Brownian diffusion and electrophoretic transport of double-stranded DNA in agarose gels

Pernodet, Nadine; Tinland, B.; Sturm, Jürgen; Weill, G.

doi:10.1002/(sici)1097-0282(199907)50:1<45::aid-bip5>3.0.co;2-2

Cited by 13 publications

(20 citation statements)

References 25 publications

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“…This would be consistent with a scaling exponent x % 0.65, a reasonable value for this gel and in agreement with [13] for low field intensities. In order to better understand the limitations of the vWBR empirical formula, we would need an experimental study of the field-dependence of their asymptotic mobility m ?…”

Section: The Asymptotic Mobilitysupporting

confidence: 89%

“…(19) and (18) as a function of the gel concentration C (in %). The pore sizes shown here are similar to those reported by other authors [12][13][14][15][16]; however, one must keep in mind that different Electrophoresis 2002, 23, 1410-1416 An empirical mobility formula for DNA gel electrophoresis methods automatically use different definitions of the "effective" mean pore size of the gel. We note that the pore size determined here is roughly equal to the Kuhn length (= 2p = 100 nm) for the largest gel concentrations used by the authors.…”

Section: The Reptation Regimesupporting

confidence: 87%

“…The data [13,15] and the theoretical understanding [1,3,4] do exist, but again as disjointed scaling regimes. With empirical formulas describing both the mobility and the diffusion, one would be able to optimize any separation system quite easily for a wide range of DNA molecular sizes.…”

Section: Discussionmentioning

confidence: 83%

“…10 of [13]) found that Eq. (7) provided excellent fits to their data for the same system with exponents in the range x = 0.35-0.7.…”

Section: The Asymptotic Mobilitymentioning

confidence: 99%

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A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Slater

2002

Electrophoresis

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The separation of DNA fragments by gel electrophoresis has been studied extensively over the last two decades. More recently, similar studies have been carried out to characterize the separation achieved by the current capillary array electrophoresis systems and their sieving polymer solutions. In all cases, at least three different mobility regimes have been shown to exist: the Ogston regime when the radius of gyration of the DNA fragment is smaller than the pore size, the reptation regime when the DNA is larger than the pore size but remains in a random coil conformation, and finally the reptation-with-orientation regime where the DNA orients in the field direction and essentially all resolution is lost. Unfortunately, although theory helps us understand the different regimes and how to properly exploit them, we still have no theory-based general equations that would apply to all regimes. Such equations would be especially useful to analyze data, optimize separation systems and interpolate mobilities to estimate unknown molecular sizes. Recently, van Winkle, Beheshti and Rill (Electrophoresis 2002, 23, 15-19) proposed an intriguing empirical formula that seems to adequately fit the mobility of dsDNA fragments across all three regimes. In this paper, I investigate the relation between this empirical formula and the known theories of gel electrophoresis, and I study the dependence of its fitting parameters upon the experimental conditions. Finally, I examine how this equation may need to be modified to capture the more subtle details predicted by fundamental theories of DNA gel electrophoresis.

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Section: The Asymptotic Mobilitysupporting

confidence: 89%

Section: The Reptation Regimesupporting

confidence: 87%

Section: Discussionmentioning

confidence: 83%

“…10 of [13]) found that Eq. (7) provided excellent fits to their data for the same system with exponents in the range x = 0.35-0.7.…”

Section: The Asymptotic Mobilitymentioning

confidence: 99%

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A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Slater

2002

Electrophoresis

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“…In particular, diffusion (translational and rotational) has been studied in a wide range of environments including the cytoplasm of cells [1], concentrated suspensions [2], gels or hydrogels [3][4][5][6][7][8][9][10][11][12][13], and mucus [14]. The diffusion of a host particle through a rigid gel matrix is reduced, relative to diffusion in "free solution", by long range hydrodynamic interaction and short range steric effects.…”

Section: Introductionmentioning

confidence: 99%

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Twahir

Davis

et al. 2011

Polymers

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Abstract:In this work, the retarding influence of a gel on the rotational motion of a macromolecule is investigated within the framework of the Effective Medium (EM) model. This is an extension of an earlier study that considered the effect of a gel on the translational motion of a macromolecule [Allison, S. et al. J. Phys. Chem. B 2008, 112, 5858-5866]. The macromolecule is modeled as an array of non-overlapping spherical beads with no restriction placed on their size or configuration. Specific applications include the rotational motion of right circular cylinders and wormlike chains modeled as strings of identical touching beads. The procedure is then used to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. At low gel concentration (M  0.010 gm/mL), good agreement between theory and experiment is achieved if the persistence length of DNA is taken to be 65 nm and the gel fiber radius of agarose is taken to be 2.5 nm. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA and this can be attributed to the onset of direct interactions that become significant when the effective particle size becomes comparable to the mean gel fiber spacing. OPEN ACCESSPolymers 2011, 3 847

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Mobility, diffusion and dispersion of single-stranded DNA in sequencing gels

Brahmasandra¹,

Burke²,

Mastrangelo

et al. 2001

Electrophoresis

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Electrophoresis of single-stranded DNA in denaturing polyacrylamide gels is presently a standard procedure for the sequencing of DNA fragments. A thorough understanding of the factors that determine the resolution of DNA fractionated in polyacrylamide gels is necessary to optimize the performance of DNA sequencers. Significant research on the mobility of double-stranded (ds)DNA molecules in agarose and polyacrylamide gels has been performed, and the phenomenon of band broadening of single-stranded (ss)DNA fragments in DNA sequencing gels has received attention only recently. In this paper, we present a detailed study of mobility, diffusion and dispersion of ssDNA in sequencing gels as a function of molecular size, gel concentration and electric field strength. DNA mobility is shown to be essentially independent of electric field in the range of 0-60 V/cm. The band broadening is greatly enhanced in the presence of an electric field and the dispersion coefficient (DE) can be an order of magnitude higher than the field-free diffusion coefficient. The measured migration parameters approximately follow the predictions of the biased reptation including fluctuations (BRF) theory. However, deviations due to nonidealities of the separation conditions are observed. The measured migration parameters can be used to optimize the performance of separation systems.

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Brownian diffusion and electrophoretic transport of double-stranded DNA in agarose gels

Cited by 13 publications

References 25 publications

A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

Rotational Diffusion of Macromolecules and Nanoparticles Modeled as Non-Overlapping Bead Arrays in an Effective Medium

Mobility, diffusion and dispersion of single-stranded DNA in sequencing gels

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