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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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Salieb-Beugelaar GB, Dorfman KD, van den Berg A, Eijkel JCT. Electrophoretic separation of DNA in gels and nanostructures. LAB ON A CHIP 2009; 9:2508-2523. [PMID: 19680576 DOI: 10.1039/b905448k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The development of nanostructure devices has opened the door to new DNA separation techniques and fundamental investigations. With advanced nanotechnologies, artificial gels (e.g. nanopillar arrays, nanofilters) can be manufactured with controlled and ordered geometries. This contrast with gels, where the pores are disordered and the range of available pore sizes is limited by the level of cross-linking and the mechanical properties of the gel. In this review, we recall the theories developed for free-solution and gel electrophoresis (extended Ogston model, biased reptation and entropic trapping) and from this perspective, suggestions for future concepts for fast DNA separation using nanostructures will be given.
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Affiliation(s)
- G B Salieb-Beugelaar
- BIOS/Lab-on-a-Chip Group, Mesa+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands.
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3
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Visualizing cells at the nanoscale. Trends Biochem Sci 2008; 34:60-70. [PMID: 19101147 DOI: 10.1016/j.tibs.2008.10.011] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/29/2008] [Accepted: 10/29/2008] [Indexed: 11/22/2022]
Abstract
Cryogenic electron tomography (cryo- ET) enables the 3D visualization of biological material at a previously unseeable scale. Carefully controlled cryogenic specimen preparation avoids the artefacts that are notorious to conventional electron microscopy specimen preparation. To date, studies employing cryo- ET have mostly been restricted to isolated macromolecular assemblies, small prokaryotic cells or thin regions of eukaryotic cells owing to the limited penetration depth of electrons through ice-embedded preparations. Recent progress in cryosectioning makes it possible to acquire tomograms from many kinds of vitrified cells and tissues. The systematic and comprehensive interpretation of such tomograms will provide unprecedented insight into the molecular organization of cellular landscapes.
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Shihabi ZK. REVIEW OF APPLICATIONS OF CAPILLARY ELECTROPHORESIS FOR CLINICAL ANALYSIS. J LIQ CHROMATOGR R T 2006. [DOI: 10.1081/jlc-100101437] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zak K. Shihabi
- a Pathology Department , Wake Forest University Baptist Medical Center , Winston-Salem, NC, 27157, U.S.A
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Shingel KI. Current knowledge on biosynthesis, biological activity, and chemical modification of the exopolysaccharide, pullulan. Carbohydr Res 2004; 339:447-60. [PMID: 15013381 DOI: 10.1016/j.carres.2003.10.034] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Accepted: 10/23/2003] [Indexed: 10/26/2022]
Abstract
The article presents an overview of the latest advances in investigations of the biosynthesis, molecular properties, and associated biological activity of pullulan. The literature survey on the pullulan biosynthesis is intended to illustrate how the great variety of environmental conditions as well as variability in strain characteristics influences the metabolic pathways of the pullulan formation and effects structural composition of the biopolymer. Molecular properties of pullulan as alpha-(1-->4)- and alpha-(1-->6)-glucan are discussed in terms of similarities with amylose and dextran structures, and an emphasis is made on the inherent biological activity of pullulan molecules. The author also attempts to summarize the concepts, options, and strategies in chemical modification of the biopolymer and to delineate future prospects in designing new biologically active derivatives.
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Affiliation(s)
- Kirill I Shingel
- Bioartificial Gel Technologies Inc, 400 Maisonneuve Ouest, suite 1156, Montreal, Quebec, Canada H3A 1L4.
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von Brocke A, Freudemann T, Bayer E. Performance of capillary gel electrophoretic analysis of oligonucleotides coupled on-line with electrospray mass spectrometry. J Chromatogr A 2003; 991:129-41. [PMID: 12703907 DOI: 10.1016/s0021-9673(03)00208-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Synthetic oligonucleotides (ODNs) are routinely analyzed using capillary gel electrophoresis (CGE) for size-sieving based separations as well as electrospray mass spectrometry (ESI-MS) for identification. On-line coupling of these methods is therefore desired in order to combine the analytical capabilities provided by both methods. Performance of on-line CGE-ESI-MS systems is influenced by various parameters, and choice of optimal conditions is crucial for successful coupling experiments. In this study, we explore characteristics of the on-line coupled CGE-ESI-MS system for ODN analysis. Effects of CGE buffer concentration, capillary length, separation and orifice voltage on CGE separation and MS detection of a phosphodiester ODN mixture were examined. Attention was paid to the influence of the interface, such as geometry of capillary alignment, sheath liquid flow-rate and sheath liquid composition on performance of the system.
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Affiliation(s)
- Alexander von Brocke
- Research Center for Nucleic Acid and Peptide Chemistry, Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany.
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Abstract
We present a mathematical model based on the models of Hubert et al. [Macromolecules 29 (1996) 1006] and Sunada and Blanch [Electrophoresis, 19 (1998) 3128] to describe the electrophoretic mobility of DNA by a transient entanglement coupling mechanism. The proposed model takes into account the interactions between molecules in the capillary and the cross-section of collision between DNA and polymer molecules. The results show that the calculated values agree remarkably well with our electrophoretic mobility data.
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Affiliation(s)
- Ho Jin Jung
- Division of Chemical Engineering and Molecular Thermodynamics Lab., Hanyang University, Seoul 133-791, South Korea
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Nkodo AE, Tinland B. Simultaneous measurements of the electrophoretic mobility, diffusion coefficient and orientation of dsDNA during electrophoresis in polymer solutions. Electrophoresis 2002; 23:2755-65. [PMID: 12210180 DOI: 10.1002/1522-2683(200208)23:16<2755::aid-elps2755>3.0.co;2-#] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We determined simultaneously the electrophoretic mobility, diffusion coefficient D and molecular orientation during electrophoresis of dsDNAs in polymer solutions ranging from the dilute to the semidilute regime. We established, for the first time, master scaling laws for the diffusion coefficient showing a universal behavior. A model found in the literature designed for the dilute regime allows, surprisingly, to describe the mobility data over the whole range of concentrations studied and at the same time the biased reptation with fluctuations (BRF) failed for the semidilute regime, even when constraint release of the network was taken into account. These quantitative determinations of D are of practical interest to evaluate band broadening during capillary electrophoresis and provide data for stimulating investigation of the physics of DNA electrophoretic motion.
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Affiliation(s)
- Axel Ekani Nkodo
- Institut Charles Sadron, Centre National de la Recherche Scientifique, 6 rue Boussingault, F-67083 Strasbourg Cedex, France
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Abstract
During the last decade, capillary electrophoresis (CE) of DNA has undergone rapid development. This improvement was especially important for DNA sequencing, where CE has now become a standard method facilitating to decipher several genomes within a very short time. Here, we give a review of the fundamentals of DNA separation in CE and the major factors influencing the performance.
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Affiliation(s)
- C Heller
- Max-Planck-Institut für molekulare Genetik, Berlin-Dahlem, Germany.
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10
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Abstract
We propose the use of a double reciprocal plot of the inflection slope and the concentration of a sieving polymer to compare sieving properties of polymers regardless of their concentration and to permit selection of appropriate sieving materials. Using this plot, the lines extrapolating the experimental values intersect the ordinate at the value corresponding to the inflection slope at the infinite concentration of the sieving polymer and the abscissa at the value characteristic for the given polymer. The latter corresponds to the polymer concentration at which the inflection slope equals half the inflection slope at an infinite polymer concentration. It is inversely proportional to intrinsic viscosity and this makes intrinsic viscosity an important physicochemical constant suitable for selection of new potent sieving polymers.
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Affiliation(s)
- V Dolník
- Molecular Dynamics, Sunnyvale, CA 94085, USA.
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Abstract
We review the wide range of polymeric materials that have been employed for DNA sequencing separations by capillary electrophoresis. Intensive research in the area has converged in showing that highly entangled solutions of hydrophilic, high molar mass polymers are required to achieve high DNA separation efficiency and long read length, system attributes that are particularly important for genomic sequencing. The extent of DNA-polymer interactions, as well as the robustness of the entangled polymer network, greatly influence the performance of a given polymer matrix for DNA separation. Further fundamental research in the field of polymer physics and chemistry is needed to elucidate the specific mechanisms by which DNA is separated in dynamic, uncross-linked polymer networks.
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Affiliation(s)
- M N Albarghouthi
- Department of Chemical Engineering, Northwestern University, Evanston, IL 60208, USA
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Abstract
This work is a continuation of earlier studies on the influence of polymer concentration and polymer composition on the capillary electrophoretic separation of DNA. The focus is on the capillary dimensions and the electric field strength as factors influencing the resolution. The aim was to establish optimum conditions for the separation of single-stranded DNA in capillaries and derive strategies for the construction of micromachined separation devices.
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Affiliation(s)
- C Heller
- Abt. Lehrach, Max-Planck-Institut für molekulare Genetik, Berlin-Dahlem, Germany.
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Abstract
The electrophoretic separation of single-stranded and double-stranded DNA has been examined, using a matrix of linear poly-N,N-dimethylacrylamide (pDMA). The dependence of peak spacing, peak width and resolution on important parameters such as polymer concentration, polymer chain length and electric field strength, has been studied. This work complements our systematic study on electrophoretic mobility under different conditions (C. Heller, Electrophoresis 1999, 20, 1962-1977), and will help to further optimize and improve high performance DNA separation in capillary electrophoresis with entangled polymer solutions.
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Affiliation(s)
- C Heller
- Abteilung Lehrach, Max-Planck-Institut für molekulare Genetik, Berlin-Dahlem, Germany.
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Abstract
We have studied the separation of single-stranded and double-stranded DNA in a matrix of entangled, linear poly-N,N-dimethylacrylamide. Our results give better insight into the mechanisms involved during separations in polymer solutions. The dependence of different parameters on DNA size, electric field, pore size and the polymer chain length are evaluated and compared to theoretical predictions. Striking differences between experimental data and predicted scaling laws are found. Our data should help to optimize DNA separation in capillary electrophoresis and to improve existing models for DNA separation in porous matrices.
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Affiliation(s)
- C Heller
- Abteilung Lehrach, Max-Planck-Institut für molekulare Genetik, Berlin-Dahlem, Germany.
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15
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Abstract
When investigating the use of different polymers for capillary electrophoresis we found that poly-N,N-dimethylacrylamide (pDMA) has a very low viscosity compared to other polymers of comparable molecular mass and resolving power. This makes it a potentially useful matrix for DNA separation in multi-capillary electrophoresis, where short cycle times or low pressure for matrix replacement are preferred. We have characterized this matrix by systematic studies on concentration, chain length and field strength dependence. It is shown that pDMA performs well for the separation of oligonucleotides and double-stranded DNA fragments. Together with the application of DNA sequencing, pDMA is a universal polymer for the separation of biological macromolecules.
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Affiliation(s)
- C Heller
- Abteilung Lehrach, Max-Planck-Institut für Molekulare Genetik, Berlin-Dahlem, Germany.
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Slater GW, Kist TB, Ren H, Drouin G. Recent developments in DNA electrophoretic separations. Electrophoresis 1998; 19:1525-41. [PMID: 9719522 DOI: 10.1002/elps.1150191003] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
DNA electrophoresis is now a fairly mature technology. Nevertheless, as we approach the 21st century, new ideas are frequently suggested that could lead to a revolution for DNA sequencing and mapping. Here, we review some of the novel concepts that have been studied since ca. 1990. Our review focuses on new separation mechanisms, new sieving matrices and recent conceptual advances.
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Affiliation(s)
- G W Slater
- Department of Physics, University of Ottawa, Ontario, Canada.
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