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Khosla NK, Lesinski JM, Colombo M, Bezinge L, deMello AJ, Richards DA. Simplifying the complex: accessible microfluidic solutions for contemporary processes within in vitro diagnostics. LAB ON A CHIP 2022; 22:3340-3360. [PMID: 35984715 PMCID: PMC9469643 DOI: 10.1039/d2lc00609j] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/15/2022] [Indexed: 05/02/2023]
Abstract
In vitro diagnostics (IVDs) form the cornerstone of modern medicine. They are routinely employed throughout the entire treatment pathway, from initial diagnosis through to prognosis, treatment planning, and post-treatment surveillance. Given the proven links between high quality diagnostic testing and overall health, ensuring broad access to IVDs has long been a focus of both researchers and medical professionals. Unfortunately, the current diagnostic paradigm relies heavily on centralized laboratories, complex and expensive equipment, and highly trained personnel. It is commonly assumed that this level of complexity is required to achieve the performance necessary for sensitive and specific disease diagnosis, and that making something affordable and accessible entails significant compromises in test performance. However, recent work in the field of microfluidics is challenging this notion. By exploiting the unique features of microfluidic systems, researchers have been able to create progressively simple devices that can perform increasingly complex diagnostic assays. This review details how microfluidic technologies are disrupting the status quo, and facilitating the development of simple, affordable, and accessible integrated IVDs. Importantly, we discuss the advantages and limitations of various approaches, and highlight the remaining challenges within the field.
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Affiliation(s)
- Nathan K Khosla
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Jake M Lesinski
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Monika Colombo
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Léonard Bezinge
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Daniel A Richards
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
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Lozeman JJA, Elsbecker T, Bohnenn S, de Boer HL, Krakers M, Mul G, van den Berg A, Odijk M. Modular microreactor with integrated reflection element for online reaction monitoring using infrared spectroscopy. LAB ON A CHIP 2020; 20:4166-4174. [PMID: 33030158 DOI: 10.1039/d0lc00704h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report on the fabrication of an internal reflection element (IRE) combined with a modular polymer microfluidic chip that can be used for attenuated total reflection (ATR) infrared spectroscopy. The IRE is fabricated from a silicon wafer. Two different polymers are used for the fabrication of the two types of modular microfluidic chips, namely polydimethylsiloxane (PDMS) and cyclic olefin copolymer (COC). The microfluidic chip is modular in the sense that several layers of mixing channels, using the herringbone mixer principle, and reactions chambers, can be stacked to facilitate the study of the desired reaction. A model Paal-Knorr reaction is carried out to prove that the chip works as intended. Furthermore, we highlight the strength of IR spectroscopy as a tool for reaction monitoring by identifying the peaks and showing the different reaction orders at the different steps of the Paal-Knorr reaction. The reduction of the aldehyde groups indicates a (pseudo) first order reaction whereas the vibrational modes associated with the ring formation indicate a zero order reaction. This zero order reaction can be explained with literature, where it is suggested that water acts as a catalyst during the dehydration step, which is the final step in the pyrrole ring formation.
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Affiliation(s)
- Jasper J A Lozeman
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
| | - Tobias Elsbecker
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
| | - Sylvie Bohnenn
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
| | - Hans L de Boer
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
| | - Max Krakers
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
| | - Guido Mul
- Photocatalytic Synthesis (PCS) Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NB, The Netherlands
| | - Albert van den Berg
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
| | - Mathieu Odijk
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, The Netherlands.
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Qiu ZD, Chen JL, Zeng W, Ma Y, Chen T, Tang JF, Lai CJS, Huang LQ. Real-time toxicity prediction of Aconitum stewing system using extractive electrospray ionization mass spectrometry. Acta Pharm Sin B 2020; 10:903-912. [PMID: 32528836 PMCID: PMC7276682 DOI: 10.1016/j.apsb.2019.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022] Open
Abstract
Due to numerous obstacles such as complex matrices, real-time monitoring of complex reaction systems (e.g., medicinal herb stewing system) has always been a challenge though great values for safe and rational use of drugs. Herein, facilitated by the potential ability on the tolerance of complex matrices of extractive electrospray ionization mass spectrometry, a device was established to realize continuous sampling and real-time quantitative analysis of herb stewing system for the first time. A complete analytical strategy, including data acquisition, data mining, and data evaluation was proposed and implemented with overcoming the usual difficulties in real-time mass spectrometry quantification. The complex Fuzi (the lateral root of Aconitum)–meat stewing systems were real-timely monitored in 150 min by qualitative and quantitative analysis of the nine key alkaloids accurately. The results showed that the strategy worked perfectly and the toxicity of the systems were evaluated and predicated accordingly. Stewing with trotters effectively accelerated the detoxification of Fuzi soup and reduced the overall toxicity to 68%, which was recommended to be used practically for treating rheumatic arthritis and enhancing immunity. The established strategy was versatile, simple, and accurate, which would have a wide application prospect in real-time analysis and evaluation of various complex reaction systems.
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Kopparthy VL, Crews ND. A versatile oscillating‐flow microfluidic PCR system utilizing a thermal gradient for nucleic acid analysis. Biotechnol Bioeng 2020; 117:1525-1532. [DOI: 10.1002/bit.27278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/20/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Varun L. Kopparthy
- Center for Biomedical Engineering and Rehabilitation Science (CBERS) Louisiana Tech University Ruston Louisiana
- Present address: Cleveland Clinic Cleveland Ohio
| | - Niel D. Crews
- Institute for Micromanufacturing (IfM) Louisiana Tech University Ruston Louisiana
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Gorgannezhad L, Stratton H, Nguyen NT. Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology. MICROMACHINES 2019; 10:E408. [PMID: 31248141 PMCID: PMC6630468 DOI: 10.3390/mi10060408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.
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Affiliation(s)
- Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane QLD 4111, Australia.
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Li X, Zhang D, Zhang H, Guan Z, Song Y, Liu R, Zhu Z, Yang C. Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis. Anal Chem 2018; 90:2570-2577. [PMID: 29350029 DOI: 10.1021/acs.analchem.7b04040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.
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Affiliation(s)
- Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Dongfeng Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China.,The MOE Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, People's Republic of China
| | - Ruochen Liu
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey United States
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and 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, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
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A disposable, continuous-flow polymerase chain reaction device: design, fabrication and evaluation. Biomed Microdevices 2017; 18:62. [PMID: 27393216 DOI: 10.1007/s10544-016-0091-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Polymerase Chain Reaction (PCR) is used to amplify a specific segment of DNA through a thermal cycling protocol. The PCR industry is shifting its focus away from macro-scale systems and towards micro-scale devices because: micro-scale sample sizes require less blood from patients, total reaction times are on the order of minutes opposed to hours, and there are cost advantages as many microfluidic devices are manufactured from inexpensive polymers. Some of the fastest PCR devices use continuous flow, but they have all been built of silicon or glass to allow sufficient heat transfer. This article presents a disposable polycarbonate (PC) device that is capable of achieving real-time, continuous flow PCR in a completely disposable polymer device in less than 13 minutes by thermally cycling the sample through an established temperature gradient in a serpentine channel. The desired temperature gradient was determined through simulations and validated by experiments which showed that PCR was achieved. Practical demonstration included amplification of foot-and-mouth disease virus (FMDV) derived cDNA.
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8
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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Development of an on-site rapid real-time polymerase chain reaction system and the characterization of suitable DNA polymerases for TaqMan probe technology. Anal Bioanal Chem 2016; 408:5641-9. [DOI: 10.1007/s00216-016-9668-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/16/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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10
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HE QD, HUANG DP, HUANG G, CHEN ZG. Advance in Research of Microfluidic Polymerase Chain Reaction Chip. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60921-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Shu B, Zhang C, Xing D. A handheld flow genetic analysis system (FGAS): towards rapid, sensitive, quantitative and multiplex molecular diagnosis at the point-of-care level. LAB ON A CHIP 2015; 15:2597-605. [PMID: 25953325 DOI: 10.1039/c5lc00139k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A handheld flow genetic analysis system (FGAS) is proposed for rapid, sensitive, multiplex and real-time quantification of nucleic acids at the point-of-care (POC) level. The FGAS includes a helical thermal-gradient microreactor and a microflow actuator, as well as control circuitry for temperature, fluid and power management, and smartphone fluorescence imaging. All of these features are integrated into a field-portable and easy-to-use molecular diagnostic platform powered by lithium batteries. Due to the unique design of the microreactor, not only steady temperatures for denaturation and annealing/extension but also a linear thermal gradient for spatial high-resolution melting can be achieved through simply maintaining a single heater at constant temperature. The smartphone fluorescence imaging system has a wide field of view that captures all PCR channels of the microreactor in a single snapshot without the need for any mechanical scanning. By these designs, the FGAS enables real-time monitoring of the temporal and spatial fluorescence signatures of amplicons during continuous-flow amplification. On the current FGAS, visual detection of as little as 10 copies per μL of genomic DNA of Salmonella enterica was achieved in 15 min, with real-time quantitative detection of the DNA over 6 orders of magnitude concentration from 10(6) to 10(1) copies per μL also completed in 7.5-15 min. In addition, multiple pathogenic DNA targets could be simultaneously discriminated with direct bar-chart readout or multiplex spatial melting in serial flow. We anticipate that the FGAS has great potential to become a next-generation gene analyzer for POC molecular diagnostics.
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Affiliation(s)
- Bowen Shu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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12
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Analysis of Thermal Performance in a Bidirectional Thermocycler by Including Thermal Contact Characteristics. MICROMACHINES 2014. [DOI: 10.3390/mi5041445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Safavieh M, Ahmed MU, Ng A, Zourob M. High-throughput real-time electrochemical monitoring of LAMP for pathogenic bacteria detection. Biosens Bioelectron 2014; 58:101-6. [DOI: 10.1016/j.bios.2014.02.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/03/2014] [Accepted: 02/04/2014] [Indexed: 02/04/2023]
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Shu B, Zhang C, Xing D. Segmented continuous-flow multiplex polymerase chain reaction microfluidics for high-throughput and rapid foodborne pathogen detection. Anal Chim Acta 2014; 826:51-60. [DOI: 10.1016/j.aca.2014.04.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/16/2014] [Accepted: 04/08/2014] [Indexed: 01/10/2023]
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Trinh KTL, Wu W, Lee NY. Bent polydimethylsiloxane–polycarbonate hybrid microdevice for on-chip flow-through polymerase chain reaction employing a single heater. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1166-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Yu Y, Li B, Baker CA, Zhang X, Roper MG. Quantitative polymerase chain reaction using infrared heating on a microfluidic chip. Anal Chem 2012; 84:2825-9. [PMID: 22385579 DOI: 10.1021/ac203307h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The IR-mediated polymerase chain reaction (IR-PCR) in microdevices is an established technique for rapid amplification of nucleic acids. In this report, we have expanded the applicability of the IR-PCR to quantitative determination of starting copy number by integrating fluorescence detection during the amplification process. Placing the microfluidic device between an IR long-pass filter and a hot mirror reduced the background to a level that enabled fluorescence measurements to be made throughout the thermal cycling process. The average fluorescence intensity during the extension step showed the expected trend of an exponential increase followed by a plateau phase in successive cycles. PUC19 templates at different starting copy numbers were amplified, and the threshold cycle showed an increase for decreasing amounts of starting DNA. The amplification efficiency was 80%, and the gel separation indicated no detectable nonspecific product. A melting curve was generated using IR heating, and this indicated a melting temperature of 85 °C for the 304 bp amplicon, which compared well to the melting temperature obtained using a conventional PCR system. This methodology will be applicable in other types of IR-mediated amplification systems, such as isothermal amplification, and in highly integrated systems that combine pre- and post-PCR processes.
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Affiliation(s)
- Yingjie Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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Zhang C, Wang H, Xing D. Multichannel oscillatory-flow multiplex PCR microfluidics for high-throughput and fast detection of foodborne bacterial pathogens. Biomed Microdevices 2012; 13:885-97. [PMID: 21691814 DOI: 10.1007/s10544-011-9558-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the field of continuous-flow PCR, the amplification throughput in a single reaction solution is low and the single-plex PCR is often used. In this work, we reported a flow-based multiplex PCR microfluidic system capable of performing high-throughput and fast DNA amplification for detection of foodborne bacterial pathogens. As a demonstration, the mixture of DNA targets associated with three different foodborne pathogens was included in a single PCR solution. Then, the solution flowed through microchannels incorporated onto three temperature zones in an oscillatory manner. The effect factors of this oscillatory-flow multiplex PCR thermocycling have been demonstrated, including effects of polymerase concentration, cycling times, number of cycles, and DNA template concentration. The experimental results have shown that the oscillatory-flow multiplex PCR, with a volume of only 5 μl, could be completed in about 13 min after 35 cycles (25 cycles) at 100 μl/min (70 μl/min), which is about one-sixth of the time required on the conventional machine (70 min). By using the presently designed DNA sample model, the minimum target concentration that could be detected at 30 μl/min was 9.8 × 10(-2) ng/μl (278-bp, S. enterica), 11.2 × 10(-2) ng/μl (168-bp, E. coli O157: H7), and 2.88 × 10(-2) ng/μl (106-bp, L. monocytogenes), which corresponds to approximately 3.72 × 10(4) copies/μl, 3.58 × 10(4) copies/μl, and 1.79 × 10(4) copies/μl, respectively. This level of speed and sensitivity is comparable to that achievable in most other continuous-flow PCR systems. In addition, the four individual channels were used to achieve multi-target PCR analysis of three different DNA samples from different food sources in parallel, thereby achieving another level of multiplexing.
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Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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Liu D, Liang G, Lei X, Chen B, Wang W, Zhou X. Highly efficient capillary polymerase chain reaction using an oscillation droplet microreactor. Anal Chim Acta 2012; 718:58-63. [PMID: 22305898 DOI: 10.1016/j.aca.2011.12.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 11/28/2022]
Abstract
The current work presents the development of a capillary-based oscillation droplet approach to maximize the potential of a continuous-flow polymerase chain reaction (PCR). Through the full utilization of interfacial chemistry, a water-in-oil (w/o) droplet was generated by allowing an oil-water plug to flow along a polytetrafluoroethylene (PTFE) capillary. The w/o droplet functioned as the reactor for oscillating-flow PCR to provide a stable reaction environment, accelerate reagent mixing, and eliminate surface adsorption. The capillary PCR approach proposed in the current research offers high amplification efficiency, fast reaction speed, and easy system control attributable to the oscillation droplet reactor. Experimental results show that the droplet-based micro-PCR assay requires lower reaction volume (2 μL) and shorter reaction time (12 min) compared with conventional PCR methods. Taking the amplification of the New Delhi metallo-beta-lactamase (NDM-1) gene as an example, the present work demonstrates that the oscillation droplet PCR assay is capable of achieving high efficiency up to 89.5% and a detection limit of 10 DNA copies. The miniature PCR protocol developed in the current work is fast, robust, and low-cost, thus exhibiting the potential for expansion into various practical applications.
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Affiliation(s)
- Dayu Liu
- Department of Laboratory Medicine, Guangzhou First Municipal People's Hospital, Affiliated to Guangzhou Medical College, Guangzhou, China.
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LIANG GT, WANG QP, WANG W, LIU DY, ZHOU XM. Droplet-based Extraction of Hepatitis B Virus DNA in a Capillary. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1016/s1872-2040(10)60441-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wang H, Zhang C, Xing D. Simultaneous detection of Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes using oscillatory-flow multiplex PCR. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0584-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Zhang C, Xing D. Single-Molecule DNA Amplification and Analysis Using Microfluidics. Chem Rev 2010; 110:4910-47. [DOI: 10.1021/cr900081z] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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Hua Z, Rouse JL, Eckhardt AE, Srinivasan V, Pamula VK, Schell WA, Benton JL, Mitchell TG, Pollack MG. Multiplexed real-time polymerase chain reaction on a digital microfluidic platform. Anal Chem 2010; 82:2310-6. [PMID: 20151681 PMCID: PMC2859674 DOI: 10.1021/ac902510u] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper details the development of a digital microfluidic platform for multiplexed real-time polymerase chain reactions (PCR). Liquid samples in discrete droplet format are programmably manipulated upon an electrode array by the use of electrowetting. Rapid PCR thermocycling is performed in a closed-loop flow-through format where for each cycle the reaction droplets are cyclically transported between different temperature zones within an oil-filled cartridge. The cartridge is fabricated using low-cost printed-circuit-board technology and is intended to be a single-use disposable device. The PCR system exhibited remarkable amplification efficiency of 94.7%. To test its potential application in infectious diseases, this novel PCR system reliably detected diagnostic DNA levels of methicillin-resistant Staphylococcus aureus (MRSA), Mycoplasma pneumoniae , and Candida albicans . Amplification of genomic DNA samples was consistently repeatable across multiple PCR loops both within and between cartridges. In addition, simultaneous real-time PCR amplification of both multiple different samples and multiple different targets on a single cartridge was demonstrated. A novel method of PCR speed optimization using variable cycle times has also been proposed and proven feasible. The versatile system includes magnetic bead handling capability, which was applied to the analysis of simulated clinical samples that were prepared from whole blood using a magnetic bead capture protocol. Other salient features of this versatile digital microfluidic PCR system are also discussed, including the configurability and scalability of microfluidic operations, instrument portability, and substrate-level integration with other pre- and post-PCR processes.
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Affiliation(s)
- Zhishan Hua
- Advanced Liquid Logic Inc., Research Triangle Park, North Carolina
| | - Jeremy L. Rouse
- Advanced Liquid Logic Inc., Research Triangle Park, North Carolina
| | | | - Vijay Srinivasan
- Advanced Liquid Logic Inc., Research Triangle Park, North Carolina
| | - Vamsee K. Pamula
- Advanced Liquid Logic Inc., Research Triangle Park, North Carolina
| | - Wiley A. Schell
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jonathan L. Benton
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Thomas G. Mitchell
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
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Rapid Detection of Tobacco Mosaic Virus from Crude Samples on an Oscillatory-flow Reverse Transcription-Polymerase Chain Reaction Microfluidics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1016/s1872-2040(08)60127-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Microfluidic chip: Next-generation platform for systems biology. Anal Chim Acta 2009; 650:83-97. [DOI: 10.1016/j.aca.2009.04.051] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 04/16/2009] [Accepted: 04/27/2009] [Indexed: 12/30/2022]
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Abstract
PCR retains a pivotal role in making accessible marker nucleic acid sequences for ready analysis in cancer diagnosis. For certain cancers such as acute lymphoblastic leukaemia, the application of quantitative procedures to assess and subsequently direct therapy has given rise to the slowly maturing field of MRD (minimal residual disease) management. Although excellent protocols exist for performing these analyses, akin to all PCR procedures the limit of detection can vary markedly between laboratories. The present paper is an overview that describes how the analytical field relating to miniaturization is likely to identify the missing link that integrates sample processing with downstream PCR, analysis and eventual therapy. Miniaturized devices are suited to the multi-parallelized handling of defined numbers of cells, and PCR-based microfluidic procedures have become reasonably established. The integration of sample processing and PCR in microfluidic devices is beginning to offer reproducible quantitative data that relate the number of biomarker nucleic acids to the defined analysed cell or cells for meaningful clinical assessment. The application of MRD may, through integrated miniaturized PCR, become more reliable and routine with additional applications in defining disease threshold levels for other cancer types. These enabling integrated platforms may facilitate biomarker measurements to predict the response and outcome, which are also of current interest for personalized medical care.
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Zhang C, Xing D. Parallel DNA amplification by convective polymerase chain reaction with various annealing temperatures on a thermal gradient device. Anal Biochem 2009; 387:102-12. [DOI: 10.1016/j.ab.2009.01.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 01/12/2009] [Accepted: 01/13/2009] [Indexed: 12/11/2022]
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27
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Zhang Y, Ozdemir P. Microfluidic DNA amplification--a review. Anal Chim Acta 2009; 638:115-25. [PMID: 19327449 DOI: 10.1016/j.aca.2009.02.038] [Citation(s) in RCA: 259] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Revised: 02/03/2009] [Accepted: 02/20/2009] [Indexed: 11/17/2022]
Abstract
The application of microfluidic devices for DNA amplification has recently been extensively studied. Here, we review the important development of microfluidic polymerase chain reaction (PCR) devices and discuss the underlying physical principles for the optimal design and operation of the device. In particular, we focus on continuous-flow microfluidic PCR on-chip, which can be readily implemented as an integrated function of a micro-total-analysis system. To overcome sample carryover contamination and surface adsorption associated with microfluidic PCR, microdroplet technology has recently been utilized to perform PCR in droplets, which can eliminate the synthesis of short chimeric products, shorten thermal-cycling time, and offers great potential for single DNA molecule and single-cell amplification. The work on chip-based PCR in droplets is highlighted.
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Affiliation(s)
- Yonghao Zhang
- Department of Mechanical Engineering, University of Strathclyde, Glasgow, G1 1XJ, UK.
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28
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West J, Becker M, Tombrink S, Manz A. Micro Total Analysis Systems: Latest Achievements. Anal Chem 2008; 80:4403-19. [PMID: 18498178 DOI: 10.1021/ac800680j] [Citation(s) in RCA: 351] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jonathan West
- ISAS, Institute for Analytical Sciences, Bunsen-Kirchhoff-Strasse 11, D-44139 Dortmund, Germany
| | - Marco Becker
- ISAS, Institute for Analytical Sciences, Bunsen-Kirchhoff-Strasse 11, D-44139 Dortmund, Germany
| | - Sven Tombrink
- ISAS, Institute for Analytical Sciences, Bunsen-Kirchhoff-Strasse 11, D-44139 Dortmund, Germany
| | - Andreas Manz
- ISAS, Institute for Analytical Sciences, Bunsen-Kirchhoff-Strasse 11, D-44139 Dortmund, Germany
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