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Zhang D, Hu Y, Gao R, Ge S, Zhang J, Zhang X, Xia N. Numerical and experimental investigation on the performance of rapid ultrasonic-assisted nucleic acid extraction based on dispersive two-phase flow. Anal Chim Acta 2024; 1288:342176. [PMID: 38220306 DOI: 10.1016/j.aca.2023.342176] [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: 09/11/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Nucleic acid extraction (NAE) is an essential step in the whole process of nucleic acid detection (NAT). Traditional manual extraction methods are time-consuming and laborious, unfavorable to the point-of-care testing of nucleic acids. Ultrasound has been emphasized due to its noncontact and easy-to-manipulate characteristics, and integration with microfluidic chip can realize rapid NAE through acoustic streaming effect. The uniformity of magnetic bead mixing in this process is a critical factor affecting the extraction effect. In this study, we developed an ultrasound-assisted NAE technique based on the magnetic bead method and optimized the chip structure to achieve rapid NAE. RESULT We use ultrasonic-assisted coupled with magnetic bead method for ultra-fast NAE. The mixing process of magnetic beads driven by acoustic streaming is simulated by a dispersive two-phase flow model, and the ultrasonic incidence angle (θin), cone structure aspect ratio (Dc/Hc) and sheet structure thickness (Hp) are optimized to enhance the mixing performance. Furthermore, the effectiveness of NAE is validated by utilizing quantitative real-time PCR (qPCR) detection. The findings reveal that a θin value of 10° yields superior mixing performance compared to other incidence angles, resulting in a maximum increase of 84 % in mixing intensity. When Dc/Hc = 0.5 and Hp = 0.5 mm, the maximum mixing index in the localized region of the chamber after 1 s of ultrasound action can reach 83.6 % and 92.5 %, respectively. Compared to the original chamber, the CT values extracted after 5 s of ultrasound action shifted forward by up to 1.9 ct and 4.1 ct, respectively. SIGNIFICANCE The dispersed two-phase flow model can effectively simulate the mixing process of magnetic beads, which plays an important role in assisting the structural design of chip extraction chambers. The single-step mixing of ultrasound-assisted NAE takes only 15s to achieve an extraction performance comparable to manual extraction. The extraction process can be completed within 7 min after integrating this technology with microfluidic chips and automated equipment, providing a solution for automated and efficient NAE.
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Affiliation(s)
- Dongxu Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics,National Innovation Platform for Industry-Education Integration in Vaccine Research,the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences,Xiamen University, Xiamen, Fujian, China
| | - Yang Hu
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics,National Innovation Platform for Industry-Education Integration in Vaccine Research,the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences,Xiamen University, Xiamen, Fujian, China; Discipline of Intelligent Instrument and Equipment, Xiamen University, Fujian, China; Department of Experimental Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Runxin Gao
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics,National Innovation Platform for Industry-Education Integration in Vaccine Research,the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences,Xiamen University, Xiamen, Fujian, China; Department of Experimental Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics,National Innovation Platform for Industry-Education Integration in Vaccine Research,the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences,Xiamen University, Xiamen, Fujian, China
| | - Jun Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics,National Innovation Platform for Industry-Education Integration in Vaccine Research,the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences,Xiamen University, Xiamen, Fujian, China
| | - Xianglei Zhang
- School of Mechanical and Electrical Engineering, Wenzhou University, Wenzhou, Zhejiang, China.
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics,National Innovation Platform for Industry-Education Integration in Vaccine Research,the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences,Xiamen University, Xiamen, Fujian, China.
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2
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Dong Y, Chen B, Cai G, Xu F, Li L, Cheng X, Shi X, Peng B, Mi S. Integrated nucleic acid purification technology based on amino-modified centrifugal microfluidic chip. Biotechnol J 2024; 19:e2300113. [PMID: 38050772 DOI: 10.1002/biot.202300113] [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: 03/14/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Nucleic acid detection is an important tool for clinical diagnosis. The purification of the sample is the most time-consuming step in the nucleic acid testing process and will affect the results of the assay. Here, we developed a surface modification-based nucleic acid purification method and designed an accompanying set of centrifugation equipment and chips to integrate the steps of nucleic acid purification on a single platform. The results of experiments with HeLa cells and HPV type 16 as samples showed that the mentioned method had good nucleic acid purification capability and the accompanying equipment greatly simplified the operation of the experimenters in the whole process. Overall, our equipment can improve the efficiency of nucleic acid purification and is suitable for application in larger-scale clinical assays.
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Affiliation(s)
- Yongkang Dong
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Bailiang Chen
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Gangpei Cai
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Fei Xu
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Linzhi Li
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaoqi Cheng
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaolu Shi
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Bo Peng
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Shengli Mi
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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3
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Liu ZJ, Yang LY, Lu TC, Huang C, Liang YQ, Xu XW, Xu YF, Liu MM, Lin XH, Chen JY. Precise Differentiation of Wobble-Type Allele via Ratiometric Design of a Ligase Chain Reaction-Based Electrochemical Biosensor for CYP2C19*2 Genotyping of Clinical Samples. Anal Chem 2023; 95:14592-14599. [PMID: 37683102 DOI: 10.1021/acs.analchem.3c01907] [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: 09/10/2023]
Abstract
Due to the comparable stability between the perfect-base pair and the wobble-base pair, a precise differentiation of the wobble-type allele has remained a challenge, often leading to false results. Herein, we proposed a ligase chain reaction (LCR)-based ratiometric electrochemical DNA sensor, namely, R-eLCR, for a precise typing of the wobble-type allele, in which the traditionally recognized "negative" signal of wobble-base pair-mediated amplification was fully utilized as a "positive" one and a ratiometric readout mode was employed to ameliorated the underlying potential external influence and improved its detection accuracy in the typing of the wobble-type allele. The results showed that the ratio between current of methylene blue (IMB) and current of ferrocene (IFc) was partitioned in three regions and three types of wobble-type allele were thus precisely differentiated (AA homozygote: IMB/IFc > 2; GG homozygote: IMB/IFc < 1; GA heterozygote: 1 < IMB/IFc < 2); the proposed R-eLCR successfully discriminated the three types of CYP2C19*2 allele in nine cases of human whole blood samples, which was consistent with those of the sequencing method. These results evidence that the proposed R-eLCR can serve as an accurate and robust alternative for the identification of wobble-type allele, which lays a solid foundation and holds great potential for precision medicine.
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Affiliation(s)
- Zhou-Jie Liu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Liang-Yong Yang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Tai-Cheng Lu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Chen Huang
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yu-Qi Liang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yan-Fang Xu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Meng-Meng Liu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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Suarez GD, Bayer S, Tang YYK, Suarez DA, Cheung PPH, Nagl S. Rapid microfluidics prototyping through variotherm desktop injection molding for multiplex diagnostics. LAB ON A CHIP 2023; 23:3850-3861. [PMID: 37534874 DOI: 10.1039/d3lc00391d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
In this work, we demonstrate an inexpensive method of prototyping microfluidics using a desktop injection molding machine. A centrifugal microfluidic device with a novel central filling mechanism was developed to demonstrate the technique. We overcame the limitations of desktop machines in replicating microfluidic features by variotherm heating and cooling the mold between 50 °C and 110 °C within two minutes. Variotherm heating enabled good replication of microfeatures, with a coefficient of variation averaging only 3.6% attained for the measured widths of 100 μm wide molded channels. Using this methodology, we produced functional polystyrene centrifugal microfluidic chips, capable of aliquoting fluids into 5.0 μL reaction chambers with 97.5% accuracy. We performed allele-specific loop-mediated isothermal amplification (AS-LAMP) reactions for genotyping CYP2C19 alleles on these chips. Readouts were generated using optical pH sensors integrated onto chips, by drop-casting sensor precursor solutions into reaction chambers before final chip assembly. Positive reactions could be discerned by decreases in pH sensor fluorescence, thresholded against negative control reactions lacking the primers for nucleic acid amplification and with time-to-results averaging 38 minutes. Variotherm desktop injection molding can enable researchers to prototype microfluidic devices more cost-effectively, in an iterative fashion, due to reduced costs of smaller, in-house molds. Designs prototyped this way can be directly translated to mass production, enhancing their commercialization potential and positive impacts.
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Affiliation(s)
- Gianmarco D Suarez
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Steevanson Bayer
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Yuki Yu Kiu Tang
- Quommni Technologies Limited, Tsuen Wan, New Territories, Hong Kong
| | | | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Stefan Nagl
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
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Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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6
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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7
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Liu Q, Zhao M, Song C, Sun J, Tao J, Sun B, Jiang J. Click Triazole as a Linker for Pretargeting Strategies: Synthesis, Docking Investigations, Fluorescence Diagnosis, and Antibacterial Action Studies. Molecules 2023; 28:molecules28062758. [PMID: 36985730 PMCID: PMC10057994 DOI: 10.3390/molecules28062758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
In this study, three compounds A1, A2, and A3 and fluorescent probes T1, T2, T3, and T4 were designed and synthesized. 1H NMR, 13C NMR, and MS characterization and elemental analysis were used to confirm A1-A3 and T1-T4. A1-A3 and T1-T4 formed diagnostic molecules by "click" reactions. A1-A3 and T1-T4 did not significantly increase cell death at concentrations of 80 μmol/L. Preliminary screening of the compounds for antibacterial activity revealed that A2 has better antibacterial activity against Agrobacterium tumefaciens. The synthesized compounds and fluorescent probes can be targeted and combined in the physiological condition to form diagnostic molecules for fluorescence detection of Agrobacterium tumefaciens. The binding sites of A1-A3 were deduced theoretically using the AutoDock Vina software docking tool. Further study of the mechanism of the antibacterial action of these compounds is likely to identify new agents against resistant bacterial strains.
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Affiliation(s)
- Qian Liu
- Department of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Mingxia Zhao
- Department of Mining Engineering, Shanxi Institute of Engineering and Technology, Yangquan 045000, China
| | - Cairong Song
- Department of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Jiankang Sun
- Department of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Jiali Tao
- Department of Mining Engineering, Shanxi Institute of Engineering and Technology, Yangquan 045000, China
| | - Bin Sun
- Department of Mining Engineering, Shanxi Institute of Engineering and Technology, Yangquan 045000, China
| | - Junbing Jiang
- Department of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Department of Mining Engineering, Shanxi Institute of Engineering and Technology, Yangquan 045000, China
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Li Z, Xu X, Wang D, Jiang X. Recent advancements in nucleic acid detection with microfluidic chip for molecular diagnostics. Trends Analyt Chem 2023; 158:116871. [PMID: 36506265 PMCID: PMC9721164 DOI: 10.1016/j.trac.2022.116871] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) has extensively promoted the application of nucleic acid testing technology in the field of clinical testing. The most widely used polymerase chain reaction (PCR)-based nucleic acid testing technology has problems such as complex operation, high requirements of personnel and laboratories, and contamination. The highly miniaturized microfluidic chip provides an essential tool for integrating the complex nucleic acid detection process. Various microfluidic chips have been developed for the rapid detection of nucleic acid, such as amplification-free microfluidics in combination with clustered regularly interspaced short palindromic repeats (CRISPR). In this review, we first summarized the routine process of nucleic acid testing, including sample processing and nucleic acid detection. Then the typical microfluidic chip technologies and new research advances are summarized. We also discuss the main problems of nucleic acid detection and the future developing trend of the microfluidic chip.
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Recent progress in microfluidic biosensors with different driving forces. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Trinh TND, Lee NY. Colorimetric detection of viable antibiotic resistant Enterococcus mediated by cordless operation of reverse transcription loop-mediated isothermal amplification. J Biotechnol 2022; 357:92-99. [PMID: 35952900 DOI: 10.1016/j.jbiotec.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/12/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022]
Abstract
In this study, we applied a tube-based reverse transcription loop-mediated isothermal amplification technique using preloaded amplification and detection reagents for simple screening of viable vancomycin-resistant Enterococcus in a cordless manner. We adopted an mRNA-based approach to detect live Enterococcus in vancomycin-treated cultures. We used agarose to preload and store all reagents for amplification and detection inside the tube, which could achieve on-site isothermal nucleic acid amplification and detection in less than 1 h without using sophisticated instruments. Moreover, the use of a portable insulated water tumbler eliminated the need for electricity, which is usually important in nucleic acid amplification-based assays. The water tumbler acted as a heat source to supply a stable heat required for the amplification reaction, which could last up to 45 min. In addition, colorimetric detection was realized using pH-based methods. The detection was triggered by shaking the tube so that the amplified solution was reacted with phenolphthalein embedded in the tube cap. The introduced one-pot strategy has many advantages such as easy and cordless operation, low cost, disposability, and less chance of contamination because the amplification and detection occur in a closed system. The system could have a great impact on nucleic acid analyses in instrument-free and low-resource areas.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, the Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, the Republic of Korea.
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Wang X, Hong XZ, Li YW, Li Y, Wang J, Chen P, Liu BF. Microfluidics-based strategies for molecular diagnostics of infectious diseases. Mil Med Res 2022; 9:11. [PMID: 35300739 PMCID: PMC8930194 DOI: 10.1186/s40779-022-00374-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/10/2022] [Indexed: 02/08/2023] Open
Abstract
Traditional diagnostic strategies for infectious disease detection require benchtop instruments that are inappropriate for point-of-care testing (POCT). Emerging microfluidics, a highly miniaturized, automatic, and integrated technology, are a potential substitute for traditional methods in performing rapid, low-cost, accurate, and on-site diagnoses. Molecular diagnostics are widely used in microfluidic devices as the most effective approaches for pathogen detection. This review summarizes the latest advances in microfluidics-based molecular diagnostics for infectious diseases from academic perspectives and industrial outlooks. First, we introduce the typical on-chip nucleic acid processes, including sample preprocessing, amplification, and signal read-out. Then, four categories of microfluidic platforms are compared with respect to features, merits, and demerits. We further discuss application of the digital assay in absolute nucleic acid quantification. Both the classic and recent microfluidics-based commercial molecular diagnostic devices are summarized as proof of the current market status. Finally, we propose future directions for microfluidics-based infectious disease diagnosis.
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Affiliation(s)
- Xin Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xian-Zhe Hong
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yi-Wei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China
| | - Jie Wang
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, School of Medicine, Stanford University, Palo Alto, CA, 94304, USA
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Cong H, Zhang N. Perspectives in translating microfluidic devices from laboratory prototyping into scale-up production. BIOMICROFLUIDICS 2022; 16:021301. [PMID: 35350441 PMCID: PMC8933055 DOI: 10.1063/5.0079045] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/23/2022] [Indexed: 05/05/2023]
Abstract
Transforming lab research into a sustainable business is becoming a trend in the microfluidic field. However, there are various challenges during the translation process due to the gaps between academia and industry, especially from laboratory prototyping to industrial scale-up production, which is critical for potential commercialization. In this Perspective, based on our experience in collaboration with stakeholders, e.g., biologists, microfluidic engineers, diagnostic specialists, and manufacturers, we aim to share our understanding of the manufacturing process chain of microfluidic cartridge from concept development and laboratory prototyping to scale-up production, where the scale-up production of commercial microfluidic cartridges is highlighted. Four suggestions from the aspect of cartridge design for manufacturing, professional involvement, material selection, and standardization are provided in order to help scientists from the laboratory to bring their innovations into pre-clinical, clinical, and mass production and improve the manufacturability of laboratory prototypes toward commercialization.
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Affiliation(s)
- Hengji Cong
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical & Materials Engineering, University College Dublin, Dublin 4, Ireland
| | - Nan Zhang
- Author to whom correspondence should be addressed:
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13
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Tortajada-Genaro LA. Design of Oligonucleotides for Allele-Specific Amplification Based on PCR and Isothermal Techniques. Methods Mol Biol 2022; 2392:35-51. [PMID: 34773613 DOI: 10.1007/978-1-0716-1799-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-nucleotide variations have been associated to various genetic diseases, variations on drug efficiency, and differences in cancer prognostics. The detection of these changes in nucleic acid sequences from patient samples is particularly useful for accurate diagnosis, therapeutics, and disease management. A reliable allele-specific amplification is still an important challenge for molecular-based diagnostic technologies. In the last years, allele-specific primers have been designed for promoting the enrichment of certain variants, based on a higher stability of primer/template duplexes. Also, several methods are based on the addition of a blocking oligonucleotide that prevent the amplification of a specific variant, enabling that other DNA variants can be observed. In this context, genotyping methods based on isothermal amplification techniques are increasing, especially those assays aimed to be deployed at point-of-care applications. The correct selection of target sequences is crucial for reaching the required analytical performances, in terms of reaction time, amplification yield, and selectivity. The present chapter describes the design criteria for the selection of primers and blockers for relevant PCR approaches and novel isothermal strategies. Several successful examples are provided in order to highlight the main design restrictions and the potential to be extended to other applications.
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Affiliation(s)
- Luis Antonio Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Valencia, Spain.
- Departamento de Química, Universitat Politècnica de València, Valencia, Spain.
- Unidad Mixta UPV-La Fe, Nanomedicine and sensors, Valencia, Spain.
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14
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Tortajada-Genaro LA. DNA Genotyping Based on Isothermal Amplification and Colorimetric Detection by Consumer Electronics Devices. Methods Mol Biol 2022; 2393:163-178. [PMID: 34837179 DOI: 10.1007/978-1-0716-1803-5_9] [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] [Indexed: 06/13/2023]
Abstract
The point-of-care testing of DNA biomarkers requires compact biosensing systems and consumer electronic technologies provide fascinating opportunities. Their portability, mass-produced components, and high-performance readout capabilities are the main advantages for the development of novel bioanalytical methods.This chapter describes the detection of single nucleotide polymorphisms (SNP) through methods based on user-friendly optical devices (e.g., USB digital microscope, flatbed scanner, smartphone, and DVD drive). Loop mediated isothermal amplification (LAMP) enables the required discrimination of each specific variant prior to the optical reading. In the first method, products are directly hybridized to the allele-specific probes attached to plastic chips in an array format. The second method, allele-specific primers are used, enabling the direct end-point detection based a colorimetric dyer and a microfluidic chamber chip. In both approaches, devices are employed for chip scanning.A representative application to the genotyping of a clinically relevant SNP from human samples is provided, showing the excellent features achieved. Consumer electronic devices are able to register sensitive precise measurements in terms of signal-to-noise ratios, image resolution, and scan-to-scan reproducibility. The integrated DNA-based method lead a low detection limit (100 genomic DNA copies), reproducible (variation <15%), high specificity (genotypes validated by reference method), and cheap assays (<10 €/test). The underlying challenge is the reliable implementation into minimal-specialized clinical laboratories, incorporating additional advantages, such as user-friendly interface, low cost, and connectivity for telemedicine needs.
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Affiliation(s)
- Luis Antonio Tortajada-Genaro
- Chemistry Department, Universitat Politècnica de València, Valencia, Spain.
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Valencia, Spain.
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15
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Zhou M, Su H, Wang B, Wan C, Du W, Chen P, Feng X, Liu BF. A magnet-actuated microfluidic array chip for high-throughput pretreatment and amplification and detection of multiple pathogens. Analyst 2022; 147:2433-2441. [DOI: 10.1039/d2an00430e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The outbreak of global infectious diseases has posed a significant threat to public health, requiring the rapid and accurate diagnosis of pathogens promptly for society to implement immediate control measures to prevent widespread pandemics.
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Affiliation(s)
- Mengfan Zhou
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huiying Su
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui 232038, China
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bangfeng Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chao Wan
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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16
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Chu H, Liu C, Liu J, Yang J, Li Y, Zhang X. Recent advances and challenges of biosensing in point-of-care molecular diagnosis. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 348:130708. [PMID: 34511726 PMCID: PMC8424413 DOI: 10.1016/j.snb.2021.130708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/07/2023]
Abstract
Molecular diagnosis, which plays a major role in infectious disease screening with successful understanding of the human genome, has attracted more attention because of the outbreak of COVID-19 recently. Since point-of-care testing (POCT) can expand the application of molecular diagnosis with the benefit of rapid reply, low cost, and working in decentralized environments, many researchers and commercial institutions have dedicated tremendous effort and enthusiasm to POCT-based biosensing for molecular diagnosis. In this review, we firstly summarize the state-of-the-art techniques and the construction of biosensing systems for POC molecular diagnosis. Then, the application scenarios of POCT-based biosensing for molecular diagnosis were also reviewed. Finally, several challenges and perspectives of POC biosensing for molecular diagnosis are discussed. This review is expected to help researchers deepen comprehension and make progresses in POCT-based biosensing field for molecular diagnosis applications.
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Affiliation(s)
- Hongwei Chu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Conghui Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jinsen Liu
- Shenzhen ENCO Instrument Co., Ltd, Shenzhen 518000, China
| | - Jiao Yang
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yingchun Li
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Xueji Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
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17
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Liu W, Yue F, Lee LP. Integrated Point-of-Care Molecular Diagnostic Devices for Infectious Diseases. Acc Chem Res 2021; 54:4107-4119. [PMID: 34699183 DOI: 10.1021/acs.accounts.1c00385] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The global outbreaks of deadly infectious diseases caused by pathogenic microorganisms have threatened public health worldwide and significantly motivated scientists to satisfy an urgent need for a rapid and accurate detection of pathogens. Traditionally, the culture-based technique is considered as the gold standard for pathogen detection, yet it has a long turnaround time due to the overnight culturing and pathogen isolation. Alternatively, nucleic acid amplification tests provide a relatively shorter turnaround time to identify whether pathogens exist in individuals with high sensitivity and high specificity. In most cases, nucleic acid amplification tests undergo three steps: sample preparation, nucleic acid amplification, and signal transduction. Despite the explosive advancement in nucleic acid amplification and signal transduction technologies, the complex and labor-intensive sample preparation steps remain a bottleneck to create a transformative integrated point-of-care (POC) molecular diagnostic device. Researchers have attempted to simplify and integrate the sample preparations for nucleic acid-based molecular diagnostic devices with innovative progress in integration strategies, engineered materials, reagent storages, and fluid actuation. Therefore, understanding the know-how and obtaining truthful knowledge of existing integrated POC molecular diagnostic devices comprising sample preparations, nucleic acid amplification, and signal transduction can generate innovative solutions to achieve personalized precision medicine and improve global health.In this Account, we discuss the challenges of automated sample preparation solutions integrated with nucleic acid amplification and signal transduction for rapid and precise home diagnostics. Blood, nasal swab, saliva, urine, and stool are emphasized as the most commonly used clinical samples for integrated POC molecular diagnostics of infectious diseases. Even though these five types of samples possess relatively correlated biomarkers due to the human body's circulatory system, each shows unique properties and exclusive advantages for molecular diagnostics in specific situations, which are included in this Account. We examine different integrated POC devices for sample preparation, which includes pathogen isolation and enrichment from the crude sample and nucleic acid purification from isolated pathogens. We present the promising on-chip integration approaches for nucleic acid amplification. We also investigate the on-chip integration methods for reagent storage, which is crucial to simplify the manual operation for end-users. Finally, we present several integrated POC molecular diagnostic devices for infectious diseases. The integrated sample preparation and nucleic acid amplification approach reviewed here can potentially impact the next generation of POC molecular home diagnostic chips, which will significantly impact public health, emergency medicine, and global biosecurity.
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Affiliation(s)
- Wenpeng Liu
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Fei Yue
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Luke P. Lee
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley 94720, California, United States
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
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18
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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19
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Zhou W, Dou M, Timilsina SS, Xu F, Li X. Recent innovations in cost-effective polymer and paper hybrid microfluidic devices. LAB ON A CHIP 2021; 21:2658-2683. [PMID: 34180494 PMCID: PMC8360634 DOI: 10.1039/d1lc00414j] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Hybrid microfluidic systems that are composed of multiple different types of substrates have been recognized as a versatile and superior platform, which can draw benefits from different substrates while avoiding their limitations. This review article introduces the recent innovations of different types of low-cost hybrid microfluidic devices, particularly focusing on cost-effective polymer- and paper-based hybrid microfluidic devices. In this article, the fabrication of these hybrid microfluidic devices is briefly described and summarized. We then highlight various hybrid microfluidic systems, including polydimethylsiloxane (PDMS)-based, thermoplastic-based, paper/polymer hybrid systems, as well as other emerging hybrid systems (such as thread-based). The special benefits of using these hybrid systems have been summarized accordingly. A broad range of biological and biomedical applications using these hybrid microfluidic devices are discussed in detail, including nucleic acid analysis, protein analysis, cellular analysis, 3D cell culture, organ-on-a-chip, and tissue engineering. The perspective trends of hybrid microfluidic systems involving the improvement of fabrication techniques and broader applications are also discussed at the end of the review.
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Affiliation(s)
- Wan Zhou
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA.
| | - Maowei Dou
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA.
| | - Sanjay S Timilsina
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA.
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - XiuJun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W University Ave., El Paso, TX 79968, USA. and Border Biomedical Research Center, Biomedical Engineering, University of Texas at El Paso, 500 West University Ave., El Paso, TX 79968, USA and Environmental Science and Engineering, University of Texas at El Paso, 500 West University Ave., El Paso, TX 79968, USA
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20
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Liu D, Shen H, Zhang Y, Shen D, Zhu M, Song Y, Zhu Z, Yang C. A microfluidic-integrated lateral flow recombinase polymerase amplification (MI-IF-RPA) assay for rapid COVID-19 detection. LAB ON A CHIP 2021; 21:2019-2026. [PMID: 34008614 DOI: 10.1039/d0lc01222j] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, currently poses an urgent global medical crisis for which there remains a lack of affordable point-of-care testing (POCT). In particular, resource-limited areas need simple and easily disseminated testing solutions to manage the outbreak. In this work, a microfluidic-integrated lateral flow recombinase polymerase amplification (MI-IF-RPA) assay was developed for rapid and sensitive detection of SARS-CoV-2, which integrates the reverse transcription recombinase polymerase amplification (RT-RPA) and a universal lateral flow (LF) dipstick detection system into a single microfluidic chip. The single-chamber RT-RPA reaction components are mixed with running buffer, and then delivered to the LF detection strips for biotin- and FAM-labelled amplified analyte sequences, which can provide easily interpreted positive or negative results. Testing requires only a simple nucleic acid extraction and loading, then incubation to obtain results, approximately 30 minutes in total. SARS-CoV-2 armored RNA particles were used to validate the MI-IF-RPA system, which showed a limit of detection of 1 copy per μL, or 30 copies per sample. Chip performance was further evaluated using clinically diagnosed cases of COVID-19 and revealed a sensitivity of 97% and specificity of 100%, highly comparable to current reverse transcription-polymerase chain reaction (RT-PCR)-based diagnostic assays. This MI-IF-RPA assay is portable and comprises affordable materials, enabling mass production and decreased risk of contamination. Without the need for specialized instrumentation and training, MI-IF-RPA assay can be used as a complement to RT-PCR for low-cost COVID-19 screening in resource-limited areas.
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Affiliation(s)
- Dan Liu
- School of Biomedical Sciences, Huaqiao University, Xiamen 362000, China.
| | - Haicong Shen
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Yuqian Zhang
- School of Biomedical Sciences, Huaqiao University, Xiamen 362000, China.
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyang Zhu
- School of Biomedical Sciences, Huaqiao University, Xiamen 362000, China.
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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21
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Hong T, Qiu L, Zhou S, Cai Z, Cui P, Zheng R, Wang J, Tan S, Jiang P. How does DNA 'meet' capillary-based microsystems? Analyst 2021; 146:48-63. [PMID: 33211035 DOI: 10.1039/d0an01336f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA possesses various chemical and physical properties which make it important in biological analysis. The opportunity for DNA to 'meet' capillary-based microsystems is rapidly increasing owing to the expanding development of miniaturization. Novel capillary-based methods can provide favourable platforms for DNA-ligand interaction assay, DNA translocation study, DNA separation, DNA aptamer selection, DNA amplification assay, and DNA digestion. Meanwhile, DNA exhibits great potential in the fabrication of new capillary-based biosensors and enzymatic bioreactors. Moreover, DNA has received significant research interest in improving capillary electrophoresis (CE) performance. We focus on highlighting the advantages of combining DNA and capillary-based microsystems. The general trend presented in this review suggests that the 'meeting' has offered a stepping stone for the application of DNA and capillary-based microsystems in the field of analytical chemistry.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
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22
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Chen Y, Mei Y, Jiang X. Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip. Chem Sci 2021; 12:4455-4462. [PMID: 34163711 PMCID: PMC8179484 DOI: 10.1039/d0sc05717g] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/07/2021] [Indexed: 12/14/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are associated with many human diseases, so accurate and efficient SNP detection is of great significance for early diagnosis and clinical prognosis. This report proposes a universal and high-fidelity genotyping method in microfluidic point-of-care equipment based on the clustered regularly interspaced short palindromic repeat (CRISPR) system. Briefly, by systematically inserting the protospacer-adjacent-motif (PAM) sequence, we improved the universality of the CRISPR/Cas12a based SNP detection; by removing the complementary ssDNA and introducing an additional nucleotide mismatch, we improved the sensitivity and specificity. We preloaded the CRISPR/Cas12a reagents into the point-of-care biochip for automating the process, increasing the stability and long-term storage. This biochip enables us to rapidly and conveniently detect the genotypes within 20 min. In a practical application, the CRISPR/Cas12a biochip successfully distinguished three genotypes (homozygous wild type; the homozygous mutant type; and the heterozygous mutant type) of the CYP1A1*2 (A4889G, rs1048943), CYP2C19*2 (G681A, rs4244285), CYP2C9*3 (A1075C, rs1057910), and CYP2C19*3 (G636A, rs4986893) genes related to multiple cancers from 17 clinical blood samples. This CRISPR/Cas12a-based SNP genotyping method, being universal, accurate, and sensitive, will have broad applications in molecular diagnostics and clinical research.
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Affiliation(s)
- Yong Chen
- Department of Biomedical Engineering, Southern University of Science and Technology No. 1088, Xueyuan Rd., Xili, Nanshan District Shenzhen Guangdong China
| | - Yixin Mei
- Department of Biomedical Engineering, Southern University of Science and Technology No. 1088, Xueyuan Rd., Xili, Nanshan District Shenzhen Guangdong China
| | - Xingyu Jiang
- Department of Biomedical Engineering, Southern University of Science and Technology No. 1088, Xueyuan Rd., Xili, Nanshan District Shenzhen Guangdong China
- Shenzhen Bay Laboratory Shenzhen Guangdong 518055 China
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23
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Ali SA, Boby N, Preena P, Singh SV, Kaur G, Ghosh SK, Nandi S, Chaudhuri P. Microcapillary LAMP for rapid and sensitive detection of pathogen in bovine semen. Anim Biotechnol 2021; 33:1025-1034. [PMID: 33427030 DOI: 10.1080/10495398.2020.1863225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A microcapillary-based loop-mediated isothermal amplification (µcLAMP) has been described for specific detection of infectious reproductive pathogens in semen samples of cattle without sophisticated instrumentation. Brucella abortus, Leptospira interrogans serovar Pomona and bovine herpesvirus 1 (BoHV-1) cultures were mixed in bovine semen samples. The µcLAMP assay is portable, user-friendly, cost-effective, and suitable to be performed as a POC diagnostic test. We have demonstrated high sensitivity and specificity of µcLAMP for detection of Brucella, Leptospira, and BoHV-1 in bovine semen samples comparable to PCR and qPCR assays. Thus, µcLAMP would be a promising field-based test for monitoring various infectious pathogens in biological samples.HighlightsDetect infectious organism in bovines semenReduction in carryover contamination is an important attribute, which may reduce the false-positive reaction.µcLAMP is a miniaturized form, which could be performed with a minimum volume of reagents.The µcLAMP assay is portable, user-friendly, and suitable to be performed as a POC diagnostic test.
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Affiliation(s)
- Syed Atif Ali
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, India
| | - Nongthombam Boby
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, India
| | - Prasanna Preena
- Division of Veterinary Medicine, Indian Veterinary Research Institute, Izatnagar, India
| | - Shiv Varan Singh
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, India
| | - Gurpreet Kaur
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, India
| | - Subrata Kumar Ghosh
- Division of Animal Reproduction, Indian Veterinary Research Institute, Izatnagar, India
| | - Sukdeb Nandi
- CADRAD, Indian Veterinary Research Institute, Izatnagar, India
| | - Pallab Chaudhuri
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar, India
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Paper-Based Molecular Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_8] [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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25
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Das D, Namboodiri S. Selection of a suitable paper membrane for Loop Mediated Isothermal DNA amplification reaction (LAMP) in a point-of-care diagnostic kit – Experimental and CFD analysis. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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26
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Paul R, Ostermann E, Wei Q. Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases. Biosens Bioelectron 2020; 169:112592. [PMID: 32942143 PMCID: PMC7476893 DOI: 10.1016/j.bios.2020.112592] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022]
Abstract
Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.
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Affiliation(s)
- Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emily Ostermann
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA; Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, 27695, USA.
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Chen Y, Mei Y, Zhao X, Jiang X. Reagents-Loaded, Automated Assay that Integrates Recombinase-Aided Amplification and Cas12a Nucleic Acid Detection for a Point-of-Care Test. Anal Chem 2020; 92:14846-14852. [DOI: 10.1021/acs.analchem.0c03883] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yong Chen
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Yixin Mei
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Xiaohui Zhao
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Xingyu Jiang
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
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Qin Z, Peng R, Baravik IK, Liu X. Fighting COVID-19: Integrated Micro- and Nanosystems for Viral Infection Diagnostics. MATTER 2020; 3:628-651. [PMID: 32838297 PMCID: PMC7346839 DOI: 10.1016/j.matt.2020.06.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) highlights the importance of rapid and sensitive diagnostics of viral infection that enables the efficient tracing of cases and the implementation of public health measures for disease containment. The immediate actions from both academia and industry have led to the development of many COVID-19 diagnostic systems that have secured fast-track regulatory approvals and have been serving our healthcare frontlines since the early stage of the pandemic. On diagnostic technologies, many of these clinically validated systems have significantly benefited from the recent advances in micro- and nanotechnologies in terms of platform design, analytical method, and system integration and miniaturization. The continued development of new diagnostic platforms integrating micro- and nanocomponents will address some of the shortcomings we have witnessed in the existing COVID-19 diagnostic systems. This Perspective reviews the previous and ongoing research efforts on developing integrated micro- and nanosystems for nucleic acid-based virus detection, and highlights promising technologies that could provide better solutions for the diagnosis of COVID-19 and other viral infectious diseases. With the summary and outlook of this rapidly evolving research field, we hope to inspire more research and development activities to better prepare our society for future public health crises.
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Affiliation(s)
- Zhen Qin
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Ran Peng
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Ilina Kolker Baravik
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Xinyu Liu
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
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Tian F, Liu C, Deng J, Han Z, Zhang L, Chen Q, Sun J. A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing. Sci China Chem 2020; 63:1498-1506. [PMID: 32837510 PMCID: PMC7387882 DOI: 10.1007/s11426-020-9800-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
The outbreak of virus-induced infectious diseases poses a global public-health challenge. Nucleic acid amplification testing (NAAT) enables early detection of pandemic viruses and plays a vital role in preventing onward transmission. However, the requirement of skilled operators, expensive instrumentation, and biosafety laboratories has hindered the use of NAAT for screening and diagnosis of suspected patients. Here we report development of a fully automated centrifugal microfluidic system with sample-in-answer-out capability for sensitive, specific, and rapid viral nucleic acid testing. The release of nucleic acids and the subsequent reverse transcription loop-mediated isothermal amplification (RT-LAMP) were integrated into the reaction units of a microfluidic disc. The whole processing steps such as injection of reagents, fluid actuation by rotation, heating and temperature control, and detection of fluorescence signals were carried out automatically by a customized instrument. We validate the centrifugal microfluidic system using oropharyngeal swab samples spiked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) armored RNA particles. The estimated limit of detection for armored RNA particles is 2 copies per reaction, the throughput is 21 reactions per disc, and the assay sample-to-answer time is approximately 70 min. This enclosed and automated microfluidic system efficiently avoids viral contamination of aerosol, and can be readily adapted for virus detection outside the diagnostic laboratory.
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Affiliation(s)
- Fei Tian
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chao Liu
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ziwei Han
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lu Zhang
- Department of Chemistry, Capital Normal University, Beijing, 100048 China
| | - Qinghua Chen
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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Tian F, Liu C, Deng J, Han Z, Zhang L, Chen Q, Sun J. A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing. SCIENCE CHINA. CHEMISTRY 2020. [PMID: 32837510 DOI: 10.1007/s11426-020-9800-6,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The outbreak of virus-induced infectious diseases poses a global public-health challenge. Nucleic acid amplification testing (NAAT) enables early detection of pandemic viruses and plays a vital role in preventing onward transmission. However, the requirement of skilled operators, expensive instrumentation, and biosafety laboratories has hindered the use of NAAT for screening and diagnosis of suspected patients. Here we report development of a fully automated centrifugal microfluidic system with sample-in-answer-out capability for sensitive, specific, and rapid viral nucleic acid testing. The release of nucleic acids and the subsequent reverse transcription loop-mediated isothermal amplification (RT-LAMP) were integrated into the reaction units of a microfluidic disc. The whole processing steps such as injection of reagents, fluid actuation by rotation, heating and temperature control, and detection of fluorescence signals were carried out automatically by a customized instrument. We validate the centrifugal microfluidic system using oropharyngeal swab samples spiked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) armored RNA particles. The estimated limit of detection for armored RNA particles is 2 copies per reaction, the throughput is 21 reactions per disc, and the assay sample-to-answer time is approximately 70 min. This enclosed and automated microfluidic system efficiently avoids viral contamination of aerosol, and can be readily adapted for virus detection outside the diagnostic laboratory. Electronic Supplementary Material Supplementary material is available for this article at 10.1007/s11426-020-9800-6 and is accessible for authorized users.
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Affiliation(s)
- Fei Tian
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chao Liu
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ziwei Han
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lu Zhang
- Department of Chemistry, Capital Normal University, Beijing, 100048 China
| | - Qinghua Chen
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement of Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Li R, Chen J, Zhang X, Cui J, Tao S, Yang L. Mini-Disk Capillary Array Coupling with LAMP for Visual Detection of Multiple Nucleic Acids using Genetically Modified Organism Analysis as an Example. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:899-906. [PMID: 31891505 DOI: 10.1021/acs.jafc.9b06979] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Convenient, portable, and low-cost multiplex nucleic acid testing (NAT) systems are the trends in the fields of food safety, environmental microorganisms, molecular diagnosis, etc. In this study, we developed a novel system for visual monitoring of multiple nucleic acids combining a mini-disk capillary array (diameter = 17 mm, embedded with 6-10 capillaries), visual loop-mediated isothermal amplification (LAMP), and quick DNA extraction called mDC-LAMP. The performance and applicability of mDC-LAMP in testing multiple nucleic acids were evaluated and verified employing genetically modified contents analysis as an example. All of the results confirmed that mDC-LAMP has the advantages of high specificity without any cross contamination, high sensitivity with a limit of detection of 25 copies/reaction, high throughput with flexible channel sensors, easy fabrication, and low costs. We believe that mDC-LAMP is a competitive choice for on-spot monitoring of multiple nucleic acids in terms of the easy fabrication/operation, low costs, and suitable performance presented in the nucleic acids test.
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Affiliation(s)
- Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jianwei Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xiujie Zhang
- Development Center of Science and Technology , Ministry of Agriculture of People's Republic of China , Beijing 100025 , China
| | - Jingjie Cui
- Institute of Cotton Research , Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology , Anyang 455000 , Henan , China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
- Institute of Cotton Research , Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology , Anyang 455000 , Henan , China
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Zeng Y, Liu M, Xia Y, Jiang X. Uracil-DNA-glycosylase-assisted loop-mediated isothermal amplification for detection of bacteria from urine samples with reduced contamination. Analyst 2020; 145:7048-7055. [PMID: 32894274 DOI: 10.1039/d0an01001d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Urine specimens are detected by conventional culture method and colonies with more than 104 are identified by MALDI-TOF MS. Meanwhile, we analyze urine samples using FTA cards for simple DNA extraction and UDG-assisted LAMP.
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Affiliation(s)
- Yingmin Zeng
- Department of Clinical Laboratory
- Third Affiliated Hospital of Guangzhou Medical University
- Guangzhou
- People's Republic of China
| | - Meiling Liu
- Department of Clinical Laboratory
- Third Affiliated Hospital of Guangzhou Medical University
- Guangzhou
- People's Republic of China
| | - Yong Xia
- Department of Clinical Laboratory
- Third Affiliated Hospital of Guangzhou Medical University
- Guangzhou
- People's Republic of China
| | - Xingyu Jiang
- Department of Biomedical Engineering
- Southern University of Science and Technology
- Shenzhen
- People's Republic of China
- Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety
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33
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Brunauer A, Ates HC, Dincer C, Früh SM. Integrated paper-based sensing devices for diagnostic applications. COMPREHENSIVE ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/bs.coac.2020.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Yin J, Suo Y, Zou Z, Sun J, Zhang S, Wang B, Xu Y, Darland D, Zhao JX, Mu Y. Integrated microfluidic systems with sample preparation and nucleic acid amplification. LAB ON A CHIP 2019; 19:2769-2785. [PMID: 31365009 PMCID: PMC8876602 DOI: 10.1039/c9lc00389d] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Rapid, efficient and accurate nucleic acid molecule detection is important in the screening of diseases and pathogens, yet remains a limiting factor at point of care (POC) treatment. Microfluidic systems are characterized by fast, integrated, miniaturized features which provide an effective platform for qualitative and quantitative detection of nucleic acid molecules. The nucleic acid detection process mainly includes sample preparation and target molecule amplification. Given the advancements in theoretical research and technological innovations to date, nucleic acid extraction and amplification integrated with microfluidic systems has advanced rapidly. The primary goal of this review is to outline current approaches used for nucleic acid detection in the context of microfluidic systems. The secondary goal is to identify new approaches that will help shape future trends at the intersection of nucleic acid detection and microfluidics, particularly with regard to increasing disease and pathogen detection for improved diagnosis and treatment.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanjie Suo
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Jingjing Sun
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Shan Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Beng Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009 China and Institute of Translational Medicine, Zhejiang University, Hangzhou, 310029 China
| | - Yawei Xu
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, Jilin, 132000 China
| | - Diane Darland
- Department of Biology, University of North Dakota, USA.
| | | | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
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35
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Li L, Geng Y, Xiang Y, Qiang H, Wang Y, Chang J, Zhao H, Zhang L. Instrument-free enrichment and detection of phosphopeptides using paper-based Phos-PAD. Anal Chim Acta 2019; 1062:102-109. [DOI: 10.1016/j.aca.2019.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/05/2019] [Indexed: 01/24/2023]
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36
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Ding S, Chen R, Chen G, Li M, Wang J, Zou J, Du F, Dong J, Cui X, Huang X, Deng Y, Tang Z. One-step colorimetric genotyping of single nucleotide polymorphism using probe-enhanced loop-mediated isothermal amplification (PE-LAMP). Am J Cancer Res 2019; 9:3723-3731. [PMID: 31281509 PMCID: PMC6587344 DOI: 10.7150/thno.33980] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphism (SNP) is the most abundant molecular marker associated with many physiologic and pathologic phenotypes. An isothermal, accurate and cost-effective SNP detection could make a great difference in point-of-care testing (POCT) or on-site diagnosis. However, there are two challenges, the expensive instrument and labor-intensive process, faced by the development of on-site SNP detection. We reported a novel SNP typing method based on the probe-enhanced loop-mediated isothermal amplification (PE-LAMP), which combines the oligonucleotide probe with a conventional LAMP to realize the SNP discrimination by analyzing the great discrepancy in amplification efficiency. Methods: We firstly constructed the genotyping method by combining the hybridization of the specific probe with the powerful amplification of LAMP. Then we validated the method by genotyping the SNP rs3741219 and we sought to realize one-step visualized typing. Finally, we applied the method to pharmacogenomic testing by genotyping CYP2C19*2 and MDR1 C3435T. Results: The PE-LAMP was successfully constructed to detect SNP and the sensitivity of our method is as low as 1000 copies of target DNA, which is sufficient to routine diagnosis. The high specificity in detecting mutant in the presence of excess wild-type allele could be achieved. It has shown good performance in helping predict the individual response of antiplatelet drug Clopidogrel through typing simply treated saliva samples. Conclusions: The proposed method is one-step, colorimetric, specific and sensitive enough to detect crudely treated samples, showing great potential in the pharmacogenomic study and POCT use.
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Zhang J, Su X, Xu J, Wang J, Zeng J, Li C, Chen W, Li T, Min X, Zhang D, Zhang S, Ge S, Zhang J, Xia N. A point of care platform based on microfluidic chip for nucleic acid extraction in less than 1 minute. BIOMICROFLUIDICS 2019; 13:034102. [PMID: 31123534 PMCID: PMC6506337 DOI: 10.1063/1.5088552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/19/2019] [Indexed: 05/25/2023]
Abstract
In view of the complex procedure of nucleic acid extraction, there exists a huge challenge for the widespread use of point-of-care diagnostics for nucleic acid testing. To achieve point-of-care applications in a more rapid and cost-efficient manner, we designed a snake pipe-shaped microfluidic chip so as to accomplish reagents-prestored, time-saving, operation-simple nucleic acid extraction. All reagents needed for this process, including lysis buffer, wash buffer, elution buffer, and so on, were preloaded in the snake pipe and securely isolated by membrane valves, without the need for using any specialized equipment. By an integrated chip and a powerful ultrasonic, this device could complete virus nucleic acid extraction from sophisticated serum samples in less than 1 min. We used hepatitis B virus (HBV) and human immunodeficiency virus (HIV) mixed with different sources of serum as samples to be extracted. The coefficient of variation of HBV and HIV extraction on-chip was 1.32% and 2.74%, respectively, and there were no significant differences between on-chip and commercial instrument extraction (P > 0.05, α = 0.05) in different dilution ratios, which showed that the extraction device we established had excellent stability and sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Shiyin Zhang
- Authors to whom correspondence should be addressed: and
| | - Shengxiang Ge
- Authors to whom correspondence should be addressed: and
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Fully integrated and slidable paper-embedded plastic microdevice for point-of-care testing of multiple foodborne pathogens. Biosens Bioelectron 2019; 135:120-128. [PMID: 31004922 DOI: 10.1016/j.bios.2019.04.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/27/2022]
Abstract
This study presents a slidable paper-embedded plastic microdevice fully integrated with DNA extraction, loop-mediated isothermal amplification (LAMP), and colorimetric detection functionalities. The developed microdevice consists of three layers that allow a sliding movement to mix the sample and reagents for DNA purification, amplification, and detection in a sequential manner. An FTA card was employed in the main chamber for DNA extraction and purification from intact bacterial cells. Subsequently, LAMP reagents and fuchsin-stored chambers were pulled toward the main chambers for DNA amplifications at 65 °C. After 30 min, the detection reagents-stored chambers were then moved to main chambers for result analysis. For the detection of LAMP amplicons, a novel colorimetric fuchsin-based method was employed. The wide applicability of the integrated microdevice was demonstrated by successfully screening three major foodborne pathogens, namely Salmonella spp., Staphylococcus aureus, and Escherichia coli O157:H7 in food, enabling highly sensitive detection of 3.0 × 101 CFU/sample of Gram-negative bacteria (Salmonella spp. and Escherichia coli O157:H7) and 3.0 × 102 CFU/sample of Gram-positive bacteria (Staphylococcus aureus) within 75 min. The portable and integrated microdevice presented in this study holds significant promise for point-of-care applications to accurately and rapidly diagnose and control diseases.
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Filipenko ML, Oscorbin IP, Khrapov EA, Shamovskaya DA, Cherednichenko AG, Shvartz Y. Detection of Ser450Leu mutation in rpoB gene of Mycobacterium tuberculosis by allele-specific loop-mediated isothermal DNA amplification method. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify genetic mutations a rather time-consuming and expensive method of polymerase chain reaction (PCR) is widely used. The aim of the present work was to evaluate the possibility of using the two schemes of the method of allele-specific isothermal loop amplification (LAMP) to detect the TCG/TTG (S450L) mutation in the rpoB gene of Mycobacterium tuberculosis. 48 clinical isolates of M. tuberculosis and 11 samples of sputum were used, randomized and obtained in the microbiological laboratory of the city of Novosibirsk from incident patients. It is shown that the use of an analysis scheme using the allele-specific primer FIP compared to F3 has the best resolution: the difference between the amplification time of the mutation and the wild type allele was 22 ± 2,4 versus 13 ± 4,1 minutes (p = 0,0011). When using 100 DNA genomic equivalents a true positive signal (amplification of the rpoB gene with a mutation using the corresponding allele-specific primer) was detected after 29,4 ± 3,4 minutes. A positive signal was visualized after adding SYBR Green I to the reaction, both when illuminated with daylight and when using a UV transilluminator. Using the developed method the DNA sample of 20 RIFR isolates from M. tuberculosis was analyzed containing the Ser450Leu mutation in the rpoB gene, 10 RIFR isolates containing other mutations in the rpoB gene and 18 RIFs isolates without any mutations; the presence of mutations in the samples was determined using classical Sanger sequencing. The sensitivity and specificity of LAMP for detecting a Ser450Leu mutation in the rpoB gene was 100%. This approach allows the use of crude lysates of mycobacteria as DNA, which reduces the total analysis time to 1,5 hour.
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Affiliation(s)
- ML Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - IP Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - EA Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - DA Shamovskaya
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - YaSh Shvartz
- Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
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Zhang H, Xu Y, Fohlerova Z, Chang H, Iliescu C, Neuzil P. LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification. Trends Analyt Chem 2019; 113:44-53. [PMID: 32287531 PMCID: PMC7112807 DOI: 10.1016/j.trac.2019.01.015] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP. Introduction of loop mediated isothermal amplification (LAMP) and its principle. Classical microfluidics-based LAMP for DNA/RNA detection. Paper-based LAMP. Microfluidic-based digital LAMP. Future of microfluidic LAMP development.
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Affiliation(s)
- Haoqing Zhang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ying Xu
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerova
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic.,Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600 Brno, Czech Republic
| | - Honglong Chang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ciprian Iliescu
- Biomedical Institute for Global Health Research and Technology (BIGHEART), National University of Singapore, MD6, 14 Medical Drive #14-01, 117599, Singapore
| | - Pavel Neuzil
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China.,Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic
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41
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Kaur N, Toley BJ. Paper-based nucleic acid amplification tests for point-of-care diagnostics. Analyst 2019; 143:2213-2234. [PMID: 29683153 DOI: 10.1039/c7an01943b] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There has been a recent resurgence in the use of paper as a substrate for developing point-of-care medical diagnostic tests, possibly triggered by expiring patents published in the 1990s. A hallmark of this resurgence has been the development of advanced shapes and structures made from paper to conduct multi-step fluidic operations using the wicking action of porous materials. Such devices indicate a distinct improvement over lateral flow immunoassays, which are restricted to conducting one-step operations. New developments in paper-based diagnostic devices have triggered interest in the development of paper-based point-of-care nucleic acid amplification tests (NAATs). NAATs can identify extremely low levels of specific nucleic acid sequences from clinical samples and are the most sensitive of all available tests for infectious disease diagnosis. Because traditional PCR-based NAATs require expensive instruments, the development of portable paper-based NAAT's has become an exciting field of research. This article aims to review and analyse the current state of development of paper-based NAATs. We project paper-based NAATs as miniaturized chemical processes and shed light on various schemes of operation used for converting the multiple steps of the chemical processes into paper microfluidic devices. We conclude by elaborating on the challenges that must be overcome in the near future so that progress can be made towards the development of fully functional and commercial paper-based NAATs.
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Affiliation(s)
- Navjot Kaur
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India560012.
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42
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Wang J, Zheng J, Zhang S, Du J, Chen Y, Liu X, Zhang H, Jiang X, Chen W. High-throughput blood sample preparation for single nucleotide polymorphism genotyping in less than 25 min. Talanta 2019; 191:119-125. [PMID: 30262040 DOI: 10.1016/j.talanta.2018.08.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/13/2018] [Accepted: 08/18/2018] [Indexed: 11/17/2022]
Abstract
Straightforward, rapid and high-throughput pretreatment for single nucleotide polymorphisms (SNP) genotyping is critically needed in clinical practice. However, all existing SNP genotyping methods require DNA purification step, which is labor-intensive and time-consuming. We develop a protocol for SNP genotyping by combining whole blood lysis (WBL) with qPCR and justify the practicality of our method in blood samples from 140 donors, including 40 samples from healthy donors, and 100 samples from donors with either low white blood cell counts, high level of serum uric acid or triglyceride. When compared with Sanger sequencing, the gold standard for SNP genotyping, our method exhibits a 100% consistency in the aspect of sensitivity and specificity. In addition, our method can obtain amplifiable DNA within 25 mins (which is the fastest to the best of our knowledge) from 48 samples. The blood samples, even with low white blood cell counts, high level of serum uric acid or triglyceride could not affect the sensitivity and specificity of our method. Our study demonstrates that the combination of WBL and qPCR genotyping can serve as a high-throughput and robust approach for routine clinical SNP genotyping.
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Affiliation(s)
- Jidong Wang
- Central Laboratory, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Jiaying Zheng
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Shaohua Zhang
- Department of Breast Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, PR China
| | - Jihui Du
- Central Laboratory, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Yongxin Chen
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Xiaolei Liu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Huisheng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology & Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing 100190, PR China.
| | - Wenwen Chen
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, PR China.
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43
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Liu C, An Y, Zhang Y, Li X, Xue Q, Wang H. Digital quantitative detection of serum circulating miRNAs using dual-enhanced magnetobiosensors based on cascaded nucleic acid circuits. Chem Commun (Camb) 2019; 55:13733-13736. [DOI: 10.1039/c9cc07841j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here, we developed a dual-enhanced magnetobiosensor based on cascaded nucleic acid circuits for sensitive, portable and digital quantitative detection of circulating miRNAs in serum by a personal glucose meter (PGM).
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Affiliation(s)
- Chunxue Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Yayun An
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Yuanfu Zhang
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Xia Li
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Qingwang Xue
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Huaisheng Wang
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
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44
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Shang Y, Sun J, Ye Y, Zhang J, Zhang Y, Sun X. Loop-mediated isothermal amplification-based microfluidic chip for pathogen detection. Crit Rev Food Sci Nutr 2018; 60:201-224. [DOI: 10.1080/10408398.2018.1518897] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuting Shang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiadi Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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45
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Jiang X, Loeb JC, Manzanas C, Lednicky JA, Fan ZH. Valve-Enabled Sample Preparation and RNA Amplification in a Coffee Mug for Zika Virus Detection. Angew Chem Int Ed Engl 2018; 57:17211-17214. [PMID: 30358036 DOI: 10.1002/anie.201809993] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/07/2018] [Indexed: 11/07/2022]
Abstract
The recent outbreaks of Zika virus (ZIKV) infection represent a public health challenge. Rapid, cost-effective, and reliable diagnostic tools for ZIKV detection at the point of care (POC) are highly desirable, especially for resource-limited nations. To address the need, we have developed an integrated device to achieve sample-to-answer ZIKV detection. The device features innovative ball-based valves enabling the storage and sequential delivery of reagents for virus lysis and a paper-based unit for RNA enrichment and purification. The paper unit is placed in a commercially available coffee mug that provides a constant temperature for reverse transcription loop-mediated isothermal amplification (RT-LAMP), followed by colorimetric detection by naked eye or a cellphone camera. Using the device, we demonstrated the reproducible detection of ZIKV in human urine and saliva samples.
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Affiliation(s)
- Xiao Jiang
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Julia C Loeb
- Department of Environmental and Global Health, and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Carlos Manzanas
- Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
| | - John A Lednicky
- Department of Environmental and Global Health, and Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Z Hugh Fan
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA.,Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL, 32611, USA
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46
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Jiang X, Loeb JC, Manzanas C, Lednicky JA, Fan ZH. Valve‐Enabled Sample Preparation and RNA Amplification in a Coffee Mug for Zika Virus Detection. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiao Jiang
- J. Crayton Pruitt Family Department of Biomedical Engineering University of Florida Gainesville FL 32611 USA
| | - Julia C. Loeb
- Department of Environmental and Global Health, and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
| | - Carlos Manzanas
- Department of Mechanical and Aerospace Engineering University of Florida P.O. Box 116250 Gainesville FL 32611 USA
| | - John A. Lednicky
- Department of Environmental and Global Health, and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
| | - Z. Hugh Fan
- J. Crayton Pruitt Family Department of Biomedical Engineering University of Florida Gainesville FL 32611 USA
- Department of Mechanical and Aerospace Engineering University of Florida P.O. Box 116250 Gainesville FL 32611 USA
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47
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Hui J, Gu Y, Zhu Y, Chen Y, Guo SJ, Tao SC, Zhang Y, Liu P. Multiplex sample-to-answer detection of bacteria using a pipette-actuated capillary array comb with integrated DNA extraction, isothermal amplification, and smartphone detection. LAB ON A CHIP 2018; 18:2854-2864. [PMID: 30105321 DOI: 10.1039/c8lc00543e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A pipette-actuated capillary array comb (PAAC) system operated on a smartphone-based hand-held device has been successfully developed for the multiplex detection of bacteria in a "sample-to-answer" manner. The PAAC consists of eight open capillaries inserted into a cylindrical plastic base with a piece of chitosan-modified glass filter paper embedded in each capillary. During the sample preparation, a PAAC was mounted into a 1 mL pipette tip with an enlarged opening and was operated with a 1 mL pipette for liquid handling. The cell lysate was drawn and expelled through the capillaries three times to facilitate the DNA capture on the embedded filter discs. Following washes with water, the loop-mediated isothermal amplification (LAMP) reagents were aspirated into the capillaries, in which the primers were pre-fixed with chitosan. After that, the PAAC was loaded into the smartphone-based device for a one-hour amplification at 65 °C and end-point detection of calcein fluorescence in the capillaries. The DNA capture efficiency of a 1.1 mm-diameter filter disc was determined to be 97% of λ-DNA and the coefficient of variation among the eight capillaries in the PAAC was only 2.2%. The multiplex detection of genomic DNA extracted from Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus provided limits of detection of 200, 500, and 500 copies, respectively, without any cross-contamination and cross reactions. "Sample-to-answer" detection of E. coli samples was successfully completed in 85 minutes, demonstrating a sensitivity of 200 cfu per capillary. The multiplex "sample-to-answer" detection, the streamlined operation, and the compact device should facilitate a broad range of applications of our PAAC system in point-of-care testing.
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Affiliation(s)
- Junhou Hui
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
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48
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Wang SX, Liu KS, Lou YF, Wang SQ, Peng YB, Chen JP, Huang JH, Xie SX, Cui L, Wang X. RNase H meets molecular beacons: an ultrasensitive fluorometric assay for nucleic acids. Mikrochim Acta 2018; 185:375. [DOI: 10.1007/s00604-018-2909-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/30/2018] [Indexed: 12/31/2022]
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49
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Liu W, Das J, Mepham AH, Nemr CR, Sargent EH, Kelley SO. A fully-integrated and automated testing device for PCR-free viral nucleic acid detection in whole blood. LAB ON A CHIP 2018; 18:1928-1935. [PMID: 29881833 DOI: 10.1039/c8lc00371h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Integrated devices for automated nucleic acid testing (NAT) are critical for infectious disease diagnosis to be performed outside of centralized laboratories. The gold standard methods for NAT are enzymatic amplification methods like the polymerase chain reaction that typically require expensive equipment and highly-trained personnel, limiting use in low-resource settings. A low-cost, integrated, rapid, portable and user-friendly point-of-care (POC) nucleic acid diagnostic device will improve the accessibility of NAT. Here, we present a fully integrated and simple-to-use POC device operated by a passive fluidic method that is able to perform a sequential multi-step assay to detect viral nucleic acids in blood. This simple device enabled the rapid detection of hepatitis C virus in blood in approximately 30 minutes with minimal sample handling by the user.
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Affiliation(s)
- Wenhan Liu
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, M5S 3G9 Canada.
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50
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Yamanaka ES, Tortajada-Genaro LA, Pastor N, Maquieira Á. Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection. Biosens Bioelectron 2018; 109:177-183. [DOI: 10.1016/j.bios.2018.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 02/07/2023]
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