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Biophys J, November 2001, p. 2558-2568, Vol. 81, No. 5

The Length Dependence of Translational Diffusion, Free Solution Electrophoretic Mobility, and Electrophoretic Tether Force of Rigid Rod-Like Model Duplex DNA

Stuart Allison,* Chuanying Chen,* and Dirk Stigterdagger

 *Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, and  dagger Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143 USA

In this work, boundary element modeling is used to study the transport of highly charged rod-like model polyions of various length under a variety of different aqueous salt conditions. Transport properties considered include free solution electrophoretic mobility, translational diffusion, and the components of the "tether force" tensor. The model parameters are chosen to coincide with transport measurements of duplex DNA carried out under six different salt/temperature conditions. The focus of the analysis is on the length dependence of the free solution electrophoretic mobility. In a solution containing 0.04 M Tris-acetate buffer at 25°C, calculated mobilities using straight rod models show a stronger dependence on fragment length than that observed experimentally. By carrying out model studies on curved rod models, it is concluded that the "leveling off" of mobility with fragment length is due, in part at least, to the finite curvature of DNA. Experimental mobilities of long duplex DNA in monovalent alkali salts are reasonably well explained once account is taken of long-range bending and the simplifying assumptions of the model studies.

Biophys J, November 2001, p. 2558-2568, Vol. 81, No. 5
© 2001 by the Biophysical Society   0006-3495/01/11/2558/11  $2.00


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