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Thormann W, Mosher RA. Dynamic computer simulations of electrophoresis: 2010-2020. Electrophoresis 2021; 43:10-36. [PMID: 34287996 PMCID: PMC9292373 DOI: 10.1002/elps.202100191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 02/05/2023]
Abstract
The transport of components in liquid media under the influence of an applied electric field can be described with the continuity equation. It represents a nonlinear conservation law that is based upon the balance laws of continuous transport processes and can be solved in time and space numerically. This procedure is referred to as dynamic computer simulation. Since its inception four decades ago, the state of dynamic computer simulation software and its use has progressed significantly. Dynamic models are the most versatile tools to explore the fundamentals of electrokinetic separations and provide insights into the behavior of buffer systems and sample components of all electrophoretic separation methods, including moving boundary electrophoresis, CZE, CGE, ITP, IEF, EKC, ACE, and CEC. This article is a continuation of previous reviews (Electrophoresis 2009, 30, S16–S26 and Electrophoresis 2010, 31, 726–754) and summarizes the progress and achievements made during the 2010 to 2020 time period in which some of the existing dynamic simulators were extended and new simulation packages were developed. This review presents the basics and extensions of the three most used one‐dimensional simulators, provides a survey of new one‐dimensional simulators, outlines an overview of multi‐dimensional models, and mentions models that were briefly reported in the literature. A comprehensive discussion of simulation applications and achievements of the 2010 to 2020 time period is also included.
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Affiliation(s)
- Wolfgang Thormann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Thormann W, Mosher RA. Instabilities of the pH gradient in carrier ampholyte-based isoelectric focusing: Elucidation of the contributing electrokinetic processes by computer simulation. Electrophoresis 2020; 42:814-833. [PMID: 33184847 DOI: 10.1002/elps.202000269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/22/2020] [Accepted: 11/05/2020] [Indexed: 11/05/2022]
Abstract
Electrokinetic processes that lead to pH gradient instabilities in carrier ampholyte-based IEF are reviewed. In addition to electroosmosis, there are four of electrophoretic nature, namely (i) the stabilizing phase with the plateau phenomenon, (ii) the gradual isotachophoretic loss of carrier ampholytes at the two column ends in presence of electrode solutions, (iii) the inequality of the mobilities of positively and negatively charged species of ampholytes, and (iv) the continuous penetration of carbonate from the catholyte into the focusing column. The impact of these factors to cathodic and anodic drifts was analyzed by simulation of carrier ampholyte-based focusing in closed and open columns. Focusing under realistic conditions within a 5 cm long capillary in which three amphoteric low molecular mass dyes were focused in a pH 3-10 gradient formed by 140 carrier ampholytes was investigated. In open columns, electroosmosis displaces the entire gradient toward the cathode or anode whereas the electrophoretic processes act bidirectionally with a transition around pH 4 (drifts for pI > 4 and pI < 4 typically toward the cathode and anode, respectively). The data illustrate that focused zones of carrier ampholytes have an electrophoretic flux and that dynamic simulation can be effectively used to assess the magnitude of each of the electrokinetic destabilizing factors and the resulting drift for a combination of these effects. Predicted drifts of focused marker dyes are compared to those observed experimentally in a setup with coated capillary and whole column optical imaging.
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Affiliation(s)
- Wolfgang Thormann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Abstract
Electrophoretic methodologies for qualitative and preparative purposes are commonly used in biological research and have been well established as an integral analytical tool for a long time in most research laboratories. Listed here are some of the more specialized innovations that have been developed in recent times for special purposes of study. These include micropreparative isoelectric focusing in liquid suspension, accelerated protease digestion by SDS-PAGE, two-dimensional SDS-PAGE for membrane protein resolution, carbon nanotube-modified page for resolution of complement C3, electrophoretic resolution of ultra-acidic proteomes in acidic media, and two-dimensional immunoelectrophoresis of pre-beta/alpha lipoprotein A-I in agarose. All these methods are briefly reviewed in this chapter.
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Affiliation(s)
- James D Fesmire
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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Mikkonen S, Jacksén J, Roeraade J, Thormann W, Emmer Å. Microfluidic Isoelectric Focusing of Amyloid Beta Peptides Followed by Micropillar-Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry. Anal Chem 2016; 88:10044-10051. [PMID: 27619937 DOI: 10.1021/acs.analchem.6b02324] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A novel method for preconcentration and purification of the Alzheimer's disease related amyloid beta (Aβ) peptides by isoelectric focusing (IEF) in 75 nL microchannels combined with their analysis by micropillar-matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) is presented. A semiopen chip-based setup, consisting of open microchannels covered by a lid of a liquid fluorocarbon, was used. IEF was performed in a mixture of four small and chemically well-defined amphoteric carriers, glutamic acid, aspartyl-histidine (Asp-His), cycloserine (cSer), and arginine, which provided a stepwise pH gradient tailored for focusing of the C-terminal Aβ peptides with a pI of 5.3 in the boundary between cSer and Asp-His. Information about the focusing dynamics and location of the foci of Aβ peptides and other compounds was obtained using computer simulation and by performing MALDI-MS analysis directly from the open microchannel. With the established configuration, detection was performed by direct sampling of a nanoliter volume containing the focused Aβ peptides from the microchannel, followed by deposition of this volume onto a chip with micropillar MALDI targets. In addition to purification, IEF preconcentration provides at least a 10-fold increase of the MALDI-MS-signal. After immunoprecipitation and concentration of the eluate in the microchannel, IEF-micropillar-MALDI-MS is demonstrated to be a suitable platform for detection of Aβ peptides in human cerebrospinal fluid as well as in blood plasma.
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Affiliation(s)
- Saara Mikkonen
- Department of Chemistry, Division of Applied Physical Chemistry-Analytical Chemistry, KTH Royal Institute of Technology , 10044 Stockholm, Sweden
| | - Johan Jacksén
- Department of Chemistry, Division of Applied Physical Chemistry-Analytical Chemistry, KTH Royal Institute of Technology , 10044 Stockholm, Sweden
| | - Johan Roeraade
- Department of Chemistry, Division of Applied Physical Chemistry-Analytical Chemistry, KTH Royal Institute of Technology , 10044 Stockholm, Sweden
| | - Wolfgang Thormann
- Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern , 3008 Bern, Switzerland
| | - Åsa Emmer
- Department of Chemistry, Division of Applied Physical Chemistry-Analytical Chemistry, KTH Royal Institute of Technology , 10044 Stockholm, Sweden
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Hao F, Li J, Zhai R, Jiao F, Zhang Y, Qian X. A novel microscale preparative gel electrophoresis system. Analyst 2016; 141:4953-60. [DOI: 10.1039/c6an00780e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel microscale preparative gel electrophoresis system is designed and manufactured for protein separation and preparation.
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Affiliation(s)
- Feiran Hao
- State Key Laboratory of Proteomics
- National Center for Protein Science
- Beijing Institute of Radiation Medicine
- Beijing 102206
- China
| | - Jiabin Li
- State Key Laboratory of Proteomics
- National Center for Protein Science
- Beijing Institute of Radiation Medicine
- Beijing 102206
- China
| | - Rui Zhai
- State Key Laboratory of Proteomics
- National Center for Protein Science
- Beijing Institute of Radiation Medicine
- Beijing 102206
- China
| | - Fenglong Jiao
- State Key Laboratory of Proteomics
- National Center for Protein Science
- Beijing Institute of Radiation Medicine
- Beijing 102206
- China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics
- National Center for Protein Science
- Beijing Institute of Radiation Medicine
- Beijing 102206
- China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics
- National Center for Protein Science
- Beijing Institute of Radiation Medicine
- Beijing 102206
- China
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Mikkonen S, Thormann W, Emmer Å. Computer simulations of sample preconcentration in carrier-free systems and isoelectric focusing in microchannels using simple ampholytes. Electrophoresis 2015; 36:2386-95. [PMID: 26036978 DOI: 10.1002/elps.201500120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/27/2015] [Accepted: 05/12/2015] [Indexed: 01/05/2023]
Abstract
In this work, electrophoretic preconcentration of protein and peptide samples in microchannels was studied theoretically using the 1D dynamic simulator GENTRANS, and experimentally combined with MS. In all configurations studied, the sample was uniformly distributed throughout the channel before power application, and driving electrodes were used as microchannel ends. In the first part, previously obtained experimental results from carrier-free systems are compared to simulation results, and the effects of atmospheric carbon dioxide and impurities in the sample solution are examined. Simulation provided insight into the dynamics of the transport of all components under the applied electric field and revealed the formation of a pure water zone in the channel center. In the second part, the use of an IEF procedure with simple well defined amphoteric carrier components, i.e. amino acids, for concentration and fractionation of peptides was investigated. By performing simulations a qualitative description of the analyte behavior in this system was obtained. Neurotensin and [Glu1]-Fibrinopeptide B were separated by IEF in microchannels featuring a liquid lid for simple sample handling and placement of the driving electrodes. Component distributions in the channel were detected using MALDI- and nano-ESI-MS and data were in agreement with those obtained by simulation. Dynamic simulations are demonstrated to represent an effective tool to investigate the electrophoretic behavior of all components in the microchannel.
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Affiliation(s)
- Saara Mikkonen
- Department of Chemistry, Analytical Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Wolfgang Thormann
- Clinical Pharmacology Laboratory, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Åsa Emmer
- Department of Chemistry, Analytical Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
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Zhao Y, Pereira F, deMello AJ, Morgan H, Niu X. Droplet-based in situ compartmentalization of chemically separated components after isoelectric focusing in a Slipchip. LAB ON A CHIP 2014; 14:555-561. [PMID: 24292781 DOI: 10.1039/c3lc51067k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Isoelectric focusing (IEF) is a powerful and widely used technique for protein separation and purification. There are many embodiments of microscale IEF that use capillary or microfluidic chips for the analysis of small sample volumes. Nevertheless, collecting the separated sample volumes without causing remixing remains a challenge. Herein, we describe a microfluidic Slipchip device that is able to efficiently compartmentalize focused analyte bands in situ into microdroplets. The device contains a microfluidic "zig-zag" separation channel that is composed of a sequence of wells formed in the two halves of the Slipchip. The analytes are focused in the channel and then compartmentalised into droplets by slipping the chip. Importantly, sample droplets can be analysed on chip or collected for subsequent analysis using electrophoresis or mass spectrometry for example. To demonstrate this approach, we perform IEF separation using standard markers and protein samples, with on-chip post-processing. Compared to alternative approaches for sample collection, the method avoids remixing, is scalable and is easily hyphenated with the other analytical methods.
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Affiliation(s)
- Yan Zhao
- Faculty of Physical Sciences and Engineering, and Institute for Life Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
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Ebara M, Hoffman JM, Hoffman AS, Stayton PS, Lai JJ. A photoinduced nanoparticle separation in microchannels via pH-sensitive surface traps. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:5388-93. [PMID: 23581256 PMCID: PMC3742372 DOI: 10.1021/la400347r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A microfluidic surface trap was developed for capturing pH-sensitive nanoparticles via a photoinitiated proton-releasing reaction of o-nitrobenzaldehyde (o-NBA) that reduces the solution pH in microchannels. The surface trap and nanoparticles were both modified with a pH-responsive polymer-poly(N-isorpopylacylamide-co-propylacrylic acid), P(NIPAAm-co-PAA). The o-NBA-coated microchannel walls demonstrated rapid proton release upon UV light irradiation, allowing the buffered solution pH in the microchannel to decrease from 7.4 to 4.5 in 60 s. The low solution pH switched the polymer-modified surfaces to be more hydrophobic, which enabled the capture of the pH-sensitive nanobeads onto the trap. When a photomask was utilized to limit the UV irradiation to a specific channel region, we were able to restrict the particle separation to only the exposed region. Via control of the UV irradiation, this technique enables not only prompt pH changes within the channel but also the capture of target molecules at specific channel locations.
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Affiliation(s)
- Mitsuhiro Ebara
- Department of Bioengineering, Box 355061, University of Washington, Seattle, WA, 98195, USA
- Biomaterials Unit, International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, JAPAN
| | - John M. Hoffman
- Department of Bioengineering, Box 355061, University of Washington, Seattle, WA, 98195, USA
| | - Allan S. Hoffman
- Department of Bioengineering, Box 355061, University of Washington, Seattle, WA, 98195, USA
| | - Patrick S. Stayton
- Department of Bioengineering, Box 355061, University of Washington, Seattle, WA, 98195, USA
| | - James J. Lai
- Department of Bioengineering, Box 355061, University of Washington, Seattle, WA, 98195, USA
- To whom correspondence should be addressed. ; Fax: +1 (206) 616-3928; Tel: +1 (206) 221-5168
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Abstract
The use of electrophoretic methodologies for use in qualitative and preparative purposes are commonly used in biological research and have been well established as an integral analytical tool for a long time in most research laboratories. Listed here are some of the more specialized innovations that have been developed in recent times for special purposes of study. These include micropreparative isoelectric focusing in liquid suspension, accelerated protease digestion by SDS-PAGE, two-dimensional SDS-PAGE for membrane protein resolution, carbon nanotube-modified page for resolution of complement C3, electrophoretic resolution of ultra-acidic proteomes in acidic media, and two-dimensional immunoelectrophoresis of pre-beta/alpha lipoprotein A-I in agarose. All these methods are briefly reviewed in this chapter.
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Affiliation(s)
- James D Fesmire
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
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Gubala V, Harris LF, Ricco AJ, Tan MX, Williams DE. Point of Care Diagnostics: Status and Future. Anal Chem 2011; 84:487-515. [DOI: 10.1021/ac2030199] [Citation(s) in RCA: 832] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vladimir Gubala
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Leanne F. Harris
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Antonio J. Ricco
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Ming X. Tan
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - David E. Williams
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
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