1
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Teixeira A, Carneiro A, Piairo P, Xavier M, Ainla A, Lopes C, Sousa-Silva M, Dias A, Martins AS, Rodrigues C, Pereira R, Pires LR, Abalde-Cela S, Diéguez L. Advances in Microfluidics for the Implementation of Liquid Biopsy in Clinical Routine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:553-590. [DOI: 10.1007/978-3-031-04039-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Zhang L, Tan J, Pei Q, Ye S. Film thickness and surface plasmon tune the contribution of SFG signals from buried interface and air surface. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Liang Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Junjun Tan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Quanbing Pei
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information Quantum Physics, University of Science and Technology of China, Hefei 230026, China
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3
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Bacolod MD, Mirza AH, Huang J, Giardina SF, Feinberg PB, Soper SA, Barany F. Application of Multiplex Bisulfite PCR-Ligase Detection Reaction-Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer. J Mol Diagn 2020; 22:885-900. [PMID: 32407802 DOI: 10.1016/j.jmoldx.2020.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
The analysis of CpG methylation in circulating tumor DNA fragments has emerged as a promising approach for the noninvasive early detection of solid tumors, including colorectal cancer (CRC). The most commonly employed assay involves bisulfite conversion of circulating tumor DNA, followed by targeted PCR, then real-time quantitative PCR (alias methylation-specific PCR). This report demonstrates the ability of a multiplex bisulfite PCR-ligase detection reaction-real-time quantitative PCR assay to detect seven methylated CpG markers (CRC or colon specific), in both simulated (approximately 30 copies of fragmented CRC cell line DNA mixed with approximately 3000 copies of fragmented peripheral blood DNA) and CRC patient-derived cell-free DNAs. This scalable assay is designed for multiplexing and incorporates steps for improved sensitivity and specificity, including the enrichment of methylated CpG fragments, ligase detection reaction, the incorporation of ribose bases in primers, and use of uracil DNA glycosylase. Six of the seven CpG markers (located in promoter regions of PPP1R16B, KCNA3, CLIP4, GDF6, SEPT9, and GSG1L) were identified through integrated analyses of genome-wide methylation data sets for 31 different types of cancer. These markers were mapped to CpG sites at the promoter region of VIM; VIM and SEPT9 are established epigenetic markers of CRC. Additional bioinformatics analyses show that the methylation at these CpG sites negatively correlates with the transcription of their corresponding genes.
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Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Aashiq H Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Steven A Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York.
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4
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Ruiz C, Huang J, Giardina SF, Feinberg PB, Mirza AH, Bacolod MD, Soper SA, Barany F. Single-molecule detection of cancer mutations using a novel PCR-LDR-qPCR assay. Hum Mutat 2020; 41:1051-1068. [PMID: 31950578 PMCID: PMC7160051 DOI: 10.1002/humu.23987] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/19/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022]
Abstract
Detection of low-abundance mutations in cell-free DNA is being used to identify early cancer and early cancer recurrence. Here, we report a new PCR-LDR-qPCR assay capable of detecting point mutations at a single-molecule resolution in the presence of an excess of wild-type DNA. Major features of the assay include selective amplification and detection of mutant DNA employing multiple nested primer-binding regions as well as wild-type sequence blocking oligonucleotides, prevention of carryover contamination, spatial sample dilution, and detection of multiple mutations in the same position. Our method was tested to interrogate the following common cancer somatic mutations: BRAF:c.1799T>A (p.Val600Glu), TP53:c.743G>A (p.Arg248Gln), KRAS:c.35G>C (p.Gly12Ala), KRAS:c.35G>T (p.Gly12Val), KRAS:c.35G>A (p.Gly12Asp), KRAS:c.34G>T (p.Gly12Cys), and KRAS:c.34G>A (p.Gly12Ser). The single-well version of the assay detected 2-5 copies of these mutations, when diluted with 10,000 genome equivalents (GE) of wild-type human genomic DNA (hgDNA) from buffy coat. A 12-well (pixel) version of the assay was capable of single-molecule detection of the aforementioned mutations at TP53, BRAF, and KRAS (specifically p.Gly12Val and p.Gly12Cys), mixed with 1,000-2,250 GE of wild-type hgDNA from plasma or buffy coat. The assay described herein is highly sensitive, specific, and robust, and potentially useful in liquid biopsies.
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Affiliation(s)
- Cristian Ruiz
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Biology, California State University Northridge, Northridge, CA, 91330, USA
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sarah F. Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Philip B. Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
- Current Address: Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Manny D. Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Steven A. Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS, 66047, USA
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
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5
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Sivakumar R, Lee NY. Microfluidic device fabrication mediated by surface chemical bonding. Analyst 2020; 145:4096-4110. [DOI: 10.1039/d0an00614a] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This review discusses on various bonding techniques for fabricating microdevices with a special emphasis on the modification of surface assisted by the use of chemicals to assemble microfluidic devices at room temperature under atmospheric pressure.
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Affiliation(s)
- Rajamanickam Sivakumar
- Department of Industrial and Environmental Engineering
- College of Industrial Environmental Engineering
- Gachon University
- Seongnam-si
- Korea
| | - Nae Yoon Lee
- Department of BioNano Technology
- Gachon University
- Seongnam-si
- Korea
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6
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Chen T, Gomez-Escoda B, Munoz-Garcia J, Babic J, Griscom L, Wu PYJ, Coudreuse D. A drug-compatible and temperature-controlled microfluidic device for live-cell imaging. Open Biol 2017; 6:rsob.160156. [PMID: 27512142 PMCID: PMC5008015 DOI: 10.1098/rsob.160156] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023] Open
Abstract
Monitoring cellular responses to changes in growth conditions and perturbation of targeted pathways is integral to the investigation of biological processes. However, manipulating cells and their environment during live-cell-imaging experiments still represents a major challenge. While the coupling of microfluidics with microscopy has emerged as a powerful solution to this problem, this approach remains severely underexploited. Indeed, most microdevices rely on the polymer polydimethylsiloxane (PDMS), which strongly absorbs a variety of molecules commonly used in cell biology. This effect of the microsystems on the cellular environment hampers our capacity to accurately modulate the composition of the medium and the concentration of specific compounds within the microchips, with implications for the reliability of these experiments. To overcome this critical issue, we developed new PDMS-free microdevices dedicated to live-cell imaging that show no interference with small molecules. They also integrate a module for maintaining precise sample temperature both above and below ambient as well as for rapid temperature shifts. Importantly, changes in medium composition and temperature can be efficiently achieved within the chips while recording cell behaviour by microscopy. Compatible with different model systems, our platforms provide a versatile solution for the dynamic regulation of the cellular environment during live-cell imaging.
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Affiliation(s)
- Tong Chen
- SyntheCell team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Blanca Gomez-Escoda
- Genome Duplication and Maintenance team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Javier Munoz-Garcia
- SyntheCell team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Julien Babic
- SyntheCell team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Laurent Griscom
- SyntheCell team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Pei-Yun Jenny Wu
- Genome Duplication and Maintenance team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
| | - Damien Coudreuse
- SyntheCell team, Institute of Genetics and Development, CNRS UMR 6290, 2 avenue du Pr. Léon Bernard, 35043 Rennes, France
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7
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Pfammatter M, Andreasen M, Meisl G, Taylor CG, Adamcik J, Bolisetty S, Sánchez-Ferrer A, Klenerman D, Dobson CM, Mezzenga R, Knowles TPJ, Aguzzi A, Hornemann S. Absolute Quantification of Amyloid Propagons by Digital Microfluidics. Anal Chem 2017; 89:12306-12313. [PMID: 28972786 PMCID: PMC5700450 DOI: 10.1021/acs.analchem.7b03279] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The
self-replicating properties of proteins into amyloid fibrils
is a common phenomenon and underlies a variety of neurodegenerative
diseases. Because propagation-active fibrils are chemically indistinguishable
from innocuous aggregates and monomeric precursors, their detection
requires measurements of their replicative capacity. Here we present
a digital amyloid quantitative assay (d-AQuA) with insulin as model
protein for the absolute quantification of single replicative units,
propagons. D-AQuA is a microfluidics-based technology that performs
miniaturized simultaneous propagon-induced amplification chain reactions
within hundreds to thousands of picoliter-sized droplets. At limiting
dilutions, the d-AQuA reactions follow a stochastic regime indicative
of the detection of single propagons. D-AQuA thus enables absolute
quantification of single propagons present in a given sample at very
low concentrations. The number of propagons quantified by d-AQuA was
similar to that of fibrillar insulin aggregates detected by atomic-force
microscopy and to an equivalent microplate-based assay, providing
independent evidence for the identity of insulin propagons with a
subset of morphologically defined protein aggregates. The sensitivity,
precision, and accuracy of d-AQuA enable it to be suitable for multiple
biotechnological and medical applications.
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Affiliation(s)
- Manuela Pfammatter
- Institute of Neuropathology, University of Zurich , CH-8091 Zurich, Switzerland
| | - Maria Andreasen
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University , DK-8000 Aarhus, Denmark
| | - Georg Meisl
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Christopher G Taylor
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Jozef Adamcik
- Department of Health Sciences and Technology, ETH Zurich , CH-8092 Zurich, Switzerland
| | - Sreenath Bolisetty
- Department of Health Sciences and Technology, ETH Zurich , CH-8092 Zurich, Switzerland
| | - Antoni Sánchez-Ferrer
- Department of Health Sciences and Technology, ETH Zurich , CH-8092 Zurich, Switzerland
| | - David Klenerman
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich , CH-8092 Zurich, Switzerland
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom.,Cavendish Laboratory, Department of Physics, University of Cambridge , Cambridge CB3 1HE, United Kingdom
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich , CH-8091 Zurich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich , CH-8091 Zurich, Switzerland
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8
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Gokaltun A, Yarmush ML, Asatekin A, Usta OB. Recent advances in nonbiofouling PDMS surface modification strategies applicable to microfluidic technology. TECHNOLOGY 2017; 5:1-12. [PMID: 28695160 PMCID: PMC5501164 DOI: 10.1142/s2339547817300013] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the last decade microfabrication processes including rapid prototyping techniques have advanced rapidly and achieved a fairly mature stage. These advances have encouraged and enabled the use of microfluidic devices by a wider range of users with applications in biological separations and cell and organoid cultures. Accordingly, a significant current challenge in the field is controlling biomolecular interactions at interfaces and the development of novel biomaterials to satisfy the unique needs of the biomedical applications. Poly(dimethylsiloxane) (PDMS) is one of the most widely used materials in the fabrication of microfluidic devices. The popularity of this material is the result of its low cost, simple fabrication allowing rapid prototyping, high optical transparency, and gas permeability. However, a major drawback of PDMS is its hydrophobicity and fast hydrophobic recovery after surface hydrophilization. This results in significant nonspecific adsorption of proteins as well as small hydrophobic molecules such as therapeutic drugs limiting the utility of PDMS in biomedical microfluidic circuitry. Accordingly, here, we focus on recent advances in surface molecular treatments to prevent fouling of PDMS surfaces towards improving its utility and expanding its use cases in biomedical applications.
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Affiliation(s)
- Aslihan Gokaltun
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School, and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
- Department of Chemical and Biological Engineering, Tufts University, 4 Colby Street, Medford, MA 02474, USA
- Department of Chemical Engineering, Hacettepe University, 06532, Beytepe, Ankara, Turkey
| | - Martin L Yarmush
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School, and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Rd., Piscataway, NJ 08854, USA
| | - Ayse Asatekin
- Department of Chemical and Biological Engineering, Tufts University, 4 Colby Street, Medford, MA 02474, USA
| | - O Berk Usta
- Center for Engineering in Medicine at Massachusetts General Hospital, Harvard Medical School, and Shriners Hospital for Children, 51 Blossom St., Boston, MA 02114, USA
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9
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Abstract
Microarray technology is a multiplex analytical technique for the detection of many different analytes in a mixture of biomolecules. The detection limits for each of the analytes for which the array is designed depend on a multiplicity of reaction parameters, the array itself, and profoundly on the label and detection technology employed. Significant improvements in assay sensitivity have been achieved by optimizing all steps that affect the generation of signal and noise. Nanoparticle technology brings a new dimension to this technology by providing not only higher sensitivity but also improved specificity for hybridization-based microarray assay systems.
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10
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Jin M, Liu X, van den Berg A, Zhou G, Shui L. Ultrasensitive DNA detection based on two-step quantitative amplification on magnetic nanoparticles. NANOTECHNOLOGY 2016; 27:335102. [PMID: 27378514 DOI: 10.1088/0957-4484/27/33/335102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sensitive detection of a specific deoxyribo nucleic acid (DNA) sequence is important for biomedical applications. In this report, a two-step amplification strategy is developed based on magnetic nanoparticles (MNPs) to achieve ultrasensitive DNA fluorescence detection. The first level amplification is obtained from multiple binding sites on MNPs to achieve thousands of probe DNA molecules on one nanoparticle surface. The second level amplification is gained by enzymatic reaction to achieve fluorescence signal enhancement. MNPs functionalized by probe DNA (DNAp) are bound to target DNA (t-DNA) molecules with a ratio of 1:1 on a substrate with capture DNA (DNAc). After the MNPs with DNAp are released from the substrate, alkaline phosphatase (AP) is labelled to MNPs via hybridization reaction between DNAp on MNPs and detection DNAs (DNAd) with AP. The AP on MNPs catalyses non-fluorescent 4-methylumbelliferyl phosphate (4-MUP) to fluorescent 4-methylumbelliferone (4-MU) with high intensity. Finally, fluorescence intensity of the 4-MU is detected by a conventional fluorescence spectrophotometer. With this two-step amplification strategy, the limit of detection (LOD) of 2.8 × 10(-18) mol l(-1) for t-DNA has been achieved.
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Affiliation(s)
- Mingliang Jin
- Institute of Electronic paper Displays, Academy of South China Advanced Optoelectronics, South China Normal University, Guangzhou 510006, People's Republic of China
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11
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Rowinska M, Kelleher SM, Soberon F, Ricco AJ, Daniels S. Fabrication and characterisation of spin coated oxidised PMMA to provide a robust surface for on-chip assays. J Mater Chem B 2015; 3:135-143. [PMID: 32261933 DOI: 10.1039/c4tb01748j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Smooth, thin PMMA layers have been oxidised using two methods on various surfaces. The longevity of activation and ability of the films to bind and retain biomolecules has been investigated.
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Affiliation(s)
- M. Rowinska
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - S. M. Kelleher
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - F. Soberon
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - A. J. Ricco
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - S. Daniels
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
- National Centre for Plasma Research and Technology
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12
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Handal MI, Ugaz VM. DNA mutation detection and analysis using miniaturized microfluidic systems. Expert Rev Mol Diagn 2014; 6:29-38. [PMID: 16359265 DOI: 10.1586/14737159.6.1.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Identification of genetic sequence variations occurring on a population-wide scale is key to unraveling the complex interactions that are the underlying cause of many medical disorders and diseases. A critical need exists, however, for advanced technology to enable DNA mutation analysis to be performed with significantly higher throughput and at significantly lower cost than is currently attainable. Microfluidic systems offer an attractive platform to address these needs by combining the ability to perform rapid analysis with a simplified device format that can be inexpensively mass-produced. This paper will review recent progress toward developing these next-generation systems and discuss challenges associated with adapting these technologies for routine laboratory use.
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Affiliation(s)
- Maria I Handal
- Texas A&M University, Department of Chemical Engineering, College Station, TX 77843-3122, USA
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13
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Watanabe S, Hagihara K, Tsukagoshi K, Hashimoto M. Microbead-Based Ligase Detection Reaction Assay Using a Molecular Beacon Probe for the Detection of Low-Abundance Point Mutations. Anal Chem 2013; 86:900-6. [DOI: 10.1021/ac403531x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sho Watanabe
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Kenta Hagihara
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering
and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
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14
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Hommatsu M, Okahashi H, Ohta K, Tamai Y, Tsukagoshi K, Hashimoto M. Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection. ANAL SCI 2013; 29:689-95. [PMID: 23842410 DOI: 10.2116/analsci.29.689] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.
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Affiliation(s)
- Manami Hommatsu
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
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15
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Zhu J, Palla M, Ronca S, Warpner R, Ju J, Lin Q. A MEMS-Based Approach to Single Nucleotide Polymorphism Genotyping. SENSORS AND ACTUATORS. A, PHYSICAL 2013; 195:175-182. [PMID: 24729659 PMCID: PMC3979494 DOI: 10.1016/j.sna.2012.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genotyping of single nucleotide polymorphisms (SNPs) allows diagnosis of human genetic disorders associated with single base mutations. Conventional SNP genotyping methods are capable of providing either accurate or high-throughput detection, but are still labor-, time-, and resource-intensive. Microfluidics has been applied to SNP detection to provide fast, low-cost, and automated alternatives, although these applications are still limited by either accuracy or throughput issues. To address this challenge, we present a MEMS-based SNP genotyping approach that uses solid-phase-based reactions in a single microchamber on a temperature control chip. Polymerase chain reaction (PCR), allele specific single base extension (SBE), and desalting on microbeads are performed in the microchamber, which is coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the SBE product. Experimental results from genotyping of the SNP on exon 1 of the HBB gene, which causes sickle cell anemia, demonstrate the potential of the device for rapid, accurate, multiplexed and high-throughput detection of SNPs.
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Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
- Department of Chemical Engineering, Columbia University,
New York, NY, USA
| | - Stefano Ronca
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
- Department of Mechanical and Industrial Engineering,
University of Brescia, Brescia, BS, Italy
| | - Ronald Warpner
- Department of Obstetrics and Gynecology, Columbia
University, New York, NY, USA
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University,
New York, NY, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
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16
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Development of a ligase detection reaction/CGE method using a LIF dual-channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild-type DNA. Electrophoresis 2013; 34:1415-22. [DOI: 10.1002/elps.201200671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 02/09/2013] [Accepted: 02/16/2013] [Indexed: 11/07/2022]
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17
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Ionic matrices pre-spotted matrix-assisted laser desorption/ionization plates for patient maker following in course of treatment, drug titration, and MALDI mass spectrometry imaging. Anal Biochem 2013; 434:187-98. [DOI: 10.1016/j.ab.2012.10.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 11/18/2022]
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18
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Horinouchi A, Tanaka K. An effect of stereoregularity on the structure of poly(methyl methacrylate) at air and water interfaces. RSC Adv 2013. [DOI: 10.1039/c3ra40631h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Chen YW, Wang H, Hupert M, Soper SA. Identification of methicillin-resistant Staphylococcus aureus using an integrated and modular microfluidic system. Analyst 2013; 138:1075-83. [DOI: 10.1039/c2an36430a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Atarashi H, Hirai T, Hori K, Hino M, Morita H, Serizawa T, Tanaka K. Uptake of water in as-spun poly(methyl methacrylate) thin films. RSC Adv 2013. [DOI: 10.1039/c3ra23066j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Chen YW, Wang H, Hupert M, Witek M, Dharmasiri U, Pingle MR, Barany F, Soper SA. Modular microfluidic system fabricated in thermoplastics for the strain-specific detection of bacterial pathogens. LAB ON A CHIP 2012; 12:3348-55. [PMID: 22859220 PMCID: PMC4386729 DOI: 10.1039/c2lc40805h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The recent outbreaks of a lethal E. coli strain in Germany have aroused renewed interest in developing rapid, specific and accurate systems for detecting and characterizing bacterial pathogens in suspected contaminated food and/or water supplies. To address this need, we have designed, fabricated and tested an integrated modular-based microfluidic system and the accompanying assay for the strain-specific identification of bacterial pathogens. The system can carry out the entire molecular processing pipeline in a single disposable fluidic cartridge and detect single nucleotide variations in selected genes to allow for the identification of the bacterial species, even its strain with high specificity. The unique aspect of this fluidic cartridge is its modular format with task-specific modules interconnected to a fluidic motherboard to permit the selection of the target material. In addition, to minimize the amount of finishing steps for assembling the fluidic cartridge, many of the functional components were produced during the polymer molding step used to create the fluidic network. The operation of the cartridge was provided by electronic, mechanical, optical and hydraulic controls located off-chip and packaged into a small footprint instrument (1 ft(3)). The fluidic cartridge was capable of performing cell enrichment, cell lysis, solid-phase extraction (SPE) of genomic DNA, continuous flow (CF) PCR, CF ligase detection reaction (LDR) and universal DNA array readout. The cartridge was comprised of modules situated on a fluidic motherboard; the motherboard was made from polycarbonate, PC, and used for cell lysis, SPE, CF PCR and CF LDR. The modules were task-specific units and performed universal zip-code array readout or affinity enrichment of the target cells with both made from poly(methylmethacrylate), PMMA. Two genes, uidA and sipB/C, were used to discriminate between E. coli and Salmonella, and evaluated as a model system. Results showed that the fluidic system could successfully identify bacteria in <40 min with minimal operator intervention and perform strain identification, even from a mixed population with the target of a minority. We further demonstrated the ability to analyze the E. coli O157:H7 strain from a waste-water sample using enrichment followed by genotyping.
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Affiliation(s)
- Yi-Wen Chen
- Department of Chemistry and Louisiana State University, Baton Rouge, LA, 70803
| | - Hong Wang
- Department of Biomedical Engineering University of North Carolina, Chapel Hill, NC, 27599
| | - Mateusz Hupert
- Department of Biomedical Engineering University of North Carolina, Chapel Hill, NC, 27599
| | - Makgorzata Witek
- Department of Biomedical Engineering University of North Carolina, Chapel Hill, NC, 27599
| | - Udara Dharmasiri
- Department of Chemistry and Louisiana State University, Baton Rouge, LA, 70803
| | | | | | - Steven A. Soper
- Department of Biomedical Engineering University of North Carolina, Chapel Hill, NC, 27599
- Department of Chemistry University of North Carolina, Chapel Hill, NC, 27599
- Nano-bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
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22
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Escorihuela J, Bañuls MJ, García Castelló J, Toccafondo V, García-Rupérez J, Puchades R, Maquieira Á. Chemical silicon surface modification and bioreceptor attachment to develop competitive integrated photonic biosensors. Anal Bioanal Chem 2012; 404:2831-40. [PMID: 22872294 DOI: 10.1007/s00216-012-6280-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/07/2012] [Accepted: 07/17/2012] [Indexed: 11/26/2022]
Abstract
Methodology for the functionalization of silicon-based materials employed for the development of photonic label-free nanobiosensors is reported. The studied functionalization based on organosilane chemistry allowed the direct attachment of biomolecules in a single step, maintaining their bioavailability. Using this immobilization approach in probe microarrays, successful specific detection of bacterial DNA is achieved, reaching hybridization sensitivities of 10 pM. The utility of the immobilization approach for the functionalization of label-free nanobiosensors based on photonic crystals and ring resonators was demonstrated using bovine serum albumin (BSA)/anti-BSA as a model system.
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Affiliation(s)
- Jorge Escorihuela
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain
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23
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Ultrathin and smooth poly(methyl methacrylate) (PMMA) films for label-free biomolecule detection with total internal reflection ellipsometry (TIRE). Biosens Bioelectron 2012; 36:250-6. [DOI: 10.1016/j.bios.2012.04.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/17/2012] [Accepted: 04/17/2012] [Indexed: 02/07/2023]
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24
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Horinouchi A, Atarashi H, Fujii Y, Tanaka K. Dynamics of Water-Induced Surface Reorganization in Poly(methyl methacrylate) Films. Macromolecules 2012. [DOI: 10.1021/ma3002559] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ayanobu Horinouchi
- Department
of Applied Chemistry and ‡International Institute for Carbon-Neutral Energy
Research (WPI- I2CNER), Kyushu University, Fukuoka 819-0395, Japan
| | - Hironori Atarashi
- Department
of Applied Chemistry and ‡International Institute for Carbon-Neutral Energy
Research (WPI- I2CNER), Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshihisa Fujii
- Department
of Applied Chemistry and ‡International Institute for Carbon-Neutral Energy
Research (WPI- I2CNER), Kyushu University, Fukuoka 819-0395, Japan
| | - Keiji Tanaka
- Department
of Applied Chemistry and ‡International Institute for Carbon-Neutral Energy
Research (WPI- I2CNER), Kyushu University, Fukuoka 819-0395, Japan
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25
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Wang H, Chen HW, Hupert ML, Chen PC, Datta P, Pittman TL, Goettert J, Murphy MC, Williams D, Barany F, Soper SA. Fully Integrated Thermoplastic Genosensor for the Highly Sensitive Detection and Identification of Multi-Drug-Resistant Tuberculosis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Wang H, Chen HW, Hupert ML, Chen PC, Datta P, Pittman TL, Goettert J, Murphy MC, Williams D, Barany F, Soper SA. Fully integrated thermoplastic genosensor for the highly sensitive detection and identification of multi-drug-resistant tuberculosis. Angew Chem Int Ed Engl 2012; 51:4349-53. [PMID: 22431490 DOI: 10.1002/anie.201200732] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Hong Wang
- Department of Chemistry and Mechanical Engineering, Louisiana State University, USA
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27
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Hashimoto M, Morimoto C, Hagihara K, Tsukagoshi K. Rapid and Convenient Sample Preparation in a Single Tube Using Magnetic Beads for Fluorescence Detection of Single Nucleotide Variation Based on Oligonucleotide Ligation. CHEM LETT 2012. [DOI: 10.1246/cl.2012.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Chika Morimoto
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Kenta Hagihara
- Department of Chemical Engineering and Materials Science, Doshisha University
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering and Materials Science, Doshisha University
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28
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Gubala V, Harris LF, Ricco AJ, Tan MX, Williams DE. Point of Care Diagnostics: Status and Future. Anal Chem 2011; 84:487-515. [DOI: 10.1021/ac2030199] [Citation(s) in RCA: 832] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vladimir Gubala
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Leanne F. Harris
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Antonio J. Ricco
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Ming X. Tan
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - David E. Williams
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
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29
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Yu L, Li Q, Gai H, Wang Z. Chemiluminescence response of murine macrophages on multilayer microfluidic chips. Appl Biochem Biotechnol 2011; 166:786-95. [PMID: 22139733 DOI: 10.1007/s12010-011-9467-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 11/15/2011] [Indexed: 11/25/2022]
Abstract
We have demonstrated an integrated platform for microfluidics and chemiluminescence (CL) detection that is capable of parallel cell culture, convenient liquid manipulation, and sensitive chemiluminescent detection. Luminol-dependent CL responses induced by three different stimuli, phytohemagglutinin (PHA), concanavalin A (ConA), and lipopolysaccharides (LPS), which can evoke a CL response in macrophages, were evaluated on this microfluidic chip. We studied the dose-dependent effect of these three stimuli on CL response in murine macrophages. PHA produced the highest CL response compared to LPS and ConA. The CL intensity produced by PHA was 6.85 and four times higher than that by LPS and ConA, respectively, at the low concentration of 100 μg/ml. We have found microfluidic based CL to be a very useful screening tool, which is less laborious and more sensitive. This microfluidic system is disposable and capable of rapid device prototyping; it may prove to be very useful in clinical and pharmaceutical applications.
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Affiliation(s)
- Linfen Yu
- Research Center of Biosensors and Medical Instruments, Shenzhen Institutes of Advanced Technology, CAS, Shenzhen, China
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30
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Wang Q, Zhang Y, Ding H, Wu J, Wang L, Zhou L, Pu Q. The use of ethylene glycol solution as the running buffer for highly efficient microchip-based electrophoresis in unmodified cyclic olefin copolymer microchips. J Chromatogr A 2011; 1218:9422-7. [PMID: 22099226 DOI: 10.1016/j.chroma.2011.10.078] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/25/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022]
Abstract
An ethylene glycol solution was used as the electrophoretic running buffer in unmodified cyclic olefin copolymer (COC) microchips to minimize the interactions between the analytes and the hydrophobic walls of the plastic microchannels, enhance the resolution of the analytes and eliminate the uncontrollable dispersion caused by uneven liquid levels and non-uniform surfaces of the separation channels. Five amino acids that were labeled with fluorescein isothiocyanate (FITC) were used as model analytes to examine the separation efficiency. The effects of ethylene glycol concentration, pH and sodium tetraborate concentration were systematically investigated. The five FITC-labeled amino acids were effectively resolved using a COC microchip with an effective length of 2.5 cm under optimum conditions, which included using a running buffer of 20 mmol/L sodium tetraborate in ethylene glycol:water (80:20, v/v), pH 6.7. A theoretical plate number of 4.8 × 10(5)/m was obtained for aspartic acid. The system exhibited good repeatability, and the relative standard deviations (n=5) of the peak areas and migration times were no more than 3.4% and 0.7%, respectively. Furthermore, the system was successfully applied to elucidate these five amino acids in human saliva.
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Affiliation(s)
- Qin Wang
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization, Gansu Province, Sate Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, 222 Southern Tianshui Road, Lanzhou, Gansu 730000, China
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31
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Abstract
Microfluidic devices exhibit a great promising development in clinical diagnosis and disease screening due to their advantages of precise controlling of fluid flow, requirement of miniamount sample, rapid reaction speed and convenient integration. In this paper, the improvements of microfluidic diagnostic technologies in recent years are reviewed. The applications and developments of on-chip disease marker detection, microfluidic cell selection and cell drug metabolism, and diagnostic micro-devices are discussed.
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Affiliation(s)
- Haifang Li
- School of Science, Beijing University of Chemical Technology, Beijing 100029, China
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32
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Chantiwas R, Park S, Soper SA, Kim BC, Takayama S, Sunkara V, Hwang H, Cho YK. Flexible fabrication and applications of polymer nanochannels and nanoslits. Chem Soc Rev 2011; 40:3677-702. [PMID: 21442106 PMCID: PMC4773912 DOI: 10.1039/c0cs00138d] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fluidic devices that employ nanoscale structures (<100 nm in one or two dimensions, slits or channels, respectively) are generating great interest due to the unique properties afforded by this size domain compared to their micro-scale counterparts. Examples of interesting nanoscale phenomena include the ability to preconcentrate ionic species at extremely high levels due to ion selective migration, unique molecular separation modalities, confined environments to allow biopolymer stretching and elongation and solid-phase bioreactions that are not constrained by mass transport artifacts. Indeed, many examples in the literature have demonstrated these unique opportunities, although predominately using glass, fused silica or silicon as the substrate material. Polymer microfluidics has established itself as an alternative to glass, fused silica, or silicon-based fluidic devices. The primary advantages arising from the use of polymers are the diverse fabrication protocols that can be used to produce the desired structures, the extensive array of physiochemical properties associated with different polymeric materials, and the simple and robust modification strategies that can be employed to alter the substrate's surface chemistry. However, while the strengths of polymer microfluidics is currently being realized, the evolution of polymer-based nanofluidics has only recently been reported. In this critical review, the opportunities afforded by polymer-based nanofluidics will be discussed using both elastomeric and thermoplastic materials. In particular, various fabrication modalities will be discussed along with the nanometre size domains that they can achieve for both elastomer and thermoplastic materials. Different polymer substrates that can be used for nanofluidics will be presented along with comparisons to inorganic nanodevices and the consequences of material differences on the fabrication and operation of nanofluidic devices (257 references).
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Affiliation(s)
- Rattikan Chantiwas
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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33
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Han K, Lee TY, Nikitopoulos DE, Soper SA, Murphy MC. A vertically stacked, polymer, microfluidic point mutation analyzer: rapid high accuracy detection of low-abundance K-ras mutations. Anal Biochem 2011; 417:211-9. [PMID: 21771577 DOI: 10.1016/j.ab.2011.06.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/15/2011] [Accepted: 06/23/2011] [Indexed: 01/06/2023]
Abstract
Recognition of point mutations in the K-ras gene can be used for the clinical management of several types of cancers. Unfortunately, several assay and hardware concerns must be addressed to allow users not well trained in performing molecular analyses the opportunity to undertake these measurements. To provide for a larger user base for these types of molecular assays, a vertically stacked microfluidic analyzer with a modular architecture and process automation was developed. The analyzer employs a primary polymerase chain reaction (PCR) coupled to an allele-specific ligase detection reaction (LDR). Each functional device, including continuous flow thermal reactors for the PCR and LDR, passive micromixers, and ExoSAP-IT purification, was designed and tested. Individual devices were fabricated in polycarbonate using hot embossing and were assembled using adhesive bonding for system assembly. The system produced LDR products from a DNA sample in approximately 1h, an 80% reduction in time compared with conventional benchtop instrumentation. Purifying the post-PCR products with the ExoSAP-IT enzyme led to optimized LDR performance, minimizing false-positive signals and producing reliable results. Mutant alleles in genomic DNA were quantified to the level of 0.25 ng of mutant DNA in 50 ng of wild-type DNA for a 25-μl sample, equivalent to DNA from 42 mutant cells.
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Affiliation(s)
- Kyudong Han
- Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.
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34
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Rapid screening of phenylketonuria using a CD microfluidic device. J Chromatogr A 2011; 1218:1907-12. [DOI: 10.1016/j.chroma.2011.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/19/2011] [Accepted: 02/01/2011] [Indexed: 11/19/2022]
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35
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Yeo LY, Chang HC, Chan PPY, Friend JR. Microfluidic devices for bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:12-48. [PMID: 21072867 DOI: 10.1002/smll.201000946] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Harnessing the ability to precisely and reproducibly actuate fluids and manipulate bioparticles such as DNA, cells, and molecules at the microscale, microfluidics is a powerful tool that is currently revolutionizing chemical and biological analysis by replicating laboratory bench-top technology on a miniature chip-scale device, thus allowing assays to be carried out at a fraction of the time and cost while affording portability and field-use capability. Emerging from a decade of research and development in microfluidic technology are a wide range of promising laboratory and consumer biotechnological applications from microscale genetic and proteomic analysis kits, cell culture and manipulation platforms, biosensors, and pathogen detection systems to point-of-care diagnostic devices, high-throughput combinatorial drug screening platforms, schemes for targeted drug delivery and advanced therapeutics, and novel biomaterials synthesis for tissue engineering. The developments associated with these technological advances along with their respective applications to date are reviewed from a broad perspective and possible future directions that could arise from the current state of the art are discussed.
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Affiliation(s)
- Leslie Y Yeo
- Micro/Nanophysics Research Laboratory, Department of Mechanical & Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
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36
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37
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Microfluidic DNA microarray analysis: a review. Anal Chim Acta 2010; 687:12-27. [PMID: 21241842 DOI: 10.1016/j.aca.2010.11.056] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 11/21/2022]
Abstract
Microarray DNA hybridization techniques have been used widely from basic to applied molecular biology research. Generally, in a DNA microarray, different probe DNA molecules are immobilized on a solid support in groups and form an array of microspots. Then, hybridization to the microarray can be performed by applying sample DNA solutions in either the bulk or the microfluidic manner. Because the immobilized probe DNA binds and retains its complementary target DNA, detection is achieved through the read-out of the tagged markers on the sample target molecules. The recent microfluidic hybridization method shows the advantages of less sample usage and reduced incubation time. Here, sample solutions are confined in microfabricated channels and flow through the probe microarray area. The high surface-to-volume ratio in microchannels of nanolitre volume greatly enhanced the sensitivity as obtained with the bulk solution method. To generate nanolitre flows, different techniques have been developed, and this including electrokinetic control, vacuum suction and syringe pumping. The latter two are pressure-driven methods which are more flexible without the need of considering the physicochemical properties of solutions. Recently, centrifugal force is employed to drive liquid movement in microchannels. This method utilizes the body force from the liquid itself and there are no additional solution interface contacts such as from electrodes or syringes and tubing. Centrifugal force driven flow also features the ease of parallel hybridizations. In this review, we will summarize the recent advances in microfluidic microarray hybridization and compare the applications of various flow methods.
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38
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Huang S, Li C, Lin B, Qin J. Microvalve and micropump controlled shuttle flow microfluidic device for rapid DNA hybridization. LAB ON A CHIP 2010; 10:2925-2931. [PMID: 20830429 DOI: 10.1039/c005227b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present a novel microfluidic device integrated with microvalves and micropumps for rapid DNA hybridization using shuttle flow. The device is composed of 48 hybridization units containing 48 microvalves and 96 micropumps for the automation of shuttle flow. We used four serotypes of Dengue Virus genes (18mer) to demonstrate that the automatic shuttle flow shortened the hybridization time to 90 s, reduced sample consumption to 1 μL and lowered detection limit to 100 pM (100 amol in a 1 μL sample). Moreover, we applied this device to realize single base discrimination and analyze 48 samples containing different DNA targets, simultaneously. For kinetic measurements of nucleotide hybridization, on-line monitoring of the processes was carried out. This rapid hybridization device has the ability for accommodating the entire hybridization process (i.e., injection, hybridization, washing, detection, signal acquisition) in an automated and high-throughput fashion.
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Affiliation(s)
- Shuqiang Huang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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39
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Microfluidic DNA microarrays in PMMA chips: streamlined fabrication via simultaneous DNA immobilization and bonding activation by brief UV exposure. Biomed Microdevices 2010; 12:673-81. [PMID: 20336488 DOI: 10.1007/s10544-010-9420-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This report presents and describes a simple and scalable method for producing functional DNA microarrays within enclosed polymeric, PMMA, microfluidic devices. Brief (30 s) exposure to UV simultaneously immobilized poly(T)poly(C)-tagged DNA probes to the surface of unmodified PMMA and activated the surface for bonding below the glass transition temperature of the bulk PMMA. Functionality and validation of the enclosed PMMA microarrays was demonstrated as 18 patients were correctly genotyped for all eight mutation sites in the HBB gene interrogated. The fabrication process therefore produced probes with desired hybridization properties and sufficient bonding between PMMA layers to allow construction of microfluidic devices. The streamlined fabrication method is suited to the production of low-cost microfluidic microarray-based diagnostic devices and, as such, is equally applicable to the development of diagnostics for both resource rich and resource limited settings.
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40
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Li S, Xia Y, Zhang J, Han J, Jiang L. Polystyrene spheres coated with gold nanoparticles for detection of DNA. Electrophoresis 2010; 31:3090-6. [DOI: 10.1002/elps.201000204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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41
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Zhang Y, Tang Z, Wang J, Wu H, Maham A, Lin Y. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Signal Amplification. Anal Chem 2010; 82:6440-6. [DOI: 10.1021/ac1006238] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Youyu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China, and Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Zhiwen Tang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China, and Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Jun Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China, and Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Hong Wu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China, and Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Aihui Maham
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China, and Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Yuehe Lin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, People’s Republic of China, and Pacific Northwest National Laboratory, Richland, Washington 99352
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42
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Lien KY, Lee GB. Miniaturization of molecular biological techniques for gene assay. Analyst 2010; 135:1499-518. [PMID: 20390199 DOI: 10.1039/c000037j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted.
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Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, National Cheng Kung University, Tainan, 701, Taiwan
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Liuni P, Rob T, Wilson DJ. A microfluidic reactor for rapid, low-pressure proteolysis with on-chip electrospray ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:315-320. [PMID: 20049884 DOI: 10.1002/rcm.4391] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A microfluidic reactor that enables rapid digestion of proteins prior to on-line analysis by electrospray ionization mass spectrometry (ESI-MS) is introduced. The device incorporates a wide (1.5 cm), shallow (10 microm) reactor 'well' that is functionalized with pepsin-agarose, a design that facilitates low-pressure operation and high clogging resistance. Electrospray ionization is carried out directly from a short metal capillary integrated into the chip outlet. Fabrication, involving laser ablation of polymethyl methacrylate (PMMA), is exceedingly straightforward and inexpensive. High sequence coverage spectra of myoglobin (Mb), ubiquitin (Ub) and bovine serum albumin (BSA) digests were obtained after <4 s of residence time in the reactor. Stress testing showed little loss of performance over approximately 2 h continuous use at high flow rates (30 microL/min). The device provides a convenient platform for a range of applications in proteomics and structural biology, i.e. to enable high-throughput workflows or to limit back-exchange in spatially resolved hydrogen/deuterium exchange (HDX) experiments.
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Affiliation(s)
- Peter Liuni
- York University Chemistry Department, Toronto, ON, M3J 1P3, Canada
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Wang L, Li PCH. Optimization of a microfluidic microarray device for the fast discrimination of fungal pathogenic DNA. Anal Biochem 2010; 400:282-8. [PMID: 20083083 DOI: 10.1016/j.ab.2010.01.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/20/2022]
Abstract
A microfluidic microarray device, which has been developed for parallel DNA detection, is now further optimized for more rapid and sensitive DNA detection and for the single-base-pair discrimination of two fungal pathogenic PCR products. Two poly(dimethylsiloxane) (PDMS)-based microfluidic chips consist of radial and spiral microchannels in which flexible probe creation and convenient sample delivery have been achieved by centrifugal pumping. The microarray hybridizations occurred at the cross sections within the spiral channels intersecting the preprinted radial probe lines. The centrifugal pumping method showed advantages over the vacuum suction method in terms of parallel solution delivery and less signal variations between replicate samples. The effect of microchannel depth was studied, and hybridization time is predictable at a certain rotation speed. Cy5 dye labels were proved to show much higher hybridization efficiency as well as less photobleaching effect as compared with the fluorescein dye labels used in our previous work. With these optimized conditions, the method was applied to the detection of three fungal pathogenic polymerase chain reaction (PCR) products with a sample load of 0.2 ng (in 1 microl). Furthermore, the single-base-pair discrimination between the PCR products of two relevant Botrytis species (B. cinerea and B. squamosa) was achieved in a duration as short as 3 min.
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Affiliation(s)
- Lin Wang
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
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Zhou J, Ellis AV, Voelcker NH. Recent developments in PDMS surface modification for microfluidic devices. Electrophoresis 2010; 31:2-16. [DOI: 10.1002/elps.200900475] [Citation(s) in RCA: 599] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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HASHIMOTO M, YOSHIDA K, TSUKAGOSHI K. Direct Detection of Mutant DNA in a Mixed Population of Higher Copy Number Wild-Type DNA Based on Ligase Detection Reaction in Conjunction with Fluorescence Resonance Energy Transfer. ANAL SCI 2010; 26:1255-9. [DOI: 10.2116/analsci.26.1255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Li C, Li H, Qin J, Lin B. Rapid discrimination of single-nucleotide mismatches based on reciprocating flow on a compact disc microfluidic device. Electrophoresis 2009; 30:4270-6. [DOI: 10.1002/elps.200900305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mairhofer J, Roppert K, Ertl P. Microfluidic systems for pathogen sensing: a review. SENSORS 2009; 9:4804-23. [PMID: 22408555 PMCID: PMC3291940 DOI: 10.3390/s90604804] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 06/04/2009] [Accepted: 06/08/2009] [Indexed: 01/21/2023]
Abstract
Rapid pathogen sensing remains a pressing issue today since conventional identification methodsare tedious, cost intensive and time consuming, typically requiring from 48 to 72 h. In turn, chip based technologies, such as microarrays and microfluidic biochips, offer real alternatives capable of filling this technological gap. In particular microfluidic biochips make the development of fast, sensitive and portable diagnostic tools possible, thus promising rapid and accurate detection of a variety of pathogens. This paper will provide a broad overview of the novel achievements in the field of pathogen sensing by focusing on methods and devices that compliment microfluidics.
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Affiliation(s)
- Jürgen Mairhofer
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Kriemhilt Roppert
- Division of Nano-System-Technologies, Austrian Research Centers GmbH – ARC, Donau-City-Street 1, 1220 Vienna, Austria
| | - Peter Ertl
- Division of Nano-System-Technologies, Austrian Research Centers GmbH – ARC, Donau-City-Street 1, 1220 Vienna, Austria
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +43-(0)50550-4305; Fax: +43-(0)50550-4399
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Emerging optofluidic technologies for point-of-care genetic analysis systems: a review. Anal Bioanal Chem 2009; 395:621-36. [PMID: 19455313 DOI: 10.1007/s00216-009-2826-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 04/24/2009] [Accepted: 04/27/2009] [Indexed: 10/20/2022]
Abstract
This review describes recently emerging optical and microfluidic technologies suitable for point-of-care genetic analysis systems. Such systems must rapidly detect hundreds of mutations from biological samples with low DNA concentration. We review optical technologies delivering multiplex sensitivity and compatible with lab-on-chip integration for both tagged and non-tagged optical detection, identifying significant source and detector technology emerging from telecommunications technology. We highlight the potential for improved hybridization efficiency through careful microfluidic design and outline some novel enhancement approaches using target molecule confinement. Optimization of fluidic parameters such as flow rate, channel height and time facilitates enhanced hybridization efficiency and consequently detection performance as compared with conventional assay formats (e.g. microwell plates). We highlight lab-on-chip implementations with integrated microfluidic control for "sample-to-answer" systems where molecular biology protocols to realize detection of target DNA sequences from whole blood are required. We also review relevant technology approaches to optofluidic integration, and highlight the issue of biomolecule compatibility. Key areas in the development of an integrated optofluidic system for DNA hybridization are optical/fluidic integration and the impact on biomolecules immobilized within the system. A wide range of technology platforms have been advanced for detection, quantification and other forms of characterization of a range of biomolecules (e.g. RNA, DNA, protein and whole cell). Owing to the very different requirements for sample preparation, manipulation and detection of the different types of biomolecules, this review is focused primarily on DNA-DNA interactions in the context of point-of-care analysis systems.
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