpret the results privately. Existing HIV self-testing methods rely on rapid diagnostic tests (RDTs) to detect the presence of HIV-1/2 antibodies, which could miss a significant portion of asymptomatic carriers during the window period. In this work, we present a fully integrated nucleic acid testing (NAT) device towards streamlined HIV self-testing using 100 μL finger-prick whole blood. The device consists of a ready-to-use microfluidic reagent cartridge and an ultra-compact NAT-on-USB analyzer. The test requires simple steps from the user to drop the finger-prick blood sample into a collection tube with lysis buffer and load the lysate onto the microfluidic cartridge, and the testing result can be easily read out by a custom-built graphical user interface (GUI). The microfluidic cartridge and the analyzer automatically handle the complexity of sample preparation, purification, and real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP). With a turnaround time of ∼60 min, we achieved a limit of detection (LoD) of 214 viral RNA copies/mL of whole blood at a 95% confidence level. Due to its ease of use and high sensitivity, we anticipate the HIV NAT-on-USB device would be particularly useful for the high-risk populations seeking private self-testing at the early stages of exposure.
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22
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Qi L, Du Y. Diagnosis of disease relevant nucleic acid biomarkers with off-the-shelf devices. J Mater Chem B 2022; 10:3959-3973. [PMID: 35575030 DOI: 10.1039/d2tb00232a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Changes in the level of nucleic acids in blood may be correlated with some clinical disorders like cancer, stroke, trauma and autoimmune diseases, and thus, nucleic acids can serve as potential biomarkers for pathological processes. The requirement of technical equipment and operator expertise in effective information readout of modern molecular diagnostic technologies significantly restricted application outside clinical laboratories. The ability to detect nucleic acid biomarkers with off-the-shelf devices, which have the advantages of portability, simplicity, low cost and short response time, is critical to provide a prompt clinical result in circumstances where the laboratory instruments are not available. This review throws light on the current strategies and challenges for nucleic acid diagnosis with commercial portable devices, indicating the future prospect of portable diagnostic devices and making a great difference in improving the healthcare and disease surveillance in resource-limited areas.
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Affiliation(s)
- Lijuan Qi
- State key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, P. R. China. .,Department of Chemistry, University of Science and Technology of China, Anhui, P. R. China
| | - Yan Du
- State key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, P. R. China. .,Department of Chemistry, University of Science and Technology of China, Anhui, P. R. China
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23
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Xiong Q, Liu J, Xie G, Mu D, Feng X, Xu H. Blocker-tailed PCR coupled with rolling circle amplification for fluorescent detection of emetic Bacillus cereus in milk. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Lateral flow-based nucleic acid detection of SARS-CoV-2 using enzymatic incorporation of biotin-labeled dUTP for POCT use. Anal Bioanal Chem 2022; 414:3177-3186. [PMID: 35044487 PMCID: PMC8766626 DOI: 10.1007/s00216-022-03880-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 12/29/2022]
Abstract
The degree of detrimental effects inflicted on mankind by the COVID-19 pandemic increased the need to develop ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable) POCT (point of care testing) to overcome the current and any future pandemics. Much effort in research and development is currently advancing the progress to overcome the diagnostic pressure built up by emerging new pathogens. LAMP (loop-mediated isothermal amplification) is a well-researched isothermal technique for specific nucleic acid amplification which can be combined with a highly sensitive immunochromatographic readout via lateral flow assays (LFA). Here we discuss LAMP-LFA robustness, sensitivity, and specificity for SARS-CoV-2 N-gene detection in cDNA and clinical swab-extracted RNA samples. The LFA readout is designed to produce highly specific results by incorporation of biotin and FITC labels to 11-dUTP and LF (loop forming forward) primer, respectively. The LAMP-LFA assay was established using cDNA for N-gene with an accuracy of 95.65%. To validate the study, 82 SARS-CoV-2-positive RNA samples were tested. Reverse transcriptase (RT)-LAMP-LFA was positive for the RNA samples with an accuracy of 81.66%; SARS-CoV-2 viral RNA was detected by RT-LAMP-LFA for as low as CT-33. Our method reduced the detection time to 15 min and indicates therefore that RT-LAMP in combination with LFA represents a promising nucleic acid biosensing POCT platform that combines with smartphone based semi-quantitative data analysis.
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25
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Cai Q, Wu D, Li H, Jie G, Zhou H. Versatile photoelectrochemical and electrochemiluminescence biosensor based on 3D CdSe QDs-DNA nanonetwork-SnO 2 nanoflower coupled with DNA walker amplification for HIV detection. Biosens Bioelectron 2021; 191:113455. [PMID: 34175650 DOI: 10.1016/j.bios.2021.113455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
A novel 3D CdSe quantum dots (QDs)-DNA nanonetwork was assembled to sensitize the mesoporous SnO2 photoelectrochemical (PEC) substrate, which was coupled with a biped-DNA walker multiple amplification technique to design a versatile electrochemiluminescence (ECL) and PEC biosensor for dual detection of HIV. Firstly, the photosensitive CdSe QDs and SnO2 nanoflowers have well-matched band-edge energy level, thus their complex can promote effective transfer of the photogenerated carriers, and show better PEC and ECL property. Then, a novel 3D CdSe QDs-DNA nanonetwork was assembled and loaded with a large amount of QDs, which was used as multifunctional PEC and ECL probes. Moreover, the target-triggered biped DNA walker-cascade amplification method was introduced to generate a large amount of output DNA, which was used to link numerous 3D CdSe QDs-DNA nanonetwork probes to the electrode, generating greatly amplified signals for sensitive assay of HIV. The highly photosensitive 3D CdSe QDs-DNA reticulated nanomaterials have high stability and controllability, and display significantly improved PEC and ECL signals of the biosensor. This method opened a new photoelectric nanocomposite of QDs-sensitized SnO2 nanoflower, and developed a versatile biosensing strategy using the 3D CdSe QDS DNA sensitization probes for ultra-sensitive detection of biomolecules, which is important for the early diagnosis of diseases.
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Affiliation(s)
- Qianqian Cai
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering. Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Di Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering. Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Hongkun Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering. Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering. Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Hong Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering. Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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26
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Zhang J, Lv H, Li L, Chen M, Gu D, Wang J, Xu Y. Recent Improvements in CRISPR-Based Amplification-Free Pathogen Detection. Front Microbiol 2021; 12:751408. [PMID: 34659186 PMCID: PMC8515055 DOI: 10.3389/fmicb.2021.751408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022] Open
Abstract
Molecular diagnostic (MDx) methods directly detect target nucleic acid sequences and are therefore an important approach for precise diagnosis of pathogen infection. In comparison with traditional MDx techniques such as PCR, the recently developed CRISPR-based diagnostic technologies, which employ the single-stranded nucleic acid trans-cleavage activities of either Cas12 or Cas13, show merits in both sensitivity and specificity and therefore have great potential in both pathogen detection and beyond. With more and more efforts in improving both the CRISPR trans-cleavage efficiencies and the signal detection sensitivities, CRISPR-based direct detection of target nucleic acids without preamplification can be a possibility. Here in this mini-review, we summarize recent research progresses of amplification-free CRISPR-Dx systems and explore the potential changes they will lead to pathogen diagnosis. In addition, discussion of the challenges for both detection sensitivity and cost of the amplification-free systems will also be covered.
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Affiliation(s)
- Jian Zhang
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hailong Lv
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, China
| | - Linxian Li
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Minjie Chen
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Dayong Gu
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jin Wang
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yong Xu
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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27
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Lin Q, Fang X, Chen H, Weng W, Liu B, Kong J. Dual-modality loop-mediated isothermal amplification for pretreatment-free detection of Septin9 methylated DNA in colorectal cancer. Mikrochim Acta 2021; 188:307. [PMID: 34453211 PMCID: PMC8396143 DOI: 10.1007/s00604-021-04979-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/07/2021] [Indexed: 12/25/2022]
Abstract
Currently, the determination of DNA methylation is still a challenge due to the limited efficiency of enrichment, bisulfite modification, and detection. In this study, a dual-modality loop-mediated isothermal amplification integrated with magnetic bead isolation is proposed for the determination of methylated Septin9 gene in colorectal cancer. Magnetic beads modified with anti-methyl cytosine antibody were prepared for fast enrichment of methylated DNA through specific immunoaffinity (30 min). One-pot real-time fluorescence and colorimetric loop-mediated isothermal amplification were simultaneously developed for detecting methylated Septin9 gene (60 min). The real-time fluorescence generating by SYTO-9 dye (excitation: 470 nm and emission: 525 nm) and pH indicator (neutral red) was used for quantitative and visualized detection of methylated DNA. This method was demonstrated to detect methylated DNA from HCT 116 cells ranging from 2 to 0.02 ng/μL with a limit of detection of 0.02 ± 0.002 ng/μL (RSD: 9.75%). This method also could discriminate methylated Septin9 in 0.1% HCT 116 cells (RSD: 6.60%), suggesting its high specificity and sensitivity. The feasibility of this assay was further evaluated by clinical plasma samples from 20 colorectal cancer patients and 20 healthy controls, which shows the potential application in simple, low cost, quantitative, and visualized detection of methylated nucleic acids.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China.
| | - Baohong Liu
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
- Shanghai Stomatological Hospital, Shanghai, 200438, People's Republic of China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
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28
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Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F, Collins JJ. CRISPR-based diagnostics. Nat Biomed Eng 2021; 5:643-656. [PMID: 34272525 DOI: 10.1038/s41551-021-00760-7] [Citation(s) in RCA: 433] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 06/02/2021] [Indexed: 02/02/2023]
Abstract
The accurate and timely diagnosis of disease is a prerequisite for efficient therapeutic intervention and epidemiological surveillance. Diagnostics based on the detection of nucleic acids are among the most sensitive and specific, yet most such assays require costly equipment and trained personnel. Recent developments in diagnostic technologies, in particular those leveraging clustered regularly interspaced short palindromic repeats (CRISPR), aim to enable accurate testing at home, at the point of care and in the field. In this Review, we provide a rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, and highlight their main applications in the sensing of a wide range of molecular targets relevant to human health.
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Affiliation(s)
- Michael M Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Feng Zhang
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, MIT, Cambridge, MA, USA. .,Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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29
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Dahiya UR, Gupt GD, Dhaka RS, Kalyanasundaram D. Functionalized Co 2FeAl Nanoparticles for Detection of SARS CoV-2 Based on Reverse Transcriptase Loop-Mediated Isothermal Amplification. ACS APPLIED NANO MATERIALS 2021; 4:5871-5882. [PMID: 37556288 PMCID: PMC8147461 DOI: 10.1021/acsanm.1c00782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/08/2021] [Indexed: 05/12/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive, efficient, and rapid nucleic acid amplification technique resulting in a large number of amplicons; however, it suffers from a high incidence of false positives due to carry-over and aerosol. Herein, we report a 10 min nano-capture system that is used in conjunction with a modified reverse transcriptase-LAMP (RT-LAMP) assay for the accurate detection of SARS CoV-2 virus. The nano-capture system employs in-house-designed probe-functionalized magnetic nanoparticles Co2FeAl (cobalt-based Heusler alloy) for efficient capture of contaminating amplicons from the reaction mixture preceding RT-LAMP. The nano-cleaned RT-LAMP assay along with engineered primers successfully detected the presence of 10 copies of SARS CoV-2 virus while completely eliminating the incidence of false positives. The presented contaminant-capture method has been compared with other approaches for elimination of contaminants and was found to be more effective. The insight brought in this work is the design of a rapid nano-capture system that hybridizes with contaminating amplicons (carry-over) with high specificity to enable easy removal from the assay for elimination of false positives. The method has been proven to be successful for RT-LAMP assays in the rapid and highly specific detection of SARS CoV-2, which is currently a major challenge for global health. To the best of our knowledge, this is the first work involving a nano-based cleaning strategy for reliable and rapid diagnosis using isothermal amplification approaches.
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Affiliation(s)
- Ujjwal Ranjan Dahiya
- Centre for Biomedical Engineering, Indian
Institute of Technology Delhi, New Delhi 110016,
India
| | - Guru Dutt Gupt
- Department of Physics, Indian Institute
of Technology Delhi, New Delhi 110016, India
| | - Rajendra S. Dhaka
- Department of Physics, Indian Institute
of Technology Delhi, New Delhi 110016, India
| | - Dinesh Kalyanasundaram
- Centre for Biomedical Engineering, Indian
Institute of Technology Delhi, New Delhi 110016,
India
- Department of Biomedical Engineering, All
India Institute of Medical Sciences, New Delhi 110029,
India
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30
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Sang P, Hu Z, Cheng Y, Yu H, Xie Y, Yao W, Guo Y, Qian H. Nucleic Acid Amplification Techniques in Immunoassay: An Integrated Approach with Hybrid Performance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5783-5797. [PMID: 34009975 DOI: 10.1021/acs.jafc.0c07980] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An immunoassay is mostly employed for the direct detection of food contaminants, and a molecular assay for targeting nucleic acids employs amplification techniques for distinguishing genes. The integration of an immunoassay with nucleic acid amplification techniques inherits the direct and rapid performance of an immunoassay and the ultrasensitive merit of a molecular assay. Enthusiastic attention has been attracted in recent years on the utilization of isothermal amplification techniques in an immunoassay, as well as the employment of a lateral flow immunoassay in a molecular assay. Thus, this Review discussed these kinds of approaches from two categories: immuno-nucleic acid amplification (I-NAA) and nucleic acid amplification-immunoassay (NAA-I). The advantages, drawbacks, and future developments were discussed for a comprehensive understanding.
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Affiliation(s)
- Panting Sang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhigang Hu
- Wuxi Children's Hospital, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi 214122, China
| | - Yuliang Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hang Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - He Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Center for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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31
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Bhadra S, Nguyen V, Torres JA, Kar S, Fadanka S, Gandini C, Akligoh H, Paik I, Maranhao AC, Molloy J, Ellington AD. Producing molecular biology reagents without purification. PLoS One 2021; 16:e0252507. [PMID: 34061896 PMCID: PMC8168896 DOI: 10.1371/journal.pone.0252507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022] Open
Abstract
We recently developed 'cellular' reagents-lyophilized bacteria overexpressing proteins of interest-that can replace commercial pure enzymes in typical diagnostic and molecular biology reactions. To make cellular reagent technology widely accessible and amenable to local production with minimal instrumentation, we now report a significantly simplified method for preparing cellular reagents that requires only a common bacterial incubator to grow and subsequently dry enzyme-expressing bacteria at 37°C with the aid of inexpensive chemical desiccants. We demonstrate application of such dried cellular reagents in common molecular and synthetic biology processes, such as PCR, qPCR, reverse transcription, isothermal amplification, and Golden Gate DNA assembly, in building easy-to-use testing kits, and in rapid reagent production for meeting extraordinary diagnostic demands such as those being faced in the ongoing SARS-CoV-2 pandemic. Furthermore, we demonstrate feasibility of local production by successfully implementing this minimized procedure and preparing cellular reagents in several countries, including the United Kingdom, Cameroon, and Ghana. Our results demonstrate possibilities for readily scalable local and distributed reagent production, and further instantiate the opportunities available via synthetic biology in general.
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Affiliation(s)
- Sanchita Bhadra
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Vylan Nguyen
- Freshman Research Initiative, DIY Diagnostics Stream, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jose-Angel Torres
- Freshman Research Initiative, DIY Diagnostics Stream, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shaunak Kar
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Inyup Paik
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Andre C. Maranhao
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
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Abstract
Isothermal nucleic acid amplification tests (iNATs), such as loop-mediated isothermal amplification (LAMP), are good alternatives to PCR-based amplification assays, especially for point-of-care and low-resource use, in part because they can be carried out with relatively simple instrumentation. However, iNATs can often generate spurious amplicons, especially in the absence of target sequences, resulting in false-positive results. This is especially true if signals are based on non-sequence-specific probes, such as intercalating dyes or pH changes. In addition, pathogens often prove to be moving, evolving targets and can accumulate mutations that will lead to inefficient primer binding and thus false-negative results. Multiplex assays targeting different regions of the analyte and logical signal readout using sequence-specific probes can help to reduce both false negatives and false positives. Here, we describe rapid conversion of three previously described SARS-CoV-2 LAMP assays that relied on a non-sequence-specific readout into individual and multiplex one-pot assays that can be visually read using sequence-specific oligonucleotide strand exchange (OSD) probes. We describe both fluorescence-based and Boolean logic-gated colorimetric lateral flow readout methods and demonstrate detection of SARS-CoV-2 virions in crude human saliva.IMPORTANCE One of the key approaches to treatment and control of infectious diseases, such as COVID-19, is accurate and rapid diagnostics that is widely deployable in a timely and scalable manner. To achieve this, it is essential to go beyond the traditional gold standard of quantitative PCR (qPCR) that is often faced with difficulties in scaling due to the complexity of infrastructure and human resource requirements. Isothermal nucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), have been long pursued as ideal, low-tech alternatives for rapid, portable testing. However, isothermal approaches often suffer from false signals due to employment of nonspecific readout methods. We describe general principles for rapidly converting nonspecifically read LAMP assays into assays that are read in a sequence-specific manner by using oligonucleotide strand displacement (OSD) probes. We also demonstrate that inclusion of OSD probes in LAMP assays maintains the simplicity of one-pot assays and a visual yes/no readout by using fluorescence or colorimetric lateral-flow dipsticks while providing accurate sequence-specific readout and the ability to logically query multiplex amplicons for redundancy or copresence. These principles not only yielded high-surety isothermal assays for SARS-CoV-2 but might also aid in the design of more sophisticated molecular assays for other analytes.
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Saengsawang N, Ruang-Areerate T, Kesakomol P, Thita T, Mungthin M, Dungchai W. Development of a fluorescent distance-based paper device using loop-mediated isothermal amplification to detect Escherichia coli in urine. Analyst 2021; 145:8077-8086. [PMID: 33078771 DOI: 10.1039/d0an01306d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The highly sensitive and selective determination of Escherichia coli (E. coli) in urine was achieved using a SYBR™ safe loop-mediated isothermal amplification (LAMP) method with a distance-based paper device. New primers set specific to multi-copy the 16s rRNA gene of E. coli were designed and used in this study. The detection sensitivity of these primers was higher than in related work and they could be incorporated with a low-cost paper-based device to quantify E. coli in urine at a concentration lower than 101 CFU mL-1. Regarding standard artificial urine, a linear range of a 10-fold dilution of E. coli concentration (105-100 CFU mL-1) with an R-square value (R2) = 0.9823 was observed directly using a fluorescent migratory distance of the 4 μL reaction mixture in the detection zone under blue light without the need for postreaction staining process. Based on the device, E. coli infection could be significantly categorized into 3 groups; none, light, and heavy levels, which is beneficial for UTI diagnosis. Hence, this paper-based device is suitable for use with the SYBR™ Safe-LAMP assay to semi-quantify E. coli, especially in resource-limited settings due to advantages of low cost, simple fabrication and operation, and no requirement for sophisticated instruments, as well as its disposability and portability.
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Affiliation(s)
- Natkrittaya Saengsawang
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Thailand.
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34
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Hoang TX, Phan LMT, Vo TAT, Cho S. Advanced Signal-Amplification Strategies for Paper-Based Analytical Devices: A Comprehensive Review. Biomedicines 2021; 9:biomedicines9050540. [PMID: 34066112 PMCID: PMC8150371 DOI: 10.3390/biomedicines9050540] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/21/2022] Open
Abstract
Paper-based analytical devices (PADs) have emerged as a promising approach to point-of-care (POC) detection applications in biomedical and clinical diagnosis owing to their advantages, including cost-effectiveness, ease of use, and rapid responses as well as for being equipment-free, disposable, and user-friendly. However, the overall sensitivity of PADs still remains weak, posing a challenge for biosensing scientists exploiting them in clinical applications. This review comprehensively summarizes the current applicable potential of PADs, focusing on total signal-amplification strategies that have been applied widely in PADs involving colorimetry, luminescence, surface-enhanced Raman scattering, photoacoustic, photothermal, and photoelectrochemical methods as well as nucleic acid-mediated PAD modifications. The advances in signal-amplification strategies in terms of signal-enhancing principles, sensitivity, and time reactions are discussed in detail to provide an overview of these approaches to using PADs in biosensing applications. Furthermore, a comparison of these methods summarizes the potential for scientists to develop superior PADs. This review serves as a useful inside look at the current progress and prospective directions in using PADs for clinical diagnostics and provides a better source of reference for further investigations, as well as innovations, in the POC diagnostics field.
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Affiliation(s)
- Thi Xoan Hoang
- Department of Life Science, Gachon University, Seongnam 13120, Gyeonggi-do, Korea; (T.X.H.); (T.A.T.V.)
| | - Le Minh Tu Phan
- Department of Electronic Engineering, Gachon University, Seongnam 13120, Gyeonggi-do, Korea
- School of Medicine and Pharmacy, The University of Danang, Danang 550000, Vietnam
- Correspondence: (L.M.T.P.); (S.C.)
| | - Thuy Anh Thu Vo
- Department of Life Science, Gachon University, Seongnam 13120, Gyeonggi-do, Korea; (T.X.H.); (T.A.T.V.)
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam 13120, Gyeonggi-do, Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea
- Correspondence: (L.M.T.P.); (S.C.)
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35
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Rapid and highly sensitive pathogen detection by real-time DNA monitoring using a nanogap impedimetric sensor with recombinase polymerase amplification. Biosens Bioelectron 2021; 179:113042. [PMID: 33662816 DOI: 10.1016/j.bios.2021.113042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/07/2021] [Accepted: 01/24/2021] [Indexed: 11/23/2022]
Abstract
Fast detection of pathogens is important for protecting our health and society. Herein, we present a high-performance nanogap impedimetric sensor for monitoring nucleic acid amplification in real time using isothermal recombinase polymerase amplification (RPA) for rapid pathogen detection. The nanogap electrode chip has two pairs of opposing gold electrodes with a 100 nm gap and was fixed to a PCB. Then, the nanogap impedimetric sensor was immersed in RPA reaction solution for the detection of E. coli O157:H7, and target DNA amplification was evaluated through bulk solution impedance changes using impedance spectroscopy every minute during RPA. In addition, target gene amplification in the sample solution during RPA was confirmed with a 2% DNA agarose gel. Our nanogap impedimetric sensor can detect down to a single copy of the eae A gene in gDNA extracted from E. coli O157:H7 as well as a single cell of pathogenic E. coli O157:H7 strain within 5 min during direct RPA, which was performed with the pathogen itself and without the extraction and purification of target gDNA. The miniaturized nanogap impedimetric sensor has potential as a cost-effective point-of-care device for fast and accurate portable pathogen detection via real-time nucleic acid analysis.
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Varona M, Eitzmann DR, Anderson JL. Sequence-Specific Detection of ORF1a, BRAF, and ompW DNA Sequences with Loop Mediated Isothermal Amplification on Lateral Flow Immunoassay Strips Enabled by Molecular Beacons. Anal Chem 2021; 93:4149-4153. [PMID: 33635624 DOI: 10.1021/acs.analchem.0c05355] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) holds great potential for point-of-care (POC) diagnostics due to its speed and sensitivity. However, differentiation between spurious amplification and amplification of the target sequence is a challenge. Herein, we develop the use of molecular beacon (MB) probes for the sequence-specific detection of LAMP on commercially available lateral flow immunoassay (LFIA) strips. The detection of three unique DNA sequences, including ORF1a from SARS-CoV-2, is demonstrated. In addition, the method is capable of detecting clinically relevant single-nucleotide polymorphisms (BRAF V600E). For all sequences tested, the LFIA method offers similar sensitivity to fluorescence detection using a qPCR instrument. We also demonstrate the coupling of the method with solid-phase microextraction to enable isolation and detection of the target sequences from human plasma, pond water, and artificial saliva. Lastly, a 3D printed device is designed and implemented to prevent contamination caused by opening the reaction containers after LAMP.
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Affiliation(s)
- Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Derek R Eitzmann
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
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37
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Sivakumar R, Dinh VP, Lee NY. Ultraviolet-induced in situ gold nanoparticles for point-of-care testing of infectious diseases in loop-mediated isothermal amplification. LAB ON A CHIP 2021; 21:700-709. [PMID: 33554994 DOI: 10.1039/d1lc00019e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The present study investigated ultraviolet-induced in situ gold nanoparticles (AuNPs) coupled with loop-mediated isothermal amplification (LAMP) for the point-of-care testing (POCT) of two major infectious pathogens, namely, Coronavirus (COVID-19) and Enterococcus faecium (E. faecium spp.). In the process, gold ions in a gold chloride (HAuCl4) solution were reduced using trisodium citrate (Na3Ct), a reducing agent, and upon UV illumination, red-colored AuNPs were produced in the presence of LAMP amplicons. The nitrogenous bases of the target deoxyribonucleic acid (DNA) acted as a physical support for capturing gold ions dissolved in the sample. The high affinity of gold with the nitrogenous bases enabled facile detection within 10 min, and the detection limit of COVID-19 plasmid DNA was as low as 42 fg μL-1. To ensure POCT, we designed a portable device that contained arrays of reagent chambers and detection chambers. In the portable device, colorimetric reagents such as HAuCl4 and Na3Ct were contained in the reagent chambers; these reagents were subsequently transferred to the detection chambers where LAMP amplicons were present and thus allowed convenient sample delivery and multiplex detection. Owing to the high sensitivity of the in situ AuNPs, simplicity of portable device fabrication, and rapid colorimetric detection, we strongly believe that the fabricated portable device could serve as a kit for rapid POCT for instantaneous detection of infectious diseases, and could be readily usable at the bedside.
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Affiliation(s)
- Rajamanickam Sivakumar
- Department of Industrial Environmental Engineering, College of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Vu Phong Dinh
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
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38
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Zhang C, Zheng T, Wang H, Chen W, Huang X, Liang J, Qiu L, Han D, Tan W. Rapid One-Pot Detection of SARS-CoV-2 Based on a Lateral Flow Assay in Clinical Samples. Anal Chem 2021; 93:3325-3330. [PMID: 33570399 PMCID: PMC7885334 DOI: 10.1021/acs.analchem.0c05059] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/05/2021] [Indexed: 01/01/2023]
Abstract
Rapid tests for pathogen identification and spread assessment are critical for infectious disease control and prevention. The control of viral outbreaks requires a nucleic acid diagnostic test that is sensitive and simple and delivers fast and reliable results. Here, we report a one-pot direct reverse transcript loop-mediated isothermal amplification (RT-LAMP) assay of SARS-CoV-2 based on a lateral flow assay in clinical samples. The entire contiguous sample-to-answer workflow takes less than 40 min from a clinical swab sample to a diagnostic result without professional instruments and technicians. The assay achieved an accuracy of 100% in 12 synthetic and 12 clinical samples compared to the data from PCR-based assays. We anticipate that our method will provide a universal platform for rapid and point-of-care detection of emerging infectious diseases.
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Affiliation(s)
- Chao Zhang
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tingting Zheng
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hua Wang
- Department
of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Chen
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Xiaoye Huang
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Jianqi Liang
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Liping Qiu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Da Han
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Weihong Tan
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute
of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy
of Sciences, Hangzhou, Zhejiang 310018, China
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Moehling TJ, Choi G, Dugan LC, Salit M, Meagher RJ. LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert Rev Mol Diagn 2021; 21:43-61. [PMID: 33474990 DOI: 10.1080/14737159.2021.1873769] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions.Areas covered: In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting.Expert opinion: Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.
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Affiliation(s)
- Taylor J Moehling
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Gihoon Choi
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Lawrence C Dugan
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Div., Livermore, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Lab and Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Robert J Meagher
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
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40
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Paper-Based Nucleic Acid Detection for Point-of-Care Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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41
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Moehling TJ, Lee DH, Henderson ME, McDonald MK, Tsang PH, Kaakeh S, Kim ES, Wereley ST, Kinzer-Ursem TL, Clayton KN, Linnes JC. A smartphone-based particle diffusometry platform for sub-attomolar detection of Vibrio cholerae in environmental water. Biosens Bioelectron 2020; 167:112497. [PMID: 32836088 PMCID: PMC7532658 DOI: 10.1016/j.bios.2020.112497] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 11/30/2022]
Abstract
Each year, 3.4 million people die from waterborne diseases worldwide. Development of a rapid and portable platform for detecting and monitoring waterborne pathogens would significantly aid in reducing the incidence and spread of infectious diseases. By combining optical methods and smartphone technology with molecular assays, the sensitivity required to detect exceedingly low concentrations of waterborne pathogens can readily be achieved. Here, we implement smartphone-based particle diffusometry (PD) detection of loop-mediated isothermal amplification (LAMP) targeting the waterborne pathogen Vibrio cholerae (V. cholerae). By measuring the diffusion of 400 nm streptavidin-coated fluorescent nanoparticles imaged at 68X magnification on a smartphone, we can detect as few as 6 V. cholerae cells per reaction (0.66 aM) in just 35 minutes. In a double-blinded study with 132 pond water samples, we establish a 91.8% sensitivity, 95.2% specificity, and 94.3% accuracy of the smartphone-based PD platform for detection of V. cholerae. Together, these results demonstrate the utility of this smartphone-based PD platform for rapid and sensitive detection of V. cholerae at the point of use.
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Affiliation(s)
- Taylor J Moehling
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Dong Hoon Lee
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Meghan E Henderson
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Mariah K McDonald
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Preston H Tsang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Seba Kaakeh
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Eugene S Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Steven T Wereley
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Katherine N Clayton
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA; OmniVis LLC, Indianapolis, IN, 46201, USA.
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA.
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42
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Ji T, Liu Z, Wang G, Guo X, Akbar Khan S, Lai C, Chen H, Huang S, Xia S, Chen B, Jia H, Chen Y, Zhou Q. Detection of COVID-19: A review of the current literature and future perspectives. Biosens Bioelectron 2020; 166:112455. [PMID: 32739797 PMCID: PMC7371595 DOI: 10.1016/j.bios.2020.112455] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) worldwide pandemic. This unprecedented situation has garnered worldwide attention. An effective strategy for controlling the COVID-19 pandemic is to develop highly accurate methods for the rapid identification and isolation of SARS-CoV-2 infected patients. Many companies and institutes are therefore striving to develop effective methods for the rapid detection of SARS-CoV-2 ribonucleic acid (RNA), antibodies, antigens, and the virus. In this review, we summarize the structure of the SARS-CoV-2 virus, its genome and gene expression characteristics, and the current progression of SARS-CoV-2 RNA, antibodies, antigens, and virus detection. Further, we discuss the reasons for the observed false-negative and false-positive RNA and antibody detection results in practical clinical applications. Finally, we provide a review of the biosensors which hold promising potential for point-of-care detection of COVID-19 patients. This review thereby provides general guidelines for both scientists in the biosensing research community and for those in the biosensor industry to develop a highly sensitive and accurate point-of-care COVID-19 detection system, which would be of enormous benefit for controlling the current COVID-19 pandemic.
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Affiliation(s)
- Tianxing Ji
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China.
| | - Zhenwei Liu
- Guangzhou Institute of Respiratory Medicine Company Limited, Guangzhou, 510535, PR China
| | - GuoQiang Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Xuguang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, PR China
| | - Shahzad Akbar Khan
- Laboratory of Pathology, Department of Pathobiology, University of Poonch Rawalakot, Rawala Kot, 12350, Pakistan
| | - Changchun Lai
- Department of Clinical Laboratory, Maoming People's Hospital, Maoming, 525000, PR China
| | - Haoyu Chen
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Shiwen Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Shaomei Xia
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Bo Chen
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Hongyun Jia
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, HongKong, PR China.
| | - Qiang Zhou
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China.
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43
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Murray LP, Mace CR. Usability as a guiding principle for the design of paper-based, point-of-care devices - A review. Anal Chim Acta 2020; 1140:236-249. [PMID: 33218486 DOI: 10.1016/j.aca.2020.09.063] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Due to their portability, versatility for supporting multiple assay formats, and potential for resulting in low-cost assays, paper-based analytical devices (PADs) are an increasingly popular format as a platform for the development of point-of-care tests. However, very few PADs have been translated successfully to their intended environments outside of academic settings. Often overlooked as a factor that inhibits translation, usability is a vital characteristic of any successful point-of-care test. Recent advancements in PAD design have demonstrated improved usability by simplifying various aspects of user operation, including sample collection, sample processing, device operation, detection, and readout/interpretation. Field testing at various stages of device design can offer critical feedback about device usability, especially when it involves the proposed end-user or other stakeholders. By highlighting advances in usability, we aim to encourage thoughtful and rigorous design at the academic prototyping stage to address one outstanding hurdle that limits the number of PADs that make it from the benchtop to the point-of-care.
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Affiliation(s)
- Lara P Murray
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Charles R Mace
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA.
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44
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Parker RW, Wilson DJ, Mace CR. Open software platform for automated analysis of paper-based microfluidic devices. Sci Rep 2020; 10:11284. [PMID: 32647203 PMCID: PMC7347888 DOI: 10.1038/s41598-020-67639-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/11/2020] [Indexed: 11/21/2022] Open
Abstract
Development of paper-based microfluidic devices that perform colorimetric measurements requires quantitative image analysis. Because the design geometries of paper-based microfluidic devices are not standardized, conventional methods for performing batch measurements of regularly spaced areas of signal intensity, such as those for well plates, cannot be used to quantify signal from most of these devices. To streamline the device development process, we have developed an open-source program called ColorScan that can automatically recognize and measure signal-containing zones from images of devices, regardless of output zone geometry or spatial arrangement. This program, which measures color intensity with the same accuracy as standard manual approaches, can rapidly process scanned device images, simultaneously measure identified output zones, and effectively manage measurement results to eliminate requirements for time-consuming and user-dependent image processing procedures.
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Affiliation(s)
- Rayleigh W Parker
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA, 021551, USA
| | - Daniel J Wilson
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA, 021551, USA
| | - Charles R Mace
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA, 021551, USA.
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45
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Liu S, Yu X, Wang J, Liu D, Wang L, Liu S. Exonuclease III-Powered Self-Propelled DNA Machine for Distinctly Amplified Detection of Nucleic Acid and Protein. Anal Chem 2020; 92:9764-9771. [DOI: 10.1021/acs.analchem.0c01197] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shuang Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Xiaoxiao Yu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Jialong Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Dengren Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Li Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Shufeng Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
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46
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Landaverde L, Wong W, Hernandez G, Fan A, Klapperich C. Method for the elucidation of LAMP products captured on lateral flow strips in a point of care test for HPV 16. Anal Bioanal Chem 2020; 412:6199-6209. [PMID: 32488390 PMCID: PMC7266737 DOI: 10.1007/s00216-020-02702-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/27/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Loop-mediated amplification (LAMP) is an isothermal amplification technique favored in diagnostics and point-of-care work due to its high sensitivity and ability to run in isothermal conditions. In addition, a visual readout by lateral flow strips (LFS) can be used in conjunction with LAMP, making the assay accessible at the point-of-care. However, the amplicons resulting from a LAMP reaction varied in length and shape, making them undiscernible on a double-stranded DNA intercalating dye stained gel. Standard characterization techniques also do not identify which amplicons specifically bind to the LFS, which generate the visual readout. We aimed to standardize our characterization of LAMP products during assay development by using fluorescein amidite (FAM) and biotin-tagged loop forward and backward primers during assay development. A pvuII restriction enzyme digest is applied to the LAMP products. FAM-tagged bands are directly correlated with the LFS visual readout. We applied this assay development workflow for an HPV 16 assay using both plasmid DNA and clinical samples to demonstrate proof of concept for generalized assay development work.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Winnie Wong
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Gabriela Hernandez
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA.
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47
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Rolando JC, Jue E, Barlow JT, Ismagilov RF. Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification. Nucleic Acids Res 2020; 48:e42. [PMID: 32103255 PMCID: PMC7144905 DOI: 10.1093/nar/gkaa099] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/08/2020] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
Isothermal amplification assays, such as loop-mediated isothermal amplification (LAMP), show great utility for the development of rapid diagnostics for infectious diseases because they have high sensitivity, pathogen-specificity and potential for implementation at the point of care. However, elimination of non-specific amplification remains a key challenge for the optimization of LAMP assays. Here, using chlamydia DNA as a clinically relevant target and high-throughput sequencing as an analytical tool, we investigate a potential mechanism of non-specific amplification. We then develop a real-time digital LAMP (dLAMP) with high-resolution melting temperature (HRM) analysis and use this single-molecule approach to analyze approximately 1.2 million amplification events. We show that single-molecule HRM provides insight into specific and non-specific amplification in LAMP that are difficult to deduce from bulk measurements. We use real-time dLAMP with HRM to evaluate differences between polymerase enzymes, the impact of assay parameters (e.g. time, rate or florescence intensity), and the effect background human DNA. By differentiating true and false positives, HRM enables determination of the optimal assay and analysis parameters that leads to the lowest limit of detection (LOD) in a digital isothermal amplification assay.
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Affiliation(s)
- Justin C Rolando
- Division of Chemistry and Chemical Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Erik Jue
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Jacob T Barlow
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
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48
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Basing LAW, Simpson SV, Adu-Sarkodie Y, Linnes JC. A Loop-Mediated Isothermal Amplification Assay for the Detection of Treponema pallidum subsp. pertenue. Am J Trop Med Hyg 2020; 103:253-259. [PMID: 32314703 DOI: 10.4269/ajtmh.19-0243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The eradication of yaws caused by Treponema pallidum subsp. pertenue is constrained by the lack of rapid, accurate diagnosis. We sought to develop a molecular point-of-care test for the diagnosis of yaws. A loop-mediated isothermal amplification (LAMP) assay with primers targeting the conserved gene, tp0967, with visual detection by lateral flow test strip was developed and optimized. The limit of detection was evaluated while 63 samples from clinical cases of yaws and five samples with polymerase chain reaction (PCR)-confirmed syphilis were used to determine the sensitivity and specificity of the assay compared with the current molecular testing protocol. The developed LAMP assay was found to be optimal when run at 65°C for 30 minutes. The limit of detection from extracted DNA was 2.7 × 104 DNA copies/mL. The sensitivity of the LAMP assay using unextracted and DNA extracted samples were 0.67 and 1.00, respectively. None of the syphilis samples tested positive in any of the assays. We show the development of a fast and sensitive LAMP assay for yaws detected by lateral flow test strip. Using extracted DNA, the assay sensitivity is at par with real-time PCR-based detection. The assay can be adapted to minimal sample processing required for infield detection without DNA extraction.
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Affiliation(s)
| | | | | | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
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Byers K, Bird AR, Cho HD, Linnes JC. Fully Dried Two-Dimensional Paper Network for Enzymatically Enhanced Detection of Nucleic Acid Amplicons. ACS OMEGA 2020; 5:4673-4681. [PMID: 32175514 PMCID: PMC7066650 DOI: 10.1021/acsomega.0c00115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/14/2020] [Indexed: 05/04/2023]
Abstract
Two-dimensional paper networks (2DPNs) have enabled the use of paper-based platforms to perform multistep immunoassays for detection of pathogenic diseases at the point-of-care. To date, however, detection has required the user to provide multiple signal enhancement solutions and been limited to protein targets. We solve these challenges by using mathematical equations to guide the device design of a novel 2DPN, which leverages multiple fluidic inputs to apply fully dried solutions of hydrogen peroxide, diaminobenzidine, and horseradish peroxidase signal enhancement reagents to enhance the limit-of-detection of numerous nucleic acid products. Upon rehydration in our unique 2DPN design, the dried signal enhancement solution reduces the limit-of-detection (LOD) of the device to 5 × 1011 nucleic acid copies/mL without increasing false positive detection. Our easy-to-use device retains activity after 28 days of dry storage and produces reliable signal enhancement 40 min after sample application. The fully integrated device demonstrated versatility in its ability to detect double-stranded and single-stranded DNA samples, as well as peptide nucleic acids.
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Affiliation(s)
| | - Anna R. Bird
- Purdue
University, West Lafayette, Indiana 47907, United States
- University
of Cambridge, Cambridge CB3 0AS, U.K.
| | - HyunDae D. Cho
- CrossLife
Technologies Inc., Carlsbad, California 92008, United States
| | - Jacqueline C. Linnes
- Purdue
University, West Lafayette, Indiana 47907, United States
- E-mail: . Phone: 1-765-496-1012
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