A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels

Calladine, C. R.; Collis, Christina M.; Drew, Horace R.; Mott, Margaret R.

doi:10.1016/0022-2836(91)80187-y

Cited by 116 publications

(61 citation statements)

References 24 publications

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“…It has been recognized for some time that the behavior of macromolecules in gel electrophoresis fall into well defined "regimes" [49], and the findings of the present study are consistent with this view. At low gel concentration where long range HI dominates, the EM model is adequate, but this breaks down at high gel concentration where reptation theories are undoubtedly more appropriate [50].…”

Section: Discussionsupporting

confidence: 90%

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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Section: Discussionsupporting

confidence: 90%

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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“…The value of R L has a maximum value between 150 and 200 bp depending on the exact nature of the mismatch and it decreases beyond the critical length of 250 bp. This fits with an idea presented by Calladine et al [1991], who suggested that the DNA molecule has an inherent flexibility and the unit of flexibility is a super helix with a pitch of roughly 200 bp. Therefore, with length increasing beyond 200 bp, the inherent flexibility of the DNA molecule obscures the effect of local change in DNA bending induced by the mismatched base.…”

Section: Parameters Affecting the Limits Of Resolution By Csgesupporting

confidence: 89%

An update on conformation sensitive gel electrophoresis

Ganguly

2002

Hum. Mutat.

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“…The porosity of agarose (determined by agarose concentration in the gel) is responsible for much of its DNA separation properties. Under these conditions, the migration velocity of the DNA fragments decreases as their length increases and is proportional to the strength of the electric field (Calladine et al, 1991;Fangman, 1978;McDonell et al, 1977). This association, however, cannot be applied once the size of DNA fragments surpasses a maximum value, which is defined basically by the composition of the gel and the electric field strength (Hervet & Bean, 1987).…”

Section: Electrophoresis Through Agarose Gelmentioning

confidence: 99%