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The Hydrodynamics of DNA Electrophoretic Stretch and Relaxation in a Polymer Solution

Department of Chemical Engineering, University of California, Berkeley, California

Correspondence: Address reprint requests to Dr. Harvey W. Blanch, Dept. of Chemical Engineering, University of California, Berkeley, CA 94720. Tel.: 510-643-1387; Fax: 510-643-1228; E-mail: blanch{at}socrates.berkeley.edu.

Theories of DNA electrophoretic separations generally treat the DNA as a free draining polymer moving in an electric field at a rate that depends on the effective charge density of the molecule. Separations can occur in sieving media ranging from ultradilute polymer solutions to tightly cross-linked gels. It has recently been shown that DNA is not free-draining when both electric and nonelectric forces simultaneously act on the molecule, as occurs when DNA collides with a polymer during electrophoretic separations. Here we show that a semidilute polymer solution screens the hydrodynamic interaction that results from the application of these forces. Fluorescently labeled DNA tethered at one end in a semidilute solution of hydroxyl-ethyl cellulose stretch more in an electric field than they stretch in free solution, and approach free-draining behavior. The steady stretching behavior is predicted without adjustable parameters by a theory developed by Stigter using a hydrodynamic screening length found from effective medium theory. Data on the relaxation of stretched molecules after the electric field is removed agree with the Rouse model prediction, which neglects hydrodynamic interactions. The slowest relaxation time constant, _R, scales with chain length as _R L^1.9±0.17 when analyzed by the data collapse method, and as _R L^2.17±0.17 when analyzed by multiexponential fit.