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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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2
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Single Fluorescence Channel-based Multiplex Detection of Avian Influenza Virus by Quantitative PCR with Intercalating Dye. Sci Rep 2015; 5:11479. [PMID: 26088868 PMCID: PMC5155576 DOI: 10.1038/srep11479] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2015] [Indexed: 12/03/2022] Open
Abstract
Since its invention in 1985 the polymerase chain reaction (PCR) has become a well-established method for amplification and detection of segments of double-stranded DNA. Incorporation of fluorogenic probe or DNA intercalating dyes (such as SYBR Green) into the PCR mixture allowed real-time reaction monitoring and extraction of quantitative information (qPCR). Probes with different excitation spectra enable multiplex qPCR of several DNA segments using multi-channel optical detection systems. Here we show multiplex qPCR using an economical EvaGreen-based system with single optical channel detection. Previously reported non quantitative multiplex real-time PCR techniques based on intercalating dyes were conducted once the PCR is completed by performing melting curve analysis (MCA). The technique presented in this paper is both qualitative and quantitative as it provides information about the presence of multiple DNA strands as well as the number of starting copies in the tested sample. Besides important internal control, multiplex qPCR also allows detecting concentrations of more than one DNA strand within the same sample. Detection of the avian influenza virus H7N9 by PCR is a well established method. Multiplex qPCR greatly enhances its specificity as it is capable of distinguishing both haemagglutinin (HA) and neuraminidase (NA) genes as well as their ratio.
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Quantitative analysis of molecular absorption into PDMS microfluidic channels. Ann Biomed Eng 2012; 40:1862-73. [PMID: 22484830 DOI: 10.1007/s10439-012-0562-z] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 03/27/2012] [Indexed: 01/07/2023]
Abstract
Microfluidic devices fabricated using poly(dimethylsiloxane) (PDMS) polymer are routinely used for in vitro cell culture for a wide range of cellular assays. These assays typically involve the incubation of cultured cells with a drug molecule or a fluorescent marker while monitoring a cellular response. The accuracy of these assays depends on achieving a consistent and reproducible concentration of solute molecules in solution. However, hydrophobic therapeutic and fluorescent molecules tend to diffuse into the PDMS walls of the microfluidic devices, which reduce their concentration in solution and consequently affect the accuracy and reliability of these assays. In this paper, we quantitatively investigate the relationship between the partition coefficient (log P) of a series of markers routinely used in in vitro cellular assays including [3H]-dexamethasone, [3H]-diazepam, [14C]-mannitol, [3H]-phenytoin, and rhodamine 6G and their absorption into PDMS microfluidic channels. Our results show that the absorption of a given solute into PDMS depends on the hydrophilic/hydrophobic balance defined by its log P value. Specifically, results demonstrate that molecules with log P less than 2.47 exhibit minimal absorption (<10%) into PDMS channels whereas molecules with log P larger than 2.62 exhibit extensive absorption (>90%) into PDMS channels. Further investigations showed that TiO(2) and glass coatings of PDMS channels reduced the absorption of hydrophobic molecules (log P > 2.62) by 2- and 4.5-folds, respectively.
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Zhang M, Gong X, Wen W. Manipulation of microfluidic droplets by electrorheological fluid. Electrophoresis 2009; 30:3116-23. [DOI: 10.1002/elps.200900119] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Law WS, Li SFY, Kricka LJ. Detection of enteropathogenic Escherichia coli by microchip capillary electrophoresis. Methods Mol Biol 2009; 509:169-179. [PMID: 19212722 DOI: 10.1007/978-1-59745-372-1_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
There is always a need to detect the presence of microorganisms, either as contaminants in food and pharmaceutical industries or bioindicators for disease diagnosis. Hence, it is important to develop efficient, rapid, and simple methods to detect microorganisms. Traditional culturing method is unsatisfactory due to its long incubation time. Molecular methods, although capable of providing a high degree of specificity, are not always useful in providing quick tests of presence or absence of microorganisms. Microchip elec-trophoresis has been recently employed to address problems associated with the detection of microorganisms due to its high versatility, selectivity, sensitivity, and short analysis times. In this work, the potential of PDMS-based microchip electrophoresis in the identification and characterization of microorganism was evaluated. Enteropathogenic E. coli (EPEC) was selected as the model microorganism. To obtain repeat-able separations, sample pretreatment was found to be essential. Microchip electrophoresis with laser-induced fluorescence detection could potentially revolutionize certain aspects of microbiology involving diagnosis, profiling of pathogens, environmental analysis, and many others areas of study.
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Affiliation(s)
- Wai S Law
- Department of Chemistry, National University of Singapore, Singapore, Republic of Singapore
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Wang F, Yang M, Burns MA. Microfabricated valveless devices for thermal bioreactions based on diffusion-limited evaporation. LAB ON A CHIP 2008; 8:88-97. [PMID: 18094766 PMCID: PMC2752386 DOI: 10.1039/b711770a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Microfluidic devices that reduce evaporative loss during thermal bioreactions such as PCR without microvalves have been developed by relying on the principle of diffusion-limited evaporation. Both theoretical and experimental results demonstrate that the sample evaporative loss can be reduced by more than 20 times using long narrow diffusion channels on both sides of the reaction region. In order to further suppress the evaporation, the driving force for liquid evaporation is reduced by two additional techniques: decreasing the interfacial temperature using thermal isolation and reducing the vapor concentration gradient by replenishing water vapor in the diffusion channels. Both thermal isolation and vapor replenishment techniques can limit the sample evaporative loss to approximately 1% of the reaction content.
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Affiliation(s)
- Fang Wang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Ming Yang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Mark A. Burns
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
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7
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Wei S, Vaidya B, Patel AB, Soper SA, McCarley RL. Photochemically patterned poly(methyl methacrylate) surfaces used in the fabrication of microanalytical devices. J Phys Chem B 2007; 109:16988-96. [PMID: 16853163 DOI: 10.1021/jp051550s] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report here the photochemical surface modification of poly(methyl methacrylate), PMMA, microfluidic devices by UV light to yield pendant carboxylic acid surface moieties. Patterns of carboxylic acid sites can be formed from the micrometer to millimeter scale by exposure of PMMA through a contact mask, and the chemical patterns allow for further functionalization of PMMA microdevice surfaces to yield arrays or other structured architectures. Demonstrated here is the relationship between UV exposure time and PMMA surface wettability, topography, surface functional group density, and electroosmotic flow (EOF) of aqueous buffer solutions in microchannels made of PMMA. It is found that the water contact angle on PMMA surfaces decreases from 70 degrees to 24 degrees after exposure to UV light as the result of the formation of carboxylic acid sites. However, upon rinsing with 2-propanol, the water contact angle increases to approximately 80 degrees , and this increase is attributed to changes in surface roughness resulting from removal of low molecular weight PMMA formed from scission events. In addition, the surface roughness and surface coverage of carboxylic acid groups exhibit a characteristic trend with UV exposure time. Electroosmotic flow (EOF) in PMMA microchannels increases upon UV modification and is pH dependent. The possible photolysis mechanism for formation of carboxylic acid groups on PMMA surfaces under the conditions outlined in this work is discussed.
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Affiliation(s)
- Suying Wei
- Department of Chemistry and Center for Biomodular Multi-scale Systems, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804, USA
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Neuzil P, Zhang C, Pipper J, Oh S, Zhuo L. Ultra fast miniaturized real-time PCR: 40 cycles in less than six minutes. Nucleic Acids Res 2006; 34:e77. [PMID: 16807313 PMCID: PMC1904101 DOI: 10.1093/nar/gkl416] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have designed, fabricated and tested a real-time PCR chip capable of conducting one thermal cycle in 8.5 s. This corresponds to 40 cycles of PCR in 5 min and 40 s. The PCR system was made of silicon micromachined into the shape of a cantilever terminated with a disc. The thin film heater and a temperature sensor were placed on the disc perimeter. Due to the system's thermal constant of 0.27 s, we have achieved a heating rate of 175°C s−1 and a cooling rate of −125°C s−1. A PCR sample encapsulated with mineral oil was dispensed onto a glass cover slip placed on the silicon disc. The PCR cycle time was then determined by heat transfer through the glass, which took only 0.5 s. A real-time PCR sample with a volume of 100 nl was tested using a FAM probe. As the single PCR device occupied an area of only a few square millimeters, devices could be combined into a parallel system to increase throughput.
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Neuzil P, Pipper J, Hsieh TM. Disposable real-time microPCR device: lab-on-a-chip at a low cost. MOLECULAR BIOSYSTEMS 2006; 2:292-8. [PMID: 16880947 DOI: 10.1039/b605957k] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have designed, fabricated and tested a real-time micro polymerase chain reaction (microPCR) system. It consists of a microscope glass cover slip placed on top of a micromachined silicon chip integrated with a heater and a temperature sensor. A single microL of a sample containing DNA was placed on the glass and encapsulated with mineral oil to prevent the evaporation of water, thus forming a virtual reaction chamber (VRC). The PCR chip required half a second to heat up from 72 to 94 degrees C and two seconds to cool from 94 to 55 degrees C, corresponding to a cooling rate of -20 K s(-1). The real-time PCR yield was determined by a fluorescence method. The melting curve analysis method as well as capillary electrophoresis was performed to determine the purity of the PCR product. As the glass slip is disposable, cross-contamination from sample to sample is eliminated. The total cost of running the PCR is given by the value of the cover slip and its treatment.
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Affiliation(s)
- Pavel Neuzil
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669.
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Seo M, Nie Z, Xu S, Mok M, Lewis PC, Graham R, Kumacheva E. Continuous microfluidic reactors for polymer particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:11614-22. [PMID: 16316091 DOI: 10.1021/la050519e] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This article provides an overview of our work in the area of the synthesis of polymer particles in continuous microfluidic reactors. The method includes (a) the generation of highly monodisperse monomer droplets in a microfluidic flow-focusing device and (b) in-situ solidification of these droplets by means of photopolymerization. We discuss the effect of monomer properties on the emulsification process, the effect of the polymerization rate on the production of high-quality particles, the role of the material of the microfluidic device in droplet formation, and the synthesis of particles with different shapes and compositions. We also demonstrate the production of highly ordered arrays of polymer particles achieved by photopolymerization of the dynamic lattices of monomer droplets in microfluidic channels. The article is concluded with a summary of future research directions in the production of polymer colloids in microfluidic reactors.
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Affiliation(s)
- Minseok Seo
- Department of Chemistry, University of Toronto, Ontario, Canada
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Panaro NJ, Lou XJ, Fortina P, Kricka LJ, Wilding P. Micropillar array chip for integrated white blood cell isolation and PCR. ACTA ACUST UNITED AC 2005; 21:157-62. [PMID: 15748689 DOI: 10.1016/j.bioeng.2004.11.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Revised: 11/10/2004] [Accepted: 11/23/2004] [Indexed: 11/25/2022]
Abstract
We report the fabrication of silicon chips containing a row of 667 pillars, 10 by 20 microm in cross-section, etched to a depth of 80 microm with adjacent pillars being separated by 3.5 microm. The chips were used to separate white blood cells from whole blood in less than 2 min and for subsequent PCR of a genomic target (eNOS). Chip fluid dynamics were validated experimentally using CoventorWare microfluidic simulation software. The amplicon concentrations were determined using microchip capillary electrophoresis and were >40% of that observed in conventional PCR tubes for chips with and without pillars. Reproducible on-chip PCR was achieved using white blood cell preparations isolated from whole human blood pumped through the chip.
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Affiliation(s)
- Nicholas J Panaro
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Lou XJ, Panaro NJ, Wilding P, Fortina P, Kricka LJ. Mutation detection using ligase chain reaction in passivated silicon-glass microchips and microchip capillary electrophoresis. Biotechniques 2005; 37:392, 394, 396-8. [PMID: 15470893 DOI: 10.2144/04373st03] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The ligase chain reaction (LCR) following PCR is one of the most sensitive and specific methods for detecting mutations, especially single nucleotide polymorphisms (SNPs). Performing LCR in microchips remains a challenge because of the inhibitory effect of the internal surfaces of silicon-glass microchips. We have tested a dynamic polymer-based surface passivation method for LCR conducted in oxide-coated silicon-glass microchips. The combination of polyvinylpyrrolidone 40 (PVP-40) at 0.75% (w/v) with an excess of the ligase produced successful LCR in the silicon-glass microchips, with yields of ligated primers comparable to reactions performed in conventional reaction tubes. Ligated primers were detected and quantified simply and conveniently using microchip capillary electrophoresis.
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Affiliation(s)
- Xing Jian Lou
- University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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13
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Nie Z, Xu S, Seo M, Lewis PC, Kumacheva E. Polymer particles with various shapes and morphologies produced in continuous microfluidic reactors. J Am Chem Soc 2005; 127:8058-63. [PMID: 15926830 DOI: 10.1021/ja042494w] [Citation(s) in RCA: 449] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a novel approach to continuous and scalable production of core-shell droplets and polymer capsules in microfluidic devices. The described method is also useful in the synthesis of polymer particles with nonspherical shapes. We used capillary instability-driven break-up of a liquid jet formed by two immiscible fluids. Precise control of emulsification of each liquid allowed for the production of highly monodisperse core-shell droplets with a predetermined diameter of cores and thickness of shells. We also achieved control over the number of cores per droplet and the location of cores in the droplet. We carried out fast throughput photopolymerization of the monomeric shells and obtained polymer particles with various shapes and morphologies, including spheres, truncated spheres and, hemispheres, and single and multicore capsules.
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Affiliation(s)
- Zhihong Nie
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, M5S 3H6 Canada
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15
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16
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McKeon J, Cho MJ, Khaledi MG. Quantitation of intracellular concentration of a delivered morpholino oligomer by capillary electrophoresis-laser- induced fluorescence: correlation with upregulation of luciferase gene expression. Anal Biochem 2001; 293:1-7. [PMID: 11373071 DOI: 10.1006/abio.2001.5087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Antisense oligonucleotides have shown great promise over the past several years as viable drugs to combat various forms of cancer and viral diseases. However, quantitative detection to monitor cellular association is difficult using conventional methods such as radiolabeling of the oligonucleotide or fluorescence confocal microscopy. In this paper quantitation of intracellular concentration of the morpholino oligonucleotide is investigated using capillary electrophoresis coupled with laser-induced fluorescence detection (CE-LIF). HeLa cells, which produce luciferase as the antisense oligomer enters the cell, were scrape-loaded with varying concentrations of the morpholino antisense. The intracellular antisense concentration measured by CE-LIF was found to correlate with those obtained with the cellular functional assay based on upregulation of luciferase. Intracellular concentrations of the antisense were found to be in the range of 6 to 29 nmol/g total cell protein, depending on the amounts that were scrape-loaded. To our best knowledge, this is the first reported quantitative correlation between delivered antisense concentration in a cell extract and the subsequent antisense upregulation of gene expression.
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Affiliation(s)
- J McKeon
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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17
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OTSUKA K. マイクロチップを用いる電気泳動分析. ELECTROCHEMISTRY 2001. [DOI: 10.5796/electrochemistry.69.624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Esch MB, Locascio LE, Tarlov MJ, Durst RA. Detection of viable Cryptosporidium parvum using DNA-modified liposomes in a microfluidic chip. Anal Chem 2001; 73:2952-8. [PMID: 11467540 DOI: 10.1021/ac001508n] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes a microfluidic chip that enables the detection of viable Cryptosporidium parvum by detecting RNA amplified by nucleic-acid-sequence-based amplification (NASBA). The mRNA serving as the template for NASBA is produced by viable C. parvum as a response to heat shock. The chip utilizes sandwich hybridization by hybridizing the NASBA-generated amplicon between capture probes and reporter probes in a microfluidic channel. The reporter probes are tagged with carboxyfluorescein-filled liposomes. These liposomes, which generate fluorescence intensities not obtainable from single fluorophores, allow the detection of very low concentrations of targets. The limit of detection of the chip is 5 fmol of amplicon in 12.5 microL of sample solution. Samples of C. parvum that underwent heat shock, extraction, and amplification by NASBA were successfully detected and clearly distinguishable from controls. This was accomplished without having to separate the amplified RNA from the NASBA mixture. The microfluidic chip can easily be modified to detect other pathogens. We envision its use in mu-total analysis systems (mu-TAS) and in DNA-array chips utilized for environmental monitoring of pathogens.
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Affiliation(s)
- M B Esch
- Analytical Chemistry Laboratories, Cornell University, Geneva, New York 14456-0462, USA
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Yuen PK, Kricka LJ, Fortina P, Panaro NJ, Sakazume T, Wilding P. Microchip module for blood sample preparation and nucleic acid amplification reactions. Genome Res 2001; 11:405-12. [PMID: 11230164 PMCID: PMC311054 DOI: 10.1101/gr.155301] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A computer numerical control-machined plexiglas-based microchip module was designed and constructed for the integration of blood sample preparation and nucleic acid amplification reactions. The microchip module is comprised of a custom-made heater-cooler for thermal cycling, a series of 254 microm x 254 microm microchannels for transporting human whole blood and reagents in and out of an 8--9 microL dual-purpose (cell isolation and PCR) glass-silicon microchip. White blood cells were first isolated from a small volume of human whole blood (<3 microL) in an integrated cell isolation--PCR microchip containing a series of 3.5-microm feature-sized "weir-type" filters, formed by an etched silicon dam spanning the flow chamber. A genomic target, a region in the human coagulation Factor V gene (226-bp), was subsequently directly amplified by microchip-based PCR on DNA released from white blood cells isolated on the filter section of the microchip mounted onto the microchip module. The microchip module provides a convenient means to simplify nucleic acid analyses by integrating two key steps in genetic testing procedures, cell isolation and PCR and promises to be adaptable for additional types of integrated assays.
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Affiliation(s)
- P K Yuen
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Zhang Z, Wu Y, Cheng W, Wu R. Single strand conformation polymorphism analysis of K-ras gene mutations by capillary electrophoresis with laser-induced fluorescence (LIF) detector. Clin Chim Acta 2000; 301:205-11. [PMID: 11020474 DOI: 10.1016/s0009-8981(00)00310-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mutations of K-ras gene play an important role in neoplastic progression. The capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) technique is available for the detection of gene mutations. Using an automated capillary electrophoresis with short-chain linear polyacrylamide, after denaturation of PCR products, injections were performed at reverse polarity of 5 kV for 15 s and the separations were carried out under a constant voltage of 8 kV. Of 16 specimens of lung cancer tissue, two specimens were found to have abnormal peaks in the electrophoretogram. CE-SSCP is rapid, automated, and has high performance.
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Affiliation(s)
- Z Zhang
- Department of Pharmacy, Henan Medical University, Zhengzhou, 450052, China.
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Abstract
Capillary electrophoresis and related techniques on microchips have made great strides in recent years. This review concentrates on progress in capillary zone electrophoresis, but also covers other capillary techniques such as isoelectric focusing, isotachophoresis, free flow electrophoresis, and micellar electrokinetic chromatography. The material and technologies used to prepare microchips, microchip designs, channel geometries, sample manipulation and derivatization, detection, and applications of capillary electrophoresis to microchips are discussed. The progress in separation of nucleic acids and proteins is particularly emphasized.
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Affiliation(s)
- V Dolník
- Molecular Dynamics, Sunnyvale, CA 94086, USA.
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Wilson VL, Wei Q, Wade KR, Chisa M, Bailey D, Kanstrup CM, Yin X, Jackson CM, Thompson B, Lee WR. Needle-in-a-haystack detection and identification of base substitution mutations in human tissues. Mutat Res 1999; 406:79-100. [PMID: 10479725 DOI: 10.1016/s1383-5726(99)00005-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Background and induced germline mutagenesis and other genotoxicity studies have been hampered by the lack of a sufficiently sensitive technique for detecting mutations in a small cluster of cells or a single cell in a tissue sample composed of millions of cells. The most frequent type of genetic alteration is intragenic. The vast majority of oncogenic mutations in human and mammalian cancer involves only single base substitutions. We have developed universally applicable techniques that not only provide the necessary sensitivity and specificity for site specific mutagenesis studies, but also identify the point mutation. The exponential amplification procedures of polymerase chain reaction (PCR) and ligase chain reaction (LCR) have been combined with restriction endonuclease (RE) digestion to enable the selective enrichment and detection of single base substitution mutations in human oncogenic loci at a sensitivity of one mutant in more than 10(7) wild type alleles. These PCR/RE/LCR procedures have been successfully designed and used for codons 12 and 248 of the Ha-ras and p53 genes, respectively, both of which contain a natural MspI restriction endonuclease recognition sequence. These procedures have also been adapted for the detection and identification of mutations in oncogenic loci that do not contain a natural restriction endonuclease recognition sequence. Using PCR techniques, a HphI site was incorporated into the codons 12/13 region of the human N-ras gene, which was then used for the selective enrichment of mutants at this oncogenic locus. These PCR/RE/LCR procedures for base substitution mutations in codon 12 of the N-ras gene were found to have the sensitivity of detection of at least one mutant allele in the presence of the DNA equivalent of 10(6) wild type cells. Only one peripheral blood leukocyte DNA specimen out of nine normal individuals displayed an observable Ha-ras mutation that was present at frequency between 10(-5) and 10(-6). These PCR/RE/LCR techniques for detecting and identifying base substitution mutations are universally applicable to almost any locus or base site within the human or animal genome. With the added advantage of the adjustability of both the amount of DNA (number of genomes) to be tested and the sensitivity (10(-2) to 10(-7)) of the assay selection or enrichment procedures, these PCR/RE/LCR techniques will be useful in addressing a broad range of important questions in mutagenesis and carcinogenesis.
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Affiliation(s)
- V L Wilson
- Institute of Environmental Studies, Louisiana State University, Baton Rouge, LA 70803, USA.
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Zorbas H. Miniatur-Durchfluß-PCR: ein Durchbruch? Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990419)111:8<1121::aid-ange1121>3.0.co;2-s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Abstract
Miniaturization has been a long-term trend in clinical diagnostics instrumentation. Now a range of new technologies, including micromachining and molecular self-assembly, are providing the means for further size reduction of analyzers to devices with micro- to nanometer dimensions and submicroliter volumes. Many analytical techniques (e.g., mass spectrometry and electrophoresis) have been successfully implemented on microchips made from silicon, glass, or plastic. The new impetus for miniaturization stems from the perceived benefits of faster, easier, less costly, and more convenient analyses and by the needs of the pharmaceutical industry for microscale, massively parallel drug discovery assays. Perfecting a user-friendly interface between a human and a microchip and determining the realistic lower limit for sample volume are key issues in the future implementation of these devices. Resolution of these issues will be important for the long-term success of microminiature analyzers; in the meantime, the scope, diversity, and rate of progress in the development of these devices promises products in the near future.
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Affiliation(s)
- Larry J Kricka
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104. Fax 215-662-7529; e-mail
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Eijkel JC, Prak A, Cowen S, Craston DH, Manz A. Micromachined heated chemical reactor for pre-column derivatisation. J Chromatogr A 1998. [DOI: 10.1016/s0021-9673(98)00459-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Abstract
A micromachined chemical amplifier was successfully used to perform the polymerase chain reaction (PCR) in continuous flow at high speed. The device is analogous to an electronic amplifier and relies on the movement of sample through thermostated temperature zones on a glass microchip. Input and output of material (DNA) is continuous, and amplification is independent of input concentration. A 20-cycle PCR amplification of a 176-base pair fragment from the DNA gyrase gene of Neisseria gonorrhoeae was performed at various flow rates, resulting in total reaction times of 90 seconds to 18.7 minutes.
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Affiliation(s)
- M U Kopp
- Zeneca/SmithKline Beecham Centre for Analytical Sciences, Department of Chemistry, Imperial College of Science, Technology and Medicine, London SW7 2AY, UK
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28
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Wilding P, Kricka LJ, Cheng J, Hvichia G, Shoffner MA, Fortina P. Integrated cell isolation and polymerase chain reaction analysis using silicon microfilter chambers. Anal Biochem 1998; 257:95-100. [PMID: 9514776 DOI: 10.1006/abio.1997.2530] [Citation(s) in RCA: 219] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
White blood cells are isolated from whole blood in silicon-glass 4.5-microliter microchips containing a series of 3.5-micron feature-sized 'weir-type' filters, formed by an etched silicon dam spanning the flow chamber. Genomic DNA targets, e.g., dystrophin gene, can be directly amplified using the polymerase chain reaction (PCR) from the white cells isolated on the filters. This dual function microchip provides a means to simplify nucleic acid analyses by integrating in a single device two key steps in the analytical procedure, namely, cell isolation and PCR.
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Affiliation(s)
- P Wilding
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia 19104, USA
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29
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Cheng J, Waters LC, Fortina P, Hvichia G, Jacobson SC, Ramsey JM, Kricka LJ, Wilding P. Degenerate oligonucleotide primed-polymerase chain reaction and capillary electrophoretic analysis of human DNA on microchip-based devices. Anal Biochem 1998; 257:101-6. [PMID: 9514777 DOI: 10.1006/abio.1997.2531] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Random amplification of the human genome using the degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) was performed in a silicon-glass chip. An aliquot of the DOP-PCR amplified genomic DNA was then introduced into another silicon-glass chip for a locus-specific, multiplex PCR of the dystrophin gene exons in order to detect deletions causing Duchenne/Becker muscular dystrophy. Amplicons were analyzed by both conventional capillary electrophoresis and microchip electrophoresis and results were compared to those obtained using standard non-chip-based PCR assays. Results from microchip electrophoresis were consistent with those from conventional capillary electrophoresis. Whole genome amplification products obtained by DOP-PCR proved to be a suitable template for multiplex PCR as long as amplicon size was < 250 bp. Successful detection and resolution of all PCR products from the multiplex PCR clearly shows the feasibility of performing complex PCR assays using microfabricated devices.
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Affiliation(s)
- J Cheng
- Department of Pathology, University of Pennsylvania, Philadelphia, USA
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30
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Mitchelson KR, Cheng J, Kricka LJ. The use of capillary electrophoresis for point-mutation screening. Trends Biotechnol 1997; 15:448-58. [PMID: 9369028 DOI: 10.1016/s0167-7799(97)01117-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Advances in capillary electrophoresis technology over the past three years have been rapid. Capillary electrophoresis offers high-throughput, high-resolution, automatic operation and on-line detection with automatic data acquisition, and this has stimulated its application to the analysis of DNA mutations. Many different PCR-based DNA-mutation assays have been developed for unknown and known mutations. This article compares conventional PCR-based mutation-detection assays with the methods developed for use with capillary electrophoresis. Future trends for mutation detection using capillary electrophoresis are also assessed, with a special emphasis on totally integrated, microchip capillary-electrophoresis-based mutation-detection systems.
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31
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Abstract
In the past year, microchips as applied to miniaturised total analysis systems, or microTAS, have benefited from technological improvements in their fabrication and been applied to analysis in many different biological areas. From a technological perspective, salient work includes fast, cheap and easy micromachining in polymers and integrated optical detection. From the bioapplications perspective, advances in DNA and protein separations, cell manipulations, immunoassays and polymerase chain reaction using on-chip electrophoretic separation stand out.
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Affiliation(s)
- M U Kopp
- Zeneca/SmithKline Beecham Centre for Analytical Science, Department of Chemistry, Imperial College, London, SW7 2AY, UK.
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32
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Colyer CL, Tang T, Chiem N, Harrison DJ. Clinical potential of microchip capillary electrophoresis systems. Electrophoresis 1997; 18:1733-41. [PMID: 9372264 DOI: 10.1002/elps.1150181006] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Clinical interest in the use of capillary electrophoresis (CE) has recently been extended to the microchip environment. Clinical analyses demand careful handling of complex samples that are often limited in quantity and in concentration. The integrated sample handling and analysis capabilities of microchip substrates thus seem ideally suited to clinical applications. This review surveys the development of sample handling (injection, mixing, and reaction) and separation elements on-chip. The integration of these elements to create a variety of clinical analyzers has been demonstrated. The application of microchip CE systems to human serum protein analysis, immunoassay, and DNA studies is reviewed, along with various other clinical applications. In addition, the clinical potential of the lab-on-a-chip concept is discussed.
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Affiliation(s)
- C L Colyer
- Department of Chemistry, University of Alberta, Edmonton, Canada
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33
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Kricka LJ, Faro I, Heyner S, Garside WT, Fitzpatrick G, McKinnon G, Ho J, Wilding P. Micromachined analytical devices: microchips for semen testing. J Pharm Biomed Anal 1997; 15:1443-7. [PMID: 9226574 DOI: 10.1016/s0731-7085(96)02046-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Micromachined devices (microchips) have been designed and tested for a range of clinically important assays. In this study we compare sperm motility determined using disposable glass microchips and a conventional Makler chamber. The 17 x 14 mm glass microchips contained three etched test structures each comprising either duplicate or quadruplicate analytical microchannels. Semen samples with sperm counts ranging from 21 to 78 million sperm per ml and forward progression scores of from 1+ to 3+ were evaluated and swimming times ranging from 360 s (3.3+ progression) to 770 s (1+,2 forward progression) observed in the microchips. Motility determined by the time taken for sperm to swim to the end of a microchannel (100 microns wide x 40 microns deep x 10 mm long) in the microchip correlated with forward progression of the sperm determined by the conventional Makler chamber method. This study demonstrates the feasibility of microchips for sperm motility testing and suggests that this technique would be applicable to the study of other types of motile cells.
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Affiliation(s)
- L J Kricka
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia 19104, USA.
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34
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Fortina P, Cheng J, Shoffner MA, Surrey S, Hitchcock WM, Kricka LJ, Wilding P. Diagnosis of Duchenne/Becker muscular dystrophy and quantitative identification of carrier status by use of entangled solution capillary electrophoresis. Clin Chem 1997. [DOI: 10.1093/clinchem/43.5.745] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Use of capillary electrophoresis, a new and useful analytical tool, offers a variety of advantages for nucleic acid analyses, including rapid analysis, automation, high resolution, qualitative and quantitative results, and low consumption of both sample and reagents. We report the first example of the use of entangled solution capillary electrophoresis (ESCE) and laser-induced fluorescence detection (LIF) for separation-based diagnostics in the quantitative analysis of multiplex PCR products for determination of carrier status of Duchenne/Becker muscular dystrophy (DMD/BMD). This ap-proach greatly improved the speed, resolution, and sensitivity of information needed for the diagnosis of DMD/BMD compared with that from conventional diagnostic methods, and is of general utility for diagnosis of genetic diseases.
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Affiliation(s)
- Paolo Fortina
- Department of Pediatrics, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | | | - Saul Surrey
- Department of Pediatrics, The Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Wendy M Hitchcock
- Department of Pathology and Clinical Laboratories, The Children’s Hospital of Philadelphia
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35
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Righetti PG, Conti M, Gelfi C. Study of haptoglobin-hemoglobin complexes by titration curves, capillary electrophoresis and capillary isoelectric focusing. J Chromatogr A 1997; 767:255-62. [PMID: 9177009 DOI: 10.1016/s0021-9673(97)00011-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A novel method is described for monitoring complex formation between macromolecules, based on combined isoelectric focusing-electrophoresis in capillaries. The example studied is the binding of serum haptoglobin (Hp) to hemoglobin (Hb). A known amount of Hb is focused in a capillary in a pH 6-8 range (pI of Hb = 7.0) and thus kept temporarily "immobilized" in the electrophoretic chamber. Subsequently, increasing amounts of ligand (Hp) are loaded cathodically and allowed to sweep past the focused Hb zone. As the complex formed has a pI value well-outside the bounds of such a pH gradient (the 1:1 molar Hb-Hp complex has a pI of 5.5, the 1 to 1/2 molar Hp-Hb complex has a pI of 5.0) it escapes immobilization and moves past the detector window, where it is monitored and quantified. Since the detector is set at 416 nm, where only Hb absorbs, and since the molar extinction coefficient of Hb is well known, it is quite easy to calculate the molar amount of Hb bound to the complex. As an additional check, the amount of unreacted Hb can now be mobilized by disrupting the pH gradient and allowing this residual free Hb to also reach the detector and be quantified. The method is easy, fast, simple and fully automated and thus could represent a valid alternative to existing methods in clinical chemistry for quantifying the amount of Hp in human sera in pathological conditions, such as hemolytic anemias and transfusion reactions.
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Affiliation(s)
- P G Righetti
- Department of Agricultural and Industrial Biotechnology, University of Verona, Italy
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