1
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Hui K, Yan L, Schneider JW. Electrophoretically Snagging Viral Genomes in Wormlike Micelle Networks Using Peptide Nucleic Acid Amphiphiles and dsDNA Oligomers. Biomacromolecules 2024. [PMID: 39017713 DOI: 10.1021/acs.biomac.4c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
We demonstrate that the attachment of 30-170 bp dsDNA oligomers to ssDNA viral genomes gives a significant additional mobility shift in micelle-tagging electrophoresis (MTE). In MTE, a modified peptide nucleic acid amphiphile is attached to the viral genome to bind drag-inducing micelles present in capillary electrophoresis running buffers. Further attachment of 30-170 bp dsDNA oligomers drastically shifts the mobility of the 5.1 kB ssDNA genome of mouse minute virus (MMV), providing a new mechanism to improve resolution in CE-based analysis of kilobase nucleic acids. A model based on biased-reptation electrophoresis, end-labeled free-solution electrophoresis, and Ferguson gel-filtration theory is presented to describe the observed mobility shifts.
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Affiliation(s)
- Kimberly Hui
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Lingxiao Yan
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - James W Schneider
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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2
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Mahmad Rasid I, Rao A, Holten-Andersen N, Olsen BD. Self-Diffusion in a Weakly Entangled Associative Network. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irina Mahmad Rasid
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ameya Rao
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Niels Holten-Andersen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley D. Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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3
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Furutani S, Furutani N, Kawai Y, Nakayama A, Nagai H. Rapid DNA Sequencing Technology Based on the Sanger Method for Bacterial Identification. SENSORS (BASEL, SWITZERLAND) 2022; 22:2130. [PMID: 35336302 PMCID: PMC8955868 DOI: 10.3390/s22062130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Antimicrobial resistance, a global health concern, has been increasing due to inappropriate use of antibacterial agents. To facilitate early treatment of sepsis, rapid bacterial identification is imperative to determine appropriate antibacterial agent for better therapeutic outcomes. In this study, we developed a rapid PCR method, rapid cycle sequencing, and microchip electrophoresis, which are the three elemental technologies for DNA sequencing based on the Sanger sequencing method, for bacterial identification. We achieved PCR amplification within 13 min and cycle sequencing within 14 min using a rapid thermal cycle system applying microfluidic technology. Furthermore, DNA analysis was completed in 14 min by constructing an algorithm for analyzing and performing microchip electrophoresis. Thus, the three elemental Sanger-based DNA sequencing steps were accomplished within 41 min. Development of a rapid purification process subsequent to PCR and cycle sequence using a microchip would help realize the identification of causative bacterial agents within one hour, and facilitate early treatment of sepsis.
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Affiliation(s)
- Shunsuke Furutani
- Advanced Photonics and Biosensing Open Innovation Laboratory (Photo-BIO OIL), National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (S.F.); (N.F.)
| | - Nozomi Furutani
- Advanced Photonics and Biosensing Open Innovation Laboratory (Photo-BIO OIL), National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (S.F.); (N.F.)
| | - Yasuyuki Kawai
- Department of Emergency and Critical Care Medicine, Nara Medical University, 840 Shijo, Kashihara 634-8522, Nara, Japan;
| | - Akifumi Nakayama
- Department of Medical Technology, School of Health Sciences, Gifu University of Medical Science, 795-1 Ichihiraga, Seki 501-3892, Gifu, Japan;
| | - Hidenori Nagai
- Advanced Photonics and Biosensing Open Innovation Laboratory (Photo-BIO OIL), National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (S.F.); (N.F.)
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4
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Damiati S, Mhanna R, Kodzius R, Ehmoser EK. Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics. Genes (Basel) 2018; 9:E144. [PMID: 29509709 PMCID: PMC5867865 DOI: 10.3390/genes9030144] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rami Mhanna
- Biomedical Engineering Program, The American University of Beirut (AUB), Beirut 1107-2020, Lebanon.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
| | - Eva-Kathrin Ehmoser
- Department of Nanobiotechnology, Institute for Synthetic Bioarchitecture, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
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5
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Anazawa T, Uchiho Y, Yokoi T, Chalkidis G, Yamazaki M. A simple and highly sensitive spectroscopic fluorescence-detection system for multi-channel plastic-microchip electrophoresis based on side-entry laser-beam zigzag irradiation. LAB ON A CHIP 2017; 17:2235-2242. [PMID: 28585967 DOI: 10.1039/c7lc00448f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A five-color fluorescence-detection system for eight-channel plastic-microchip electrophoresis was developed. In the eight channels (with effective electrophoretic lengths of 10 cm), single-stranded DNA fragments were separated (with single-base resolution up to 300 bases within 10 min), and seventeen-loci STR genotyping for forensic human identification was successfully demonstrated. In the system, a side-entry laser beam is passed through the eight channels (eight A channels), with alternately arrayed seven sacrificial channels (seven B channels), by a technique called "side-entry laser-beam zigzag irradiation." Laser-induced fluorescence from the eight A channels and Raman-scattered light from the seven B channels are then simultaneously, uniformly, and spectroscopically detected, in the direction perpendicular to the channel array plane, through a transmission grating and a CCD camera. The system is therefore simple and highly sensitive. Because the microchip is fabricated by plastic-injection molding, it is inexpensive and disposable and thus suitable for actual use in various fields.
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Affiliation(s)
| | | | | | | | - Motohiro Yamazaki
- Hitachi High-Technologies Corporation, Science & Medical Systems Business Group, Japan
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6
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Pollnau M, Hammer M, Dongre C, Hoekstra HJWM. Combined microfluidic-optical DNA analysis with single-base-pair sizing capability. BIOMEDICAL OPTICS EXPRESS 2016; 7:5201-5207. [PMID: 28018736 PMCID: PMC5175563 DOI: 10.1364/boe.7.005201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Abstract
DNA sequencing by microchip capillary electrophoresis (CE) enables cheap, high-speed analysis of low reagent volumes. One of its potential applications is the identification of genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant size range of 150-1000 base-pairs requires a variance of σ2 < 10-3. In a microfluidic chip post-processed by femtosecond-laser writing of an optical waveguide we CE-separated 12 blue-labeled and 23 red-labeled DNA fragments in size. Each set was excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue and red signals distinguished by Fourier analysis. We tested different calibration strategies. Choice of the fluorescent label as well as the applied fit function strongly influence the obtained variance, whereas fluctuations between two consecutive experiments are less detrimental in a laboratory environment. We demonstrate a variance of σ2 ≈4 × 10-4, lower than required for the detection of single base-pair insertion or deletion in an optofluidic chip.
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Affiliation(s)
- Markus Pollnau
- Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
- Department of Materials and Nano Physics, School of Information and Communication Technology, KTH−Royal Institute of Technology, Electrum 229, Isafjordsgatan 22−24, 16440 Kista, Sweden
| | - Manfred Hammer
- Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
- Theoretical Electrical Engineering, University of Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany
| | - Chaitanya Dongre
- Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
| | - Hugo J. W. M. Hoekstra
- Integrated Optical Microsystems Group, MESA + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
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7
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Anazawa T, Yokoi T, Uchiho Y. Side-Entry Laser-Beam Zigzag Irradiation of Multiple Channels in a Microchip for Simultaneous and Highly Sensitive Detection of Fluorescent Analytes. Anal Chem 2015; 87:8623-8. [DOI: 10.1021/acs.analchem.5b02222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Takashi Anazawa
- Hitachi, Ltd., Research and Development Group, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Takahide Yokoi
- Hitachi, Ltd., Research and Development Group, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Yuichi Uchiho
- Hitachi, Ltd., Research and Development Group, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
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8
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Chung M, Kim D, Herr AE. Polymer sieving matrices in microanalytical electrophoresis. Analyst 2014; 139:5635-54. [DOI: 10.1039/c4an01179a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Abstract
We develop a non-convex non-linear programming problem that determines the minimum run time to resolve different lengths of DNA using a gel-free micelle end-labeled free solution electrophoresis separation method. Our optimization framework allows for efficient determination of the utility of different DNA separation platforms and enables the identification of the optimal operating conditions for these DNA separation devices. The non-linear programming problem requires a model for signal spacing and signal width, which is known for many DNA separation methods. As a case study, we show how our approach is used to determine the optimal run conditions for micelle end-labeled free-solution electrophoresis and examine the trade-offs between a single capillary system and a parallel capillary system. Parallel capillaries are shown to only be beneficial for DNA lengths above 230 bases using a polydisperse micelle end-label otherwise single capillaries produce faster separations.
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10
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Yu MH, Huang YC, Chang PL. Rapid screening of the heterogeneity of DNA methylation by single-strand conformation polymorphism and CE-LIF in the presence of electro-osmotic flow. Electrophoresis 2014; 35:2378-85. [DOI: 10.1002/elps.201300502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/14/2013] [Accepted: 12/16/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Meng-Hsuan Yu
- Department of Chemistry; Tunghai University; Taichung Taiwan
| | - Ya-Chi Huang
- Department of Chemistry; Tunghai University; Taichung Taiwan
| | - Po-Ling Chang
- Department of Chemistry; Tunghai University; Taichung Taiwan
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11
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Hamon M, Hong JW. New tools and new biology: recent miniaturized systems for molecular and cellular biology. Mol Cells 2013; 36:485-506. [PMID: 24305843 PMCID: PMC3887968 DOI: 10.1007/s10059-013-0333-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 01/09/2023] Open
Abstract
Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.
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Affiliation(s)
- Morgan Hamon
- Materials Research and Education Center, Department of Mechanical Engineering, Auburn University, Auburn, AL 36849,
USA
| | - Jong Wook Hong
- Materials Research and Education Center, Department of Mechanical Engineering, Auburn University, Auburn, AL 36849,
USA
- College of Pharmacy, Seoul National University, Seoul 151-741,
Korea
- Department of Bionano Engineering, Hanyang University, Ansan 426-791,
Korea
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12
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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13
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Albrecht JC, Kotani A, Lin JS, Soper SA, Barron AE. Simultaneous detection of 19 K-ras mutations by free-solution conjugate electrophoresis of ligase detection reaction products on glass microchips. Electrophoresis 2013; 34:590-7. [PMID: 23192597 PMCID: PMC4361093 DOI: 10.1002/elps.201200462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 01/08/2023]
Abstract
We demonstrate here the power and flexibility of free-solution conjugate electrophoresis (FSCE) as a method of separating DNA fragments by electrophoresis with no sieving polymer network. Previous work introduced the coupling of FSCE with ligase detection reaction (LDR) to detect point mutations, even at low abundance compared to the wild-type DNA. Here, four large drag-tags are used to achieve free-solution electrophoretic separation of 19 LDR products ranging in size from 42 to 66 nt that correspond to mutations in the K-ras oncogene. LDR-FSCE enabled electrophoretic resolution of these 19 LDR-FSCE products by CE in 13.5 min (E = 310 V/cm) and by microchip electrophoresis in 140 s (E = 350 V/cm). The power of FSCE is demonstrated in the unique characteristic of free-solution separations where the separation resolution is constant no matter the electric field strength. By microchip electrophoresis, the electric field was increased to the maximum of the power supply (E = 700 V/cm), and the 19 LDR-FSCE products were separated in less than 70 s with almost identical resolution to the separation at E = 350 V/cm. These results will aid the goal of screening K-ras mutations on integrated "sample-in/answer-out" devices with amplification, LDR, and detection all on one platform.
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Affiliation(s)
| | - Akira Kotani
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Jennifer S. Lin
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Steven A. Soper
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Annelise E. Barron
- Department of Bioengineering, Stanford University, Stanford, California, USA
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14
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Meagher RJ, Thaitrong N. Microchip electrophoresis of DNA following preconcentration at photopatterned gel membranes. Electrophoresis 2012; 33:1236-46. [DOI: 10.1002/elps.201100675] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Fredlake CP, Hert DG, Niedringhaus TP, Lin JS, Barron AE. Divergent dispersion behavior of ssDNA fragments during microchip electrophoresis in pDMA and LPA entangled polymer networks. Electrophoresis 2012; 33:1411-20. [PMID: 22648809 PMCID: PMC4362670 DOI: 10.1002/elps.201100686] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Resolution of DNA fragments separated by electrophoresis in polymer solutions ("matrices") is determined by both the spacing between peaks and the width of the peaks. Prior research on the development of high-performance separation matrices has been focused primarily on optimizing DNA mobility and matrix selectivity, and gave less attention to peak broadening. Quantitative data are rare for peak broadening in systems in which high electric field strengths are used (>150 V/cm), which is surprising since capillary and microchip-based systems commonly run at these field strengths. Here, we report results for a study of band broadening behavior for ssDNA fragments on a glass microfluidic chip, for electric field strengths up to 320 V/cm. We compare dispersion coefficients obtained in a poly(N,N-dimethylacrylamide) (pDMA) separation matrix that was developed for chip-based DNA sequencing with a commercially available linear polyacrylamide (LPA) matrix commonly used in capillaries. Much larger DNA dispersion coefficients were measured in the LPA matrix as compared to the pDMA matrix, and the dependence of dispersion coefficient on DNA size and electric field strength were found to differ quite starkly in the two matrices. These observations lead us to propose that DNA migration mechanisms differ substantially in our custom pDMA matrix compared to the commercially available LPA matrix. We discuss the implications of these results in terms of developing optimal matrices for specific separation (microchip or capillary) platforms.
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Affiliation(s)
- Christopher P. Fredlake
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Daniel G. Hert
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | | | - Jennifer S. Lin
- Department of Bioengineering, Stanford University, Stanford, CA USA
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16
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Duarte GRM, Coltro WKT, Borba JC, Price CW, Landers JP, Carrilho E. Disposable polyester-toner electrophoresis microchips for DNA analysis. Analyst 2012; 137:2692-8. [PMID: 22545263 DOI: 10.1039/c2an16220b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microchip electrophoresis has become a powerful tool for DNA separation, offering all of the advantages typically associated with miniaturized techniques: high speed, high resolution, ease of automation, and great versatility for both routine and research applications. Various substrate materials have been used to produce microchips for DNA separations, including conventional (glass, silicon, and quartz) and alternative (polymers) platforms. In this study, we perform DNA separation in a simple and low-cost polyester-toner (PeT)-based electrophoresis microchip. PeT devices were fabricated by a direct-printing process using a 600 dpi-resolution laser printer. DNA separations were performed on PeT chip with channels filled with polymer solutions (0.5% m/v hydroxyethylcellulose or hydroxypropylcellulose) at electric fields ranging from 100 to 300 V cm(-1). Separation of DNA fragments between 100 and 1000 bp, with good correlation of the size of DNA fragments and mobility, was achieved in this system. Although the mobility increased with increasing electric field, separations showed the same profile regardless of the electric field. The system provided good separation efficiency (215,000 plates per m for the 500 bp fragment) and the separation was completed in 4 min for 1000 bp fragment ladder. The cost of a given chip is approximately $0.15 and it takes less than 10 minutes to prepare a single device.
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Affiliation(s)
- Gabriela R M Duarte
- Instituto de Química de São Carlos, Universidade de São Paulo, Grupo de Bioanalítica, Microfabricação e Separações, Brazil
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17
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Chen HC, Chang YS, Chen SJ, Chang PL. Determination of the heterogeneity of DNA methylation by combined bisulfite restriction analysis and capillary electrophoresis with laser-induced fluorescence. J Chromatogr A 2012; 1230:123-9. [DOI: 10.1016/j.chroma.2012.01.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 01/13/2012] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
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18
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Haynes RD, Meagher RJ, Barron AE. A chemically synthesized peptoid-based drag-tag enhances free-solution DNA sequencing by capillary electrophoresis. Biopolymers 2012; 96:702-7. [PMID: 22180915 DOI: 10.1002/bip.21627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report a capillary-based DNA sequencing read length of 100 bases in 16 min using end-labeled free-solution conjugate electrophoresis (FSCE) with a monodisperse poly-N-substituted glycine (polypeptoid) as a synthetic drag-tag. FSCE enabled rapid separation of single-stranded (ss) DNA sequencing fragments with single-base resolution without the need for a viscous DNA separation matrix. Protein-based drag-tags previously used for FSCE sequencing, for example, streptavidin, are heterogeneous in molar mass (polydisperse); the resultant band-broadening can make it difficult to obtain the single-base resolution necessary for DNA sequencing. In this study, we synthesized and HPLC-purified a 70mer poly-N-(methoxyethyl)glycine (NMEG) drag-tag with a molar mass of - 11 kDa. The NMEG monomers that comprise this peptoid drag-tag are interesting for bioanalytical applications, because the methoxyethyl side chain's chemical structure is reminiscent of the basic monomer unit of polyethylene glycol, a highly biocompatible commercially available polymer, which, however, is not available in monodisperse preparation at an - 11 kDa molar mass. This is the first report of ssDNA separation and of four-color, base-by-base DNA sequencing by FSCE through the use of a chemically synthesized drag-tag. These results show that high-molar mass, chemically synthesized drag-tags based on the polyNMEG structure, if obtained in monodisperse preparation, would serve as ideal drag-tags and could help FSCE reach the commercially relevant read lengths of 100 bases or more.
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Affiliation(s)
- Russell D Haynes
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, IL 60208, USA
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19
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Cho SW, Kang DK, Choo JB, Demllo AJ, Chang SI. Recent advances in microfluidic technologies for biochemistry and molecular biology. BMB Rep 2011; 44:705-12. [DOI: 10.5483/bmbrep.2011.44.11.705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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20
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Huang J, Zheng Z, Andersson AF, Engstrand L, Ye W. Rapid screening of complex DNA samples by single-molecule amplification and sequencing. PLoS One 2011; 6:e19723. [PMID: 21625543 PMCID: PMC3098247 DOI: 10.1371/journal.pone.0019723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 04/08/2011] [Indexed: 11/19/2022] Open
Abstract
Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample.
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Affiliation(s)
- Jiaqi Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Zongli Zheng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Anders F. Andersson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Swedish Institute for Communicable Infectious Disease Control, Solna, Sweden
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Albrecht JC, Kerby MB, Niedringhaus TP, Lin JS, Wang X, Barron AE. Free-solution electrophoretic separations of DNA-drag-tag conjugates on glass microchips with no polymer network and no loss of resolution at increased electric field strength. Electrophoresis 2011; 32:1201-8. [PMID: 21500207 PMCID: PMC3416026 DOI: 10.1002/elps.201000574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/10/2010] [Accepted: 01/03/2011] [Indexed: 11/08/2022]
Abstract
Here, we demonstrate the potential for high-resolution electrophoretic separations of ssDNA-protein conjugates in borosilicate glass microfluidic chips, with no sieving media and excellent repeatability. Using polynucleotides of two different lengths conjugated to moderately cationic protein polymer drag-tags, we measured separation efficiency as a function of applied electric field. In excellent agreement with prior theoretical predictions of Slater et al., resolution is found to remain constant as applied field is increased up to 700 V/cm, the highest field we were able to apply. This remarkable result illustrates the fundamentally different physical limitations of free-solution conjugate electrophoresis (FSCE)-based DNA separations relative to matrix-based DNA electrophoresis. ssDNA separations in "gels" have always shown rapidly declining resolution as the field strength is increased; this is especially true for ssDNA > 400 bases in length. FSCE's ability to decouple DNA peak resolution from applied electric field suggests the future possibility of ultra-rapid FSCE sequencing on chips. We investigated sources of peak broadening for FSCE separations on borosilicate glass microchips, using six different protein polymer drag-tags. For drag-tags with four or more positive charges, electrostatic and adsorptive interactions with poly(N-hydroxyethylacrylamide)-coated microchannel walls led to appreciable band-broadening, while much sharper peaks were seen for bioconjugates with nearly charge-neutral protein drag-tags.
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Affiliation(s)
| | - Matthew B. Kerby
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Jennifer S. Lin
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Xiaoxiao Wang
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Annelise E. Barron
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
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Albrecht JC, Lin JS, Barron AE. A 265-base DNA sequencing read by capillary electrophoresis with no separation matrix. Anal Chem 2011; 83:509-15. [PMID: 21182303 PMCID: PMC3271724 DOI: 10.1021/ac102188p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrophoretic DNA sequencing without a polymer matrix is currently possible only with the use of some kind of "drag-tag" as a mobility modifier. In free-solution conjugate electrophoresis (FSCE), a drag-tag attached to each DNA fragment breaks linear charge-to-friction scaling, enabling size-based separation in aqueous buffer alone. Here we report a 265-base read for free-solution DNA sequencing by capillary electrophoresis using a random-coil protein drag-tag of unprecedented length and purity. We identified certain methods of protein expression and purification that allow the production of highly monodisperse drag-tags as long as 516 amino acids, which are almost charge neutral (+1 to +6) and yet highly water-soluble. Using a four-color LIF detector, 265 bases could be read in 30 min with a 267-amino acid drag-tag, on par with the average read of current next-gen sequencing systems. New types of multichannel systems that allow much higher throughput electrophoretic sequencing should be much more accessible in the absence of a requirement for viscous separation matrix.
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Affiliation(s)
| | - Jennifer S. Lin
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Annelise E. Barron
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
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Szita N, Polizzi K, Jaccard N, Baganz F. Microfluidic approaches for systems and synthetic biology. Curr Opin Biotechnol 2010; 21:517-23. [PMID: 20829028 DOI: 10.1016/j.copbio.2010.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 08/03/2010] [Accepted: 08/03/2010] [Indexed: 01/04/2023]
Abstract
Microfluidic systems miniaturise biological experimentation leading to reduced sample volume, analysis time and cost. Recent innovations have allowed the application of -omics approaches on the microfluidic scale. It is now possible to perform 1.5 million PCR reactions simultaneously, obtain transcriptomic data from as little as 150 cells (as few as 2 transcripts per gene of interest) and perform mass-spectrometric analyses online. For synthetic biology, unit operations have been developed that allow de novo construction of synthetic systems from oligonucleotide synthesis through to high-throughput, high efficiency electroporation of single cells or encapsulation into abiotic chassis enabling the processing of thousands of synthetic organisms per hour. Future directions include a push towards integrating more processes into a single device and replacing off-chip analyses where possible.
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Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics 2010; 11:469. [PMID: 20701770 PMCID: PMC3091665 DOI: 10.1186/1471-2164-11-469] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology. RESULTS A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp. CONCLUSIONS We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops.
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Affiliation(s)
- Xiaolei Wu
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Chengwei Ren
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
- Beta Seed Inc., Tangent, OR 97389, USA
| | - Trupti Joshi
- Digital Biology Laboratory, Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tri Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Digital Biology Laboratory, Computer Science Department and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
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Arora A, Simone G, Salieb-Beugelaar GB, Kim JT, Manz A. Latest Developments in Micro Total Analysis Systems. Anal Chem 2010; 82:4830-47. [PMID: 20462185 DOI: 10.1021/ac100969k] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Arun Arora
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Giuseppina Simone
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Georgette B. Salieb-Beugelaar
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Jung Tae Kim
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Andreas Manz
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
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Kaji N, Okamoto Y, Tokeshi M, Baba Y. Nanopillar, nanoball, and nanofibers for highly efficient analysis of biomolecules. Chem Soc Rev 2010; 39:948-56. [DOI: 10.1039/b900410f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Oakley JA, Robinson S, Dyer CE, Greenman J, Greenway GM, Haswell SJ. Development of a gel-to-gel electro-kinetic pinched injection method for an integrated micro-fluidic based DNA analyser. Anal Chim Acta 2009; 652:239-44. [DOI: 10.1016/j.aca.2009.07.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 07/23/2009] [Accepted: 07/24/2009] [Indexed: 10/20/2022]
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28
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Liu P, Mathies RA. Integrated microfluidic systems for high-performance genetic analysis. Trends Biotechnol 2009; 27:572-81. [DOI: 10.1016/j.tibtech.2009.07.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/30/2009] [Accepted: 07/02/2009] [Indexed: 01/09/2023]
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Forster RE, Hert DG, Chiesl TN, Fredlake CP, Barron AE. DNA migration mechanism analyses for applications in capillary and microchip electrophoresis. Electrophoresis 2009; 30:2014-24. [PMID: 19582705 DOI: 10.1002/elps.200900264] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In 2009, electrophoretically driven DNA separations in slab gels and capillaries have the sepia tones of an old-fashioned technology in the eyes of many, even while they remain ubiquitously used, fill a unique niche, and arguably have yet to reach their full potential. For comic relief, what is old becomes new again: agarose slab gel separations are used to prepare DNA samples for "next-gen" sequencing platforms (e.g. the Illumina and 454 machines) - dsDNA molecules within a certain size range are "cut out" of a gel and recovered for subsequent "massively parallel" pyrosequencing. In this review, we give a Barron lab perspective on how our comprehension of DNA migration mechanisms in electrophoresis has evolved, since the first reports of DNA separations by CE ( approximately 1989) until now, 20 years later. Fused-silica capillaries and borosilicate glass and plastic microchips quietly offer increasing capacities for fast (and even "ultra-fast"), efficient DNA separations. While the channel-by-channel scaling of both old and new electrophoresis platforms provides key flexibility, it requires each unique DNA sample to be prepared in its own micro or nanovolume. This Achilles' heel of electrophoresis technologies left an opening through which pooled sample, next-gen DNA sequencing technologies rushed. We shall see, over time, whether sharpening understanding of transitions in DNA migration modes in crosslinked gels, nanogel solutions, and uncrosslinked polymer solutions will allow electrophoretic DNA analysis technologies to flower again. Microchannel electrophoresis, after a quiet period of metamorphosis, may emerge sleeker and more powerful, to claim its own important niche applications.
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Affiliation(s)
- Ryan E Forster
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
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31
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Zhang Y, Wang J, Okamoto Y, Tokeshi M, Kaji N, Baba Y. Velocity Gap Theory Developed for Magnifying Resolutions without Changing Separation Mechanisms or Separation Lengths. Anal Chem 2009; 81:2745-50. [DOI: 10.1021/ac802671m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yong Zhang
- Department of Applied Chemistry, Graduate School of Engineering, MEXT Innovative Research Center for Preventive Medical Engineering, Health Technology Research Center, Plasma Nanotechnology Research Center, Nagoya University, Nagoya 464-8603, Japan, National Institute of Advanced Industrial Science and Technology (AIST) Hayashi-cho 2217-14, Takamatsu 761-0395, Japan, and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Jun Wang
- Department of Applied Chemistry, Graduate School of Engineering, MEXT Innovative Research Center for Preventive Medical Engineering, Health Technology Research Center, Plasma Nanotechnology Research Center, Nagoya University, Nagoya 464-8603, Japan, National Institute of Advanced Industrial Science and Technology (AIST) Hayashi-cho 2217-14, Takamatsu 761-0395, Japan, and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Yukihiro Okamoto
- Department of Applied Chemistry, Graduate School of Engineering, MEXT Innovative Research Center for Preventive Medical Engineering, Health Technology Research Center, Plasma Nanotechnology Research Center, Nagoya University, Nagoya 464-8603, Japan, National Institute of Advanced Industrial Science and Technology (AIST) Hayashi-cho 2217-14, Takamatsu 761-0395, Japan, and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Manabu Tokeshi
- Department of Applied Chemistry, Graduate School of Engineering, MEXT Innovative Research Center for Preventive Medical Engineering, Health Technology Research Center, Plasma Nanotechnology Research Center, Nagoya University, Nagoya 464-8603, Japan, National Institute of Advanced Industrial Science and Technology (AIST) Hayashi-cho 2217-14, Takamatsu 761-0395, Japan, and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering, MEXT Innovative Research Center for Preventive Medical Engineering, Health Technology Research Center, Plasma Nanotechnology Research Center, Nagoya University, Nagoya 464-8603, Japan, National Institute of Advanced Industrial Science and Technology (AIST) Hayashi-cho 2217-14, Takamatsu 761-0395, Japan, and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Yoshinobu Baba
- Department of Applied Chemistry, Graduate School of Engineering, MEXT Innovative Research Center for Preventive Medical Engineering, Health Technology Research Center, Plasma Nanotechnology Research Center, Nagoya University, Nagoya 464-8603, Japan, National Institute of Advanced Industrial Science and Technology (AIST) Hayashi-cho 2217-14, Takamatsu 761-0395, Japan, and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
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32
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Stellwagen NC, Stellwagen E. Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A 2009; 1216:1917-29. [PMID: 19100556 PMCID: PMC2643323 DOI: 10.1016/j.chroma.2008.11.090] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/24/2008] [Accepted: 11/27/2008] [Indexed: 11/18/2022]
Abstract
DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.
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Affiliation(s)
- Nancy C Stellwagen
- Department of Biochemistry, University of Iowa, 4403 Bowen Science Building, Iowa City, IA 52242, USA.
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Slater GW, Holm C, Chubynsky MV, de Haan HW, Dubé A, Grass K, Hickey OA, Kingsburry C, Sean D, Shendruk TN, Zhan L. Modeling the separation of macromolecules: A review of current computer simulation methods. Electrophoresis 2009; 30:792-818. [DOI: 10.1002/elps.200800673] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Forster RE, Chiesl TN, Fredlake CP, White CV, Barron AE. Hydrophobically modified polyacrylamide block copolymers for fast, high-resolution DNA sequencing in microfluidic chips. Electrophoresis 2009; 29:4669-76. [PMID: 19053064 DOI: 10.1002/elps.200800353] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
By using a microfluidic electrophoresis platform to perform DNA sequencing, genomic information can be obtained more quickly and affordably than the currently employed capillary array electrophoresis instruments. Previous research in our group has shown that physically cross-linked, hydrophobically modified polyacrylamide matrices separate dsDNA more effectively than linear polyacrylamide (LPA) solutions. Expanding upon this work, we have synthesized a series of LPA-co-dihexylacrylamide block copolymers specifically designed to electrophoretically sequence ssDNA quickly and efficiently on a microfluidic device. By incorporating very small amounts of N,N-dihexylacrylamide, a hydrophobic monomer, these copolymer solutions achieved up to approximately 10% increases in average DNA sequencing read length over LPA homopolymer solutions of matched molar mass. Additionally, the inclusion of the small amount of hydrophobe does not significantly increase the polymer solution viscosities, relative to LPA solutions, so that channel loading times between the copolymers and the homopolymers are similar. The resulting polymer solutions are capable of providing enhanced sequencing separations in a short period of time without compromising the ability to rapidly load and unload the matrix from a microfluidic device.
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Affiliation(s)
- Ryan E Forster
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
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Root BE, Hammock ML, Barron AE. Thermoresponsive N-alkoxyalkylacrylamide polymers as a sieving matrix for high-resolution DNA separations on a microfluidic chip. Electrophoresis 2009; 29:4677-83. [PMID: 19053065 DOI: 10.1002/elps.200800354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In recent years, there has been an increasing demand for a wide range of DNA separations that require the development of materials to meet the needs of high resolution and high throughput. Here, we demonstrate the use of thermoresponsive N-alkoxyalkylacrylamide polymers as a sieving matrix for DNA separations on a microfluidic chip. The viscosities of the N-alkoxyalkylacrylamide polymers are more than an order of magnitude lower than that of a linear polyacrylamide (LPA) of corresponding molecular weight, allowing rapid loading of the microchip. At 25 degrees C, N-alkoxyalkylacrylamide polymers can provide improved DNA separations compared with LPA in terms of reduced separation time and increased separation efficiency, particularly for the larger DNA fragments. The improved separation efficiency in N-alkoxyalkylacrylamide polymers is attributed to the peak widths increasing only slightly with DNA fragment size, while the peak widths increase appreciably above 150 bp using an LPA matrix. Upon elevating the temperature to 50 degrees C, the increase in viscosity of the N-alkoxyalkylacrylamide solutions is dependent upon their overall degree of hydrophobicity. The most hydrophobic polymers exhibit a lower critical solution temperature below 50 degrees C, undergoing a coil-to-globule transition followed by chain aggregation. DNA separation efficiency at 50 degrees C therefore decreases significantly with increasing hydrophobic character of the polymers, and no separations were possible with solutions with a lower critical solution temperature below 50 degrees C. The work reported here demonstrates the potential for this class of polymers to be used for applications such as PCR product and RFLP sizing, and provides insight into the effect of polymer hydrophobicity on DNA separations.
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Affiliation(s)
- Brian E Root
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
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Kumagai H, Utsunomiya S, Nakamura S, Yamamoto R, Harada A, Kaji T, Hazama M, Ohashi T, Inami A, Ikegami T, Miyamoto K, Endo N, Yoshimi K, Toyoda A, Hattori M, Sakaki Y. Large-scale microfabricated channel plates for high-throughput, fully automated DNA sequencing. Electrophoresis 2009; 29:4723-32. [PMID: 19016243 DOI: 10.1002/elps.200800301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have described a new DNA sequencing platform based on the Sanger chemistry, in which the large-scale microfabricated channel plates and electrophoretic system result in higher-throughput DNA sequencing. Three hundred and eighty-four channels are arranged in a fan-like shape on a 25x47 cm glass plate, on which 384 oval sample holes are connected to each channel coupled to the opposite anode access holes. Two microfabricated plates are set on the sequencing apparatus, in which sequencing electrophoresis is conducted on one plate and the preparation process is on another plate. Each sample hole is loaded with 2.3 microL volume of sample and injected into separation channels electrokinetically. High-quality sequencing data were acquired using the pUC18 template, achieving an average read-length of 1001 bases with 99% accuracy and a throughput of 5 Mbases per day per instrument. To assess the performance in actual sequencing field, the bacterial artificial chromosome shotgun library of the Pseudorca crassidens genome was sequenced, using 1/80 of the quantity of Sanger reagent (0.1 microL). We believe that this is the first demonstration of the useful performance of DNA sequencing using monolithic microfabricated devices with walk-away operation.
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Hert DG, Fredlake CP, Barron AE. DNA sequencing by microchip electrophoresis using mixtures of high- and low-molar mass poly(N,N-dimethylacrylamide) matrices. Electrophoresis 2008; 29:4663-8. [PMID: 19053157 PMCID: PMC3064962 DOI: 10.1002/elps.200800389] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Previous studies have reported that mixed molar mass polymer matrices show enhanced DNA sequencing fragment separation compared with matrices formulated from a single average molar mass. Here, we describe a systematic study to investigate the effects of varying the amounts of two different average molar mass polymers on the DNA sequencing ability of poly(N,N-dimethylacrylamide) (pDMA) sequencing matrices in microfluidic chips. Two polydisperse samples of pDMA, with weight-average molar masses of 3.5 MDa and 770 kDa, were mixed at various fractional concentrations while maintaining the overall polymer concentration at 5% w/v. We show that although the separation of short DNA fragments depends strongly on the overall solution concentration of the polymer, inclusion of the high-molar mass polymer is essential to achieve read lengths of interest (>400 bases) for many sequencing applications. Our results also show that one of the blended matrices, comprised of 3% 3.5 MDa pDMA and 2% 770 kDa pDMA, yields similar sequencing read lengths (>520 bases on average) to the high-molar mass matrix alone, while also providing a fivefold reduction in zero-shear viscosity. These results indicate that the long read lengths achieved in a viscous, high-molar mass polymer matrix are also possible to achieve in a tuned, blended matrix of high- and low-molar mass polymers with a much lower overall solution viscosity.
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Affiliation(s)
- Daniel G. Hert
- Department of Chemical and Biological Engineering, Northwestern University, Evanston IL 60208
| | - Christopher P. Fredlake
- Department of Chemical and Biological Engineering, Northwestern University, Evanston IL 60208
| | - Annelise E. Barron
- Department of Chemical and Biological Engineering, Northwestern University, Evanston IL 60208
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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Lo RC, Ugaz VM. Microchip DNA electrophoresis with automated whole-gel scanning detection. LAB ON A CHIP 2008; 8:2135-45. [PMID: 19023477 DOI: 10.1039/b811033f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Gel electrophoresis continues to play an important role in miniaturized bioanalytical systems, both as a stand alone technique and as a key component of integrated lab-on-a-chip diagnostics. Most implementations of microchip electrophoresis employ finish-line detection methods whereby fluorescently labeled analytes are observed as they migrate past a fixed detection point near the end of the separation channel. But tradeoffs may exist between the simultaneous goals of maximizing resolution (normally achieved by using longer separation channels) and maximizing the size range of analytes that can be studied (where shorter separation distances reduce the time required for the slowest analytes to reach the detector). Here we show how the miniaturized format can offer new opportunities to employ alternative detection schemes that can help address these issues by introducing an automated whole-gel scanning detection system that enables the progress of microchip-based gel electrophoresis of DNA to be continuously monitored along an entire microchannel. This permits flexibility to selectively observe smaller faster moving fragments during the early stages of the separation before they have experienced significant diffusive broadening, while allowing the larger slower moving fragments to be observed later in the run when they can be better resolved but without the need for them to travel the entire length of the separation channel. Whole-gel scanning also provides a continuous and detailed picture of the electrophoresis process as it unfolds, allowing fundamental physical parameters associated with DNA migration phenomena (e.g., mobility, diffusive broadening) to be rapidly and accurately measured in a single experiment. These capabilities are challenging to implement using finish-line methods, and make it possible to envision a platform capable of enabling separation performance to be rapidly screened in a wide range of gel matrix materials and operating conditions, even allowing separation and matrix characterization steps to be performed simultaneously in a single self-calibrating experiment.
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Affiliation(s)
- Roger C Lo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA.
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Hert DG, Fredlake CP, Barron AE. Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 2008; 29:4618-26. [DOI: 10.1002/elps.200800456] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Fredlake CP, Hert DG, Root BE, Barron AE. Polymer systems designed specifically for DNA sequencing by microchip electrophoresis: a comparison with commercially available materials. Electrophoresis 2008; 29:4652-62. [PMID: 19053156 PMCID: PMC3517007 DOI: 10.1002/elps.200800352] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Electrophoresis-based DNA sequencing is the only proven technology for the de novo sequencing of large and complex genomes. Miniaturization of capillary array electrophoresis (CAE) instruments can increase sequencing throughput and decrease cost while maintaining the high quality and long read lengths that has made CAE so successful for de novo sequencing. The limited availability of high-performance polymer matrices and wall coatings designed specifically for microchip-sequencing platforms continues to be a major barrier to the successful development of a commercial microchip-sequencing instrument. It has been generally assumed that the matrices and wall coatings that have been developed for use in commercial CAE instruments will be able to be implemented directly into microchip devices with little to no change in sequencing performance. Here, we show that sequencing matrices developed specifically for microchip electrophoresis systems can deliver read lengths that are 150-300 bases longer on chip than some of the most widely used polymer-sequencing matrices available commercially. Additionally, we show that the coating ability of commercial matrices is much less effective in the borosilicate chips used in this study. These results lead to the conclusion that new materials must be developed to make high-performance microfabricated DNA-sequencing instruments a reality.
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Affiliation(s)
- Christopher P. Fredlake
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Daniel G. Hert
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Brian E. Root
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL USA
| | - Annelise E. Barron
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
- Department of Bioengineering, Stanford University, Stanford, CA USA
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Gupta PK. Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 2008; 26:602-11. [DOI: 10.1016/j.tibtech.2008.07.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 07/05/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
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Lamoril J, Ameziane N, Deybach JC, Bouizegarène P, Bogard M. Les techniques de séquençage de l’ADN : une révolution en marche. Première partie. IMMUNO-ANALYSE & BIOLOGIE SPÉCIALISÉE 2008. [PMCID: PMC7147846 DOI: 10.1016/j.immbio.2008.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- J. Lamoril
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
- Auteur correspondant.
| | - N. Ameziane
- Laboratoire de biologie polyvalente, centre hospitalier de Sens, 89100 Sens, France
| | - J.-C. Deybach
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
| | - P. Bouizegarène
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
| | - M. Bogard
- Laboratoire de biochimie et biologie moléculaire, centre hospitalier de Meaux, 77100 Meaux, France
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Yeung SHI, Seo TS, Crouse CA, Greenspoon SA, Chiesl TN, Ban JD, Mathies RA. Fluorescence energy transfer-labeled primers for high-performance forensic DNA profiling. Electrophoresis 2008; 29:2251-9. [DOI: 10.1002/elps.200700772] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Liu P, Yeung SHI, Crenshaw KA, Crouse CA, Scherer JR, Mathies RA. Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer. Forensic Sci Int Genet 2008; 2:301-9. [PMID: 19083840 DOI: 10.1016/j.fsigen.2008.03.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/10/2008] [Accepted: 03/31/2008] [Indexed: 11/19/2022]
Abstract
An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2h and 30min with <or=0.8bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful "mock" CODIS hit was generated on the suspect's sample within 6h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.
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Affiliation(s)
- Peng Liu
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, CA 94720, USA
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Kumaresan P, Yang CJ, Cronier SA, Blazej RG, Mathies RA. High-Throughput Single Copy DNA Amplification and Cell Analysis in Engineered Nanoliter Droplets. Anal Chem 2008; 80:3522-9. [DOI: 10.1021/ac800327d] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Palani Kumaresan
- Department of Mechanical Engineering, Department of Chemistry, and UCSF/UC Berkeley Joint Bioengineering Graduate Group, University of California, Berkeley, California 94720
| | - Chaoyong James Yang
- Department of Mechanical Engineering, Department of Chemistry, and UCSF/UC Berkeley Joint Bioengineering Graduate Group, University of California, Berkeley, California 94720
| | - Samantha A. Cronier
- Department of Mechanical Engineering, Department of Chemistry, and UCSF/UC Berkeley Joint Bioengineering Graduate Group, University of California, Berkeley, California 94720
| | - Robert G. Blazej
- Department of Mechanical Engineering, Department of Chemistry, and UCSF/UC Berkeley Joint Bioengineering Graduate Group, University of California, Berkeley, California 94720
| | - Richard A. Mathies
- Department of Mechanical Engineering, Department of Chemistry, and UCSF/UC Berkeley Joint Bioengineering Graduate Group, University of California, Berkeley, California 94720
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Beachcombing for bioscience. NATURE MATERIALS 2008; 7:165. [PMID: 18297117 DOI: 10.1038/nmat2138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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