title: DNA electrophoresis in agarose gels: effects of field and gel concentration on the exponential dependence of reciprocal mobility on DNA length.
abstract: Electrophoretic mobilities of DNA molecules ranging in length from 200 to 48 502 base pairs (bp) were measured in agarose gels with concentrations T = 0.5% to 1.3% at electric fields from E = 0.71 to 5.0 V/cm. This broad data set determines a range of conditions over which the new interpolation equation nu(L) = (beta+alpha(1+exp(-L/gamma))(-1) can be used to relate mobility to length with high accuracy. Mobility data were fit with chi(2) > 0.999 for all gel concentrations and fields ranging from 2.5 to 5 V/cm, and for lower fields at low gel concentrations. Analyses using so-called reptation plots (Rousseau, J., Drouin, G., Slater, G. W., Phys. Rev. Lett. 1997, 79, 1945-1948) indicate that this simple exponential relation is obeyed well when there is a smooth transition from the Ogston sieving regime to the reptation regime with increasing DNA length. Deviations from this equation occur when DNA migration is hindered, apparently by entropic-trapping, which is favored at low fields and high gel concentrations in the ranges examined.
authors.affiliation: Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4350, USA.
authors.forename: Randolph L
authors.initials: RL
authors.lastname: Rill
authors.forename: Afshin
authors.initials: A
authors.lastname: Beheshti
authors.forename: David H
authors.initials: DH
authors.lastname: Van Winkle
mesh_terms: D004247:DNA / Q000302:isolation & purification*; D004563:Electrochemistry; D004587:Electrophoresis, Agar Gel / Q000379:methods*; D005782:Gels; D008956:Models, Chemical; D008970:Molecular Weight
chemical_list: D005782:Gels; D004247:DNA