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 c ross-linked polyacrylamide gels. This separation process is called trapping electrophoresis because the dynamical properties of the analytes are stron gly affected by random steric trapping in the gel. End-labeled ssDNA molecu les can also be electrophoretically separated in free solution. This proces s is called end-labeled free solution electrophoresis, and the separation i s 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-cros slinked polymer solutions ranging from semidilute to ultradilute conditions . In the semidilute limit, sieving interactions dominate, and small DNA mol ecules move faster than larger ones. In the ultradilute limit, however, we recover free-solution-like separations where small molecules are more retar ded than larger ones. We also observe a fascinating transition between thes e 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 suggest s a universal relationship between the mobility of labeled and unlabeled DN A molecules in all electrophoretic conditions.