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  • 1
    Electronic Resource
    Electronic Resource
    Ogston gel electrophoretic sieving: How is the fractional volume available to a particle related to its mobility and diffusion coefficient(s)? (1995)
    Weinheim : Wiley-Blackwell
    Electrophoresis 16 (1995), S. 11-15 
    Details
    ISSN: 0173-0835
    Keywords: Ogston model ; Ferguson plot ; Gel electrophoresis ; Diffusion ; Einstein relation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The Ogston-Morris-Rodbard-Chrambach model (OMRCM) of gel electrophoresis assumes that the mobility μ of charged particles is proportional to the fractional volume (f) of the gel that is available to them. If the gel is random, as described by Ogston, the (semi-log) Ferguson plot is the method of choice for analyzing experimental data since it permits an estimate of the gel's mean pore size to be made. However, the Ferguson plot is rarely linear; this is usually “explained” by the deformation of the anisotropy of the particle, the nonrandom or variable architecture or the gel, or the onset of some other migration mechanism. Many authors have refined this model, but the original assumption that μ ∝ f has not been seriously examined. Also, the model says nothing of the effect of the field intensity, the connectivity of the gel pores, nor anything about the diffusion coefficient. We have developed a Monte-Carlo computer simulation algorithm to study the electrophoretic sieving of simple particles in gels. In this brief communication, we report important preliminary results which indicate that the basic assumptions of the OMRCM are wrong. We use a two-dimensional periodic gel since the OMRCM becomes trivial in this case. Our results show that the relationship between f and μ is not the one assumed by the OMRCM. Moreover, we find that the Einstein relation between the diffusion coefficient and the mobility is not valid. This is due to the fact that the particles do not have a uniform probability of visiting the various sites that are available to them. We thus conclude that the Ferguson plot is intrinsically nonlinear; the curvature of the plot is, in fact, related to the intensity of the electric field as well as to the degree of randomness of the gel fibers.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150160104
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  • 2
    Electronic Resource
    Electronic Resource
    An exactly solvable Ogston model of gel electrophoresis: I. The role of the symmetry and randomness of the gel structure (1996)
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 977-988 
    Details
    ISSN: 0173-0835
    Keywords: Ogston model ; Ferguson plots ; Gel electrophoresis ; Gel structure ; Electrophoretic mobility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The Ogston-Morris-Rodbard-Chrambach model (OMRCM) of gel electrophoresis assumes that the mobility (μ) of charged particles is directly proportional to the fractional volume (f) of the gel that is available to them. Many authors have studied the fractional volume f in detail for various particle shapes, but the original assumption, that μsf, has not been scrutinized seriously. In fact, this geometrical model of electrophoresis does not take into account the connectivity of the gel pores or the precise gel architecture. Recently (G. W. Slater and H. L. Guo, Electrophoresis 1995, 16, 11-15) we developed a Monte Carlo computer simulation algorithm to study the electrophoretic motion of simple particles in gels in the presence of fields of arbitrary strength. Our preliminary results indicated that the mobility and the fractional volume were not generally proportional to one another. In this article, we show how to calculate, in the limit where the field intensity is vanishingly small, the exact electrophoretic mobility of particles in any type of gel in two or more dimensions. Our results, presented here for some simple two-dimensional systems, indicate that a particle can have different electrophoretic mobilities in gels in which it has access to the same fractional available volume f. The curvature of the Ferguson plot is shown to be related to the symmetry and the degree of randomness that characterize the gel. We also demonstrate that the OMRCM is, in fact, a mean field approximation that corresponds to a uniform, annealed gel. We thus conclude that the relation between the electrophoretic mobility and the gel concentration (C) is a delicate function of the gel architecture, and that one needs more than the fractional volume f to fully characterize the transport properties of migrating particles in separation media. Exact relationships between the mobility μ and the gel concentration C are given for our model gels.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150170604
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  • 3
    Electronic Resource
    Electronic Resource
    Trapping gel electrophoresis of end-labeled DNA: An analytical model for mobility and diffusion (1995)
    Weinheim : Wiley-Blackwell
    Electrophoresis 16 (1995), S. 704-712 
    Details
    ISSN: 0173-0835
    Keywords: Gel electrophoresis ; DNA sequencing ; Trapping electrophoresis ; Reptation model ; Streptavidin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: As shown by Ulanovsky, Drouin and Gilbert (Nature 1990, 343, 190-192), the gel electrophoretic migration of DNA is severely reduced by steric trapping when streptavidin is attached to one end of the polyelectrolyte. We present a model that allows us to calculate both the mobility and the diffusion coefficient, hence the resolution factor of the resulting separation. We compare our results to those of Défontaines and Viovy (Electrophoresis 1993, 14, 8-17) and we show that the averages over the molecular conformations must be done carefully. We also show that trapping increases diffusion substantially and that this makes constant-field trapping electrophoresis incapable of increasing the number of bases read per sequencing run. Finally, we conclude that severe trapping may lead to highly anomalous transport behavior where one cannot define a velocity or a diffusion constant.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.11501601114
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  • 4
    Electronic Resource
    Electronic Resource
    An exactly solvable Ogston model of gel electrophoresis II. Sieving through periodic gels (1996)
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 1407-1415 
    Details
    ISSN: 0173-0835
    Keywords: Ogston model ; Ferguson plot ; Gel electrophoresis ; Gel pore size ; Gel fiber radius ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Recently, we developed a lattice model to study the dynamics of particles being electrophoresed in gels (G. W. Slater, H. L. Guo, Electrophoresis 1995, 16, 11-15). In Part I of this series (G. W. Slater, H. L. Guo, Electrophoresis 1996, 17, 977-988), we showed how to calculate the exact electrophoretic mobility of one-site particles in the limit where the electric field intensity E is vanishingly small. Since we can solve the model for arbitrary gel structures in two or more dimensions, we compared our results with those of the Ogston-Morris-Rodbard-Chrambach model (OMRCM) of gel electrophoresis, which assumes that the mobility (μ) of charged particles is directly proportional to the fractional gel volume (f) that is available to them. Our results and theoretical analysis indicated that the OMRCM is a mean-field approximation that can be useful as a rough guide; however, it generally misses the subtle sieving effects related to the correlations between the position of the obstacles in a given gel structure. In this paper (Part II) we study, for two-dimensional periodic gels, the exact relationships between the zero-field mobility μ and the gel concentration C for larger particle sizes. The fact that μ is a strong function of the particle size suggests that we can separate large particles using two-dimensional periodic gels (similar to those fabricated by W. D. Volkmuth and R. H. Austin, Nature 1992, 358, 600-602). We analyze our data using Ferguson-like plots and we show that one can indeed use a generalized retardation coefficient, K, to estimate the effective pore size, aK and effective fiber size rK for these model gels. We conclude that the retardation coefficient is a useful concept to characterize a sieving structure even though it does not permit the inference of the exact gel structure.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150170903
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