DNA electrophoresis in agarose gels: Effects of field and gel concentration on the exponential dependence of reciprocal mobility on DNA length

✍ Scribed by Randolph L. Rill; Afshin Beheshti; David H. Van Winkle

• Publisher: John Wiley and Sons
• Year: 2002
• Tongue: English
• Weight: 190 KB
• Volume: 23
• Category: Article
• ISSN: 0173-0835
• DOI: 10.1002/1522-2683(200208)23:16<2710::aid-elps2710>3.0.co;2-0

✦ Synopsis

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.