Probing the mechanisms of the electrophoretic separation of DNA

COLL 35

Harvey W. Blanch and Sean M. Ferree. Department of Chemical Engineering, University of California, Tan Hall, Berkeley, CA 94720-1462
Electrophoresis has been a powerful and ubiquitous tool for the separation and analysis of DNA molecules. However our understanding of the mechanisms of separation, beyond the traditional sieving and reptation models for gel electrophoresis, is incomplete, particularly in dilute polymer solutions. We examine the electrophoresis of restriction fragment DNA molecules in dilute and ultra-dilute polymer solutions. DNA undergoes large conformational changes during electrophoresis, and these conformational dynamics must be included in models of the electrophoretic separation. We present epifluorescent microscopy data of the electrophoretic stretching of tethered DNA molecules to probe the influence DNA dynamics on the separation process and discuss a theory to describe these single molecule DNA stretching dynamics