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Kulkarni MB, Goel S. Mini-thermal platform integrated with microfluidic device with on-site detection for real-time DNA amplification. Biotechniques 2023; 74:158-171. [PMID: 37139914 DOI: 10.2144/btn-2022-0091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The recent cases of COVID-19 have brought the prospect of and requirement for point-of-care diagnostic devices into the limelight. Despite all the advances in point-of-care devices, there is still a huge requirement for a rapid, accurate, easy-to-use, low-cost, field-deployable and miniaturized PCR assay device to amplify and detect genetic material. This work aims to develop an Internet-of-Things automated, integrated, miniaturized and cost-effective microfluidic continuous flow-based PCR device capable of on-site detection. As a proof of application, the 594-bp GAPDH gene was successfully amplified and detected on a single system. The presented mini thermal platform with an integrated microfluidic device has the potential to be used for the detection of several infectious diseases.
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Affiliation(s)
- Madhusudan B Kulkarni
- MEMS, Microfluidics & Nano Electronics (MMNE) Lab, Department of Electrical & Electronics Engineering, Birla Institute of Technology & Sciences (BITS), Pilani, Hyderabad Campus, Hyderabad, 500078, Telangana, India
| | - Sanket Goel
- MEMS, Microfluidics & Nano Electronics (MMNE) Lab, Department of Electrical & Electronics Engineering, Birla Institute of Technology & Sciences (BITS), Pilani, Hyderabad Campus, Hyderabad, 500078, Telangana, India
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Wang J, Jiang H, Pan L, Gu X, Xiao C, Liu P, Tang Y, Fang J, Li X, Lu C. Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems. Front Bioeng Biotechnol 2023; 11:1020430. [PMID: 36815884 PMCID: PMC9930993 DOI: 10.3389/fbioe.2023.1020430] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.
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Affiliation(s)
- Jingwen Wang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Han Jiang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Leiming Pan
- Zhejiang Hongzheng Testing Co., Ltd., Ningbo, China
| | - Xiuying Gu
- Zhejiang Gongzheng Testing Center Co., Ltd., Hangzhou, China
| | - Chaogeng Xiao
- Institute of Food Science, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Pengpeng Liu
- Key Laboratory of Biosafety detection for Zhejiang Market Regulation, Zhejiang Fangyuan Testing Group LO.T, Hangzhou, China
| | - Yulong Tang
- Hangzhou Tiannie Technology Co., Ltd., Hangzhou, China
| | - Jiehong Fang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoqian Li
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Chenze Lu
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
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Sheu SC, Song YS, Chen JJ. A Portable Continuous-Flow Polymerase Chain Reaction Chip Device Integrated with Arduino Boards for Detecting Colla corii asini. MICROMACHINES 2022; 13:1289. [PMID: 36014212 PMCID: PMC9412515 DOI: 10.3390/mi13081289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Food security is a significant issue in modern society. Because morphological characters are not reliable enough to distinguish authentic traditional Chinese medicines, it is essential to establish an effective and applicable method to identify them to protect people's health. Due to the expensive cost of the manufacturing process and the large volume of the analytical system, the need to build a portable and cheap device is urgent. This work describes the development of a portable nucleic acid amplification device integrated with thermal control and liquid pumping connecting to Arduino boards. We present a novel microfluidic polymerase chain reaction (PCR) chip with symmetric isothermal zones. The total chip volume is small, and only one Arduino board is needed for thermal control. We assemble a miniaturized liquid pump and program an Arduino file to push the sample mixture into the chip to implement the PCR process. In the proposed operation, the Nusselt number of the sample flow is less than one, and the heat transfer is conduction only. Then we can ensure temperature uniformity in specific reaction regions. A Colla corii asini DNA segment of 200 bp is amplified to evaluate the PCR performance under the various operational parameters. The initial concentration for accomplishing the PCR process is at least 20 ng/μL at the flow rate of 0.4 μL/min in the portable continuous flow PCR (CFPCR) device. To our knowledge, our group is the first to introduce Arduino boards into the heat control and sample pumping modules for a CFPCR device.
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Affiliation(s)
- Shyang-Chwen Sheu
- Department of Food Science, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
| | - Yi-Syuan Song
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
| | - Jyh-Jian Chen
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
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Li B, Li Y, Jiang Y, Manz A, Wu W. A digital PCR system based on the thermal cycled chip with multi helix winding capillary. Sci Rep 2020; 10:17824. [PMID: 33082428 PMCID: PMC7576587 DOI: 10.1038/s41598-020-74711-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
This paper presents a digital PCR system based on a novel thermal cycled chip, which wraps microchannels on a trapezoidal structure made of polydimethylsiloxane (PDMS) in a multi-helix manner for the first time. It is found that compared to the single helix chip commonly used in previous reports, this kind of novel multi-helix chip can make the surface temperature in the renaturation zone more uniform, and even in the case of rapid fluid flow, it can improve the efficiency of the polymerase chain reaction. What’s more, the winding method of multi helix (such as double helix, six helix and eight helix) can obtain better temperature uniformity than the winding of odd helix (such as single helix and three helix). As a proof of concept, the temperature-optimized double-helical chip structure is applied to continuous-flow digital PCR and there is no need to add any surfactant to both the oil phase and reagent. In addition, we successfully analyzed the fluorescence signal of continuous-flow digital PCR by using CMOS camera. Finally, this method is applied for the absolute quantification of the clinical serum sample infected by HBV. The accuracy of the test results has been confirmed by commercial instruments.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanming Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Andreas Manz
- Systems Engineering Department, Saarland University, 66123, Saarbrücken, Germany.,Bio Sensor & Materials Group, KIST Europe, 66123, Saarbrücken, Germany
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.
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Enhanced chromosome extraction from cells using a pinched flow microfluidic device. Biomed Microdevices 2020; 22:25. [DOI: 10.1007/s10544-020-0477-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Shu JI, Baysal O, Qian S, Qiu X. Computational Design of a Single Heater Convective Polymerase Chain Reaction for Point-of-Care. J Med Device 2019. [DOI: 10.1115/1.4045130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Abstract
Recently, researchers have started working to develop polymerase chain reaction (PCR) devices as a means for point-of-care (POC) applications. Among the requirements are portability, affordability, and performing reliably and quickly. Proposed by the present study is a process to design a convective-PCR (CPCR) device with only a single heater. It is assumed that such a design developed using microfluidics and capillary tube should help make a CPCR to be portable and more economical for POC use. One of the challenges is to achieve steadily the prerequisite three temperature zones with a single heater. It is demonstrated that this can be done with the present methodology. The underlying physics of the convection driving the CPCR function is mathematically modeled, then verified by our experimental results. In search of better designs, the following parameters that affect the CPCR performance are considered: the heater's height, and the diameter, the height, and the wall thickness of the capillary tube. A large design space consisting of design candidates is defined by combining the values within the range of each of these parameters. The results of the corresponding design cases are obtained from our mathematical model, and the performance of each case is evaluated by their deoxyribonucleic acid (DNA) doubling time. The two best CPCR performing reactors are selected and discussed. It is, therefore, demonstrated that the present methodology is capable of enhancing the CPCR reactor performance with a single heater.
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Affiliation(s)
- Jung Il Shu
- Institute of Micro/Nanotechnology, Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529
| | - Oktay Baysal
- Institute of Micro/Nanotechnology, Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529
| | - Shizhi Qian
- Institute of Micro/Nanotechnology, Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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Wu D, Wu W. Battery Powered Portable Thermal Cycler for Continuous-Flow Polymerase Chain Reaction Diagnosis by Single Thermostatic Thermoelectric Cooler and Open-Loop Controller. SENSORS 2019; 19:s19071609. [PMID: 30987195 PMCID: PMC6479314 DOI: 10.3390/s19071609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/28/2022]
Abstract
Temperature control is the most important and fundamental part of a polymerase chain reaction (PCR). To date, there have been several methods to realize the periodic heating and cooling of the thermal-cycler system for continuous-flow PCR reactions, and three of them were widely used: the thermo-cycled thermoelectric cooler (TEC), the heating block, and the thermostatic heater. In the present study, a new approach called open-loop controlled single thermostatic TEC was introduced to control the thermal cycle during the amplification process. Differing from the former three methods, the size of this microdevice is much smaller, especially when compared to the microdevice used in the heating block method. Furthermore, the rising and cooling speed of this method is much rapider than that in a traditional TEC cycler, and is nearly 20-30% faster than a single thermostatic heater. Thus, a portable PCR system was made without any external heat source, and only a Teflon tube-wrapped TEC chip was used to achieve the continuous-flow PCR reactions. This provides an efficient way to reduce the size of the system and simplify it. In addition, through further experiments, the microdevice is not only found to be capable of amplification of a PCR product from Human papillomavirus type 49 (Genbank ref: X74480.1) and Rubella virus (RUBV), but also enables clinical diagnostics, such as a test for hepatitis B virus.
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Affiliation(s)
- Di Wu
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130000, China.
| | - Wenming Wu
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130000, China.
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Shi B, He G, Wu W. A PCR microreactor machinery with passive micropump and battery-powered heater for thermo-cycled amplifications of clinical-level and multiplexed DNA targets. Mikrochim Acta 2018; 185:467. [DOI: 10.1007/s00604-018-3007-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023]
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Shen H, Qu F, Xia Y, Jiang X. Straightforward and Ultrastable Surface Modification of Microfluidic Chips with Norepinephrine Bitartrate Improves Performance in Immunoassays. Anal Chem 2018; 90:3697-3702. [PMID: 29478312 DOI: 10.1021/acs.analchem.7b05186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Polymers are commonly used materials for microfluidic chip fabrication, because they are standardized in fabrication and low in cost. However, most polymeric materials that are readily fabricated on the industrial scale are hydrophobic, which is inconvenient for the injection and flow of the aqueous solution, resulting in poor analytical performance for biochemical assays. In this work, we present a straightforward and ultrastable surface modification process for polymeric chips. A one-step modification by using norepinephrine bitartrate monohydrate as a modification reagent is completed at room temperature. The hydrophilicity of the polymeric surfaces increases dramatically. Surface modification is stable for at least 2.5 years, allowing for autoinjection of aqueous solution into the channels. The chips are applied in the immunoassay of alpha-fetoprotein (AFP). The low nonspecific adsorption after modification results in significantly decreased background noise, optimized signal-to-noise ratios (SNR), and dramatically enhanced reproducibility of the immunoassay. Thirty clinical human serum samples are analyzed; these results strongly correlated with the values obtained using commercial test kits. We anticipate that this surface modification method can be used for immunoassay devices in analytical and biosensing technology.
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Affiliation(s)
- Haiying Shen
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , People's Republic of China.,Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nano-materials Nanosafety , National Center for Nanoscience and Technology , Beijing 100190 , People's Republic of China
| | - Feng Qu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , People's Republic of China
| | - Yong Xia
- Department of Clinical Laboratory , Third Affiliated Hospital of Guangzhou Medical University , Guangzhou 510150 , People's Republic of China
| | - Xingyu Jiang
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nano-materials Nanosafety , National Center for Nanoscience and Technology , Beijing 100190 , People's Republic of China.,Department of Clinical Laboratory , Third Affiliated Hospital of Guangzhou Medical University , Guangzhou 510150 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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Chen JJ, Li KT. Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System. MICROMACHINES 2018; 9:mi9020048. [PMID: 30393324 PMCID: PMC6187668 DOI: 10.3390/mi9020048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/18/2018] [Accepted: 01/25/2018] [Indexed: 02/07/2023]
Abstract
In order to analyze the DNA amplification numerically with integration of the DNA kinetics, three-dimensional simulations, including flow and thermal fields, and one-dimensional polymerase chain reaction (PCR) kinetics are presented. The simulated results are compared with experimental data that have been applied to the operation of a continuous-flow PCR device. Microchannels fabricated by Micro Electro-Mechanical Systems (MEMS) technologies are shown. Comprehensive simulations of the flow and thermal fields and experiments measuring temperatures during thermal cycling are presented first. The resultant velocity and temperature profiles from the simulations are introduced to the mathematical models of PCR kinetics. Then kinetic equations are utilized to determine the evolution of the species concentrations inside the DNA mixture along the microchannel. The exponential growth of the double-stranded DNA concentration is investigated numerically with the various operational parameters during PCR. Next a 190-bp segment of Bartonella DNA is amplified to evaluate the PCR performance. The trends of the experimental results and numerical data regarding the DNA amplification are similar. The unique architecture built in this study can be applied to a low-cost portable PCR system in the future.
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Affiliation(s)
- Jyh Jian Chen
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan.
| | - Kun Tze Li
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1 Shuefu Road, Neipu, Pingtung 91201, Taiwan.
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Song IH, Park T. PMMA Solution Assisted Room Temperature Bonding for PMMA⁻PC Hybrid Devices. MICROMACHINES 2017; 8:mi8090284. [PMID: 30400474 PMCID: PMC6189942 DOI: 10.3390/mi8090284] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/15/2017] [Accepted: 09/17/2017] [Indexed: 11/16/2022]
Abstract
Recently, thermoplastic polymers have become popular materials for microfluidic chips due to their easy fabrication and low cost. A polymer based microfluidic device can be formed in various fabrication techniques such as laser machining, injection molding, and hot embossing. A new bonding process presented in this paper uses a 2.5% (w/w) polymethyl methacrylate (PMMA) solution as an adhesive layer to bond dissimilar polymers-PMMA to polycarbonate (PC)-to enclose the PMMA microfluidic channels with PC. This technique has been successfully demonstrated to bond PMMA microchip to PC film. This paper presents bonding strength using a shear strength test and a crack opening method in addition to the fluidic leakage inspection.
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Affiliation(s)
- In-Hyouk Song
- Department of Engineering Technology, Texas State University, San Marcos, TX 78666, USA.
| | - Taehyun Park
- School of Mechanical Engineering, Kyungnam University, Changwon 51767, Korea.
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Unloading of cryoprotectants from cryoprotectant-loaded cells on a microfluidic platform. Biomed Microdevices 2017; 19:15. [DOI: 10.1007/s10544-017-0155-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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