Electrophoresis of composite molecular objects. 2. Competition between sieving and frictional effects in polymer solutions

We previously showed that labeling one end of single-stranded DNA molecules with a neutral label like streptavidin increases the interband separation of these hybrid DNA molecules when they are electrophoresed in denaturing cross-linked polyacrylamide gels. This separation process is called trapping electrophoresis because the dynamical properties of the analytes are strongly affected by random steric trapping in the gel. End-labeled ssDNA molecules can also be electrophoretically separated in free solution. This process is called end-labeled free solution electrophoresis, and the separation is then due to the extra hydrodynamic friction provided by the streptavidin label. In this article, Re present a study of the capillary electrophoresis of DNA molecules end-labeled with streptavidin in the presence of non-crosslinked polymer solutions ranging from semidilute to ultradilute conditions. In the semidilute limit, sieving interactions dominate, and small DNA molecules move faster than larger ones. In the ultradilute limit, however, we recover free-solution-like separations where small molecules are more retarded than larger ones. We also observe a fascinating transition between these two regimes, for intermediate polymer concentrations and DNA sizes, where the competition between trapping, sieving, and frictional effects leads to nonmonotonic mobility-size relationships. Our theoretical analysis suggests a universal relationship between the mobility of labeled and unlabeled DNA molecules in all electrophoretic conditions.