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

✍ Scribed by Nadine Pernodet; Bernard Tinland; Jean Sturm; Gilbert Weill

• Publisher: Wiley (John Wiley & Sons)
• Year: 1999
• Tongue: English
• Weight: 216 KB
• Volume: 50
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/(sici)1097-0282(199907)50:1<45::aid-bip5>3.0.co;2-2

✦ Synopsis

The field free diffusion constant and the electric field dependence of the electrophoretic mobility and molecular orientation of DNA samples from 5 to 164 kilobase pairs in agarose gels from 0.5 to 2% have been measured by fluorescence recovery after photobleaching and birefringence. In conditions where the reptation predictions hold for the field free diffusion, they partially fail for the DNA size dependence of the low field limit of the electrophoretic mobility. The linear field dependencies of the electrophoretic mobility and orientation factor seem to favor the biased reptation model with fluctuations over the standard biased reptation model, which predicts a quadratic field dependence. The quantitative analysis of the molecular parameters shows, however, that most experiments have been carried out at values of the field where the difference between the two models may be less conclusive. The pore size dependence of the different quantities has been given a particular attention and the role of the distribution of pore sizes in the departures from the reptation predictions is discussed.