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Review
. 2009 Mar 6;1216(10):1917-29.
doi: 10.1016/j.chroma.2008.11.090. Epub 2008 Dec 6.

Effect of the matrix on DNA electrophoretic mobility

Nancy C Stellwagen  1 , Earle Stellwagen
Affiliations
Review

Effect of the matrix on DNA electrophoretic mobility

Nancy C Stellwagen et al. J Chromatogr A. .

Abstract

DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.

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Figures

Fig. 1
Fig. 1
Ferguson plots observed for dsDNA fragments of different sizes. The logarithm of the mobility, μ, is plotted as a function of agarose concentration, %A. At each gel concentration, the mobilities were measured as a function of electric field strength and extrapolated to E = 0. From top to bottom, the sizes of the DNAs are: 0.5, 1.6, 3.1, 6.1, 9.2, and 12.2 kbp. Adapted from Ref. [46], with permission.
Fig. 2
Fig. 2
Log-log plots of the dependence of the mobility, μ, observed in agarose gels of various concentrations on DNA molecular mass, in kilobase pairs, at two different electric field strengths. (A) 3.8 V/cm; (B), 0.64 V/cm. From top to bottom, the agarose gel concentrations are 0.2%, 0.4%, 0.6%, 0.9%, 1.25%, and 1.5%. Adapted from Ref. [53], with permission.
Fig. 3
Fig. 3
Ferguson plots observed for dsDNA fragments in polyacrylamide gels containing 3.0%C and various %T. From top to bottom, the sizes of the DNAs are: 123, 246, 369, 615, 984, and 1599 bp. Adapted from Ref. [139], with permission.
Fig. 4
Fig. 4
Log-log plots of the dependence of the mobility, μ, observed in poly-N,N'-dimethylacrylamide (pDMA) solutions of various concentrations on DNA size. (A), dsDNA, 25°C; (B), ssDNA, 50°C with 4M urea. From top to bottom, the pDMA concentrations are 1%, 2%, 5%, and 10%. Adapted from Ref. [5] with permission.
Fig. 5
Fig. 5
Dependence of the mobility, μ, observed for dsDNA on the concentration of hydroxypropyl cellulose (HPC) in the solution. The threshold overlap concentration, Φ*, is indicated. From top to bottom, the DNA increases in size from 72 to 23130 bp. Adapted from Ref. [225] with permission.
Fig. 6
Fig. 6
Dependence of the free solution mobility, μ, of curved (open circle) and normal (closed circle) DNA molecules on DNA molecular mass, in base pairs. Adapted from Ref. [241] with permission.
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References

    1. Viovy J-L. Rev. Mod. Phys. 2000;72:813.
    1. Upcroft P, Upcroft JA. J. Chromatogr. 1993;618:79. - PubMed
    1. Slater GW, Guillouzic S, Gauthier MG, Mercier J-F, Kenward M, McCormick LC, Tessier F. Electrophoresis. 2002;23:3791. - PubMed
    1. Slater GW, Kist TBL, Ren H, Drouin G. Electrophoresis. 1998;19:1525. - PubMed
    1. Heller C. Electrophoresis. 2001;22:629. - PubMed

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