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Gumuscu B, Bomer JG, de Boer HL, van den Berg A, Eijkel JCT. Exploiting biased reptation for continuous flow preparative DNA fractionation in a versatile microfluidic platform. MICROSYSTEMS & NANOENGINEERING 2017; 3:17001. [PMID: 31057856 PMCID: PMC6444976 DOI: 10.1038/micronano.2017.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 12/02/2016] [Accepted: 12/12/2016] [Indexed: 06/07/2023]
Abstract
A new approach is presented for preparative, continuous flow fractionation of sub-10-kbp DNA fragments, which exploits the variation in the field-dependent mobility of the DNA molecules based on their length. Orthogonally pulsed electric fields of significantly different magnitudes are applied to a microchip filled with a sieving matrix of 1.2% agarose gel. Using this method, we demonstrate a high-resolution separation of 0.5, 1, 2, 5, and 10 kbp DNA fragments within 2 min. During the separation, DNA fragments are also purified from other ionic species. Preparative fractionation of sub-10-kbp DNA molecules plays an important role in second-generation sequencing. The presented device performs rapid high-resolution fractionation and it can be reliably manufactured with simple microfabrication procedures.
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Affiliation(s)
- Burcu Gumuscu
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Johan G. Bomer
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Hans L. de Boer
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Albert van den Berg
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Jan C. T. Eijkel
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
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Sikorsky AA, Fourkas JT, Ross D. Gradient Elution Moving Boundary Electrophoresis with Field-Amplified Continuous Sample Injection. Anal Chem 2014; 86:3625-32. [DOI: 10.1021/ac500242a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alison A. Sikorsky
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Material
Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20878, United States
| | - John T. Fourkas
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Institute for Physical
Science and Technology, Maryland NanoCenter, and Center for Nanophysics
and Advanced Materials, University of Maryland, College Park, Maryland 20742, United States
| | - David Ross
- Material
Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20878, United States
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Terranova GR, Mártin HO, Aldao CM. Separation of long linear polymers in gel electrophoresis with alternating electric fields: a theoretical study using the necklace model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061801. [PMID: 23005118 DOI: 10.1103/physreve.85.061801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Indexed: 06/01/2023]
Abstract
The necklace model, which mimics the reptation of a chain of N beads in a square lattice, is used to study the drift velocity of charged linear polymers in gels under an applied electric field that periodically changes its direction. The characteristics of the model allow us to determine the effects of the alternating electric field on the chains' dynamics. We explain why chains of different N can be made to move in opposite directions with a nonuniform electric field with certain values of intensity and frequency. The key point is that, when alternating electric fields are applied, longer chains spend more time out of the steady-state regime than lower chains. Numerical results are obtained by means of Monte Carlo simulations and they are qualitatively in agreement with experiments of DNA migration in gel electrophoresis.
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Affiliation(s)
- G R Terranova
- Instituto de Investigaciones Físicas de Mar del Plata (IFIMAR), Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata-CONICET Deán Funes 3350, B7602AYL Mar del Plata, Argentina
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Das S, Chakraborty S. Transport and separation of charged macromolecules under nonlinear electromigration in nanochannels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:7704-7710. [PMID: 18620440 DOI: 10.1021/la703892q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work, we theoretically investigate the implications of nonlinear electrophoretic effects on the transport and size-based separation of charged macromolecules in nanoscale confinements. By employing a regular perturbation analysis, we address certain nontrivial features of interconnection among wall-induced transverse migrative fluxes, electrophoretic and electroosmotic transport, confinement-induced hindered diffusive effects, and hydrodynamic interactions in detail. We demonstrate that there occurs an optimal regime of influence of the nonlinear electrophoretic effects, within which high values of separation resolution may be achieved. This size-based optimal regime, however, can be effectively exploited only for nanochannel flows, as attributed to the strong electric double layer interactions prevalent within the same.
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Affiliation(s)
- Siddhartha Das
- Department of Mechanical Engineering, IIT Kharagpur-721302, India
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Tsai H, Low TY, Freeby S, Paulus A, Ramnarayanan K, Cheng CPP, Leung HCE. Increase in local protein concentration by field-inversion gel electrophoresis. Proteome Sci 2007; 5:18. [PMID: 17897441 PMCID: PMC2211458 DOI: 10.1186/1477-5956-5-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Accepted: 09/26/2007] [Indexed: 11/20/2022] Open
Abstract
Background Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE). Results Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE) in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE) showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS), which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. Conclusion The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein separation tool.
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Affiliation(s)
- Henghang Tsai
- Medical Proteomics and Bioanalysis Section, Genome Institute of Singapore, Singapore
| | - Teck Yew Low
- Medical Proteomics and Bioanalysis Section, Genome Institute of Singapore, Singapore
| | | | | | - Kalpana Ramnarayanan
- Medical Proteomics and Bioanalysis Section, Genome Institute of Singapore, Singapore
| | - Chung-pui Paul Cheng
- Medical Proteomics and Bioanalysis Section, Genome Institute of Singapore, Singapore
| | - Hon-chiu Eastwood Leung
- Department of Molecular and Cellular Biology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, USA
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Sideris D. Focusing of macromolecules using equilibrium between centrifugal and electric force. IET Nanobiotechnol 2007; 1:58-61. [PMID: 17672806 DOI: 10.1049/iet-nbt:20060011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A focusing separation model for macromolecules has been theoretically investigated. The method involves an ultracentrifugation device, which however, deploys an electric field gradient oriented longitudinally along the radial direction. When a macromolecular sample solution is centrifuged, the molecules which have different density to the surrounding solvent and a non-zero electric charge, experience a combination of centrifugal and electric forces. This forces the molecules to move to the equilibrium positions along the radius of the rotor, which are characterised by the charge over mass ratio of the molecules. Therefore a molecular sample will be separated into its constituents and bands will form, akin to electrophoresis. The bands are, however, focused at their equilibrium position. An example configuration has been examined whereby four proteins with masses between 20 and 100 kDa can be separated within a radial distance of 20 cm, for a rotor spinning at approximately 130,000 rpm and with a varying electric field between 0 and 100 V/cm.
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Affiliation(s)
- D Sideris
- Institute of Biomedical Engineering, Imperial College London, London, UK.
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Marziali A, Pel J, Bizzotto D, Whitehead LA. Novel electrophoresis mechanism based on synchronous alternating drag perturbation. Electrophoresis 2005; 26:82-90. [PMID: 15624147 DOI: 10.1002/elps.200406140] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We present a novel means of transporting molecules in solution by applying a zero-time-average alternating motive force to the molecules, and perturbing the molecular drag coefficient synchronously with the applied force, thus causing a net drift in a direction determined by the phase of the alternating drag perturbation relative to the alternating force. We apply an electrophoretic form of the method to transport and concentrate DNA in a gel, such that all molecules migrate on average away from the nearest electrode and toward a central region. Since an electrode does not occupy this central region, this method presents the possibility of transporting and focusing DNA and other charged molecules in regions free from electrodes and the associated electrochemistry.
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Affiliation(s)
- Andre Marziali
- Department of Physicsand Astronomy, University of British Columbia, Vancouver, BC, Canada.
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Petsev DN, Lopez GP, Ivory CF, Sibbett SS. Microchannel protein separation by electric field gradient focusing. LAB ON A CHIP 2005; 5:587-97. [PMID: 15915250 DOI: 10.1039/b501538c] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A microchannel device is presented which separates and focuses charged proteins based on electric field gradient focusing. Separation is achieved by setting a constant electroosmotic flow velocity against step changes in electrophoretic velocity. Where these two velocities are balanced for a given analyte, the analyte focuses at that point because it is driven to it from all points within the channel. We demonstrate the separation and focusing of a binary mixture of bovine serum albumin and phycoerythrin. The device is constructed of intersecting microchannels in poly(dimethylsiloxane)(PDMS) inlaid with hollow dialysis fibers. The device uses no exotic chemicals such as antibodies or synthetic ampholytes, but operates instead by purely physical means involving the independent manipulation of electrophoretic and electroosmotic velocities. One important difference between this apparatus and most other devices designed for field-gradient focusing is the injection of current at discrete intersections in the channel rather than continuously along the length of a membrane-bound separation channel.
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Affiliation(s)
- Dimiter N Petsev
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque 87131, USA
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Ying L, White SS, Bruckbauer A, Meadows L, Korchev YE, Klenerman D. Frequency and voltage dependence of the dielectrophoretic trapping of short lengths of DNA and dCTP in a nanopipette. Biophys J 2004; 86:1018-27. [PMID: 14747337 PMCID: PMC1303895 DOI: 10.1016/s0006-3495(04)74177-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The study of the properties of DNA under high electric fields is of both fundamental and practical interest. We have exploited the high electric fields produced locally in the tip of a nanopipette to probe the motion of double- and single-stranded 40-mer DNA, a 1-kb single-stranded DNA, and a single-nucleotide triphosphate (dCTP) just inside and outside the pipette tip at different frequencies and amplitudes of applied voltages. We used dual laser excitation and dual color detection to simultaneously follow two fluorophore-labeled DNA sequences with millisecond time resolution, significantly faster than studies to date. A strong trapping effect was observed during the negative half cycle for all DNA samples and also the dCTP. This effect was maximum below 1 Hz and decreased with higher frequency. We assign this trapping to strong dielectrophoresis due to the high electric field and electric field gradient in the pipette tip. Dielectrophoresis in electrodeless tapered nanostructures has potential applications for controlled mixing and manipulation of short lengths of DNA and other biomolecules, opening new possibilities in miniaturized biological analysis.
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Affiliation(s)
- Liming Ying
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
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