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The electrophoretic mobility of short 18 and 20 bp duplex DNAs is modeled by an iterative boundary element procedure that numerically solves the coupled Poisson, low Reynolds Number Navier-Stokes, and ion transport equations. Both capped cylinder (CC) and "detailed" models derived from the secondary structure of the fragments are examined. Translation-rotation coupling is examined with regard to the transport of the detailed models, and it is concluded that this coupling has very little effect on either diffusion or electrophoresis. When the buffer consists primarily of KCl, the calculated mobility is about 4-6% larger than the experimental mobility for either the CC or "detailed" models, but when the buffer is Tris acetate, the descrepancy is significantly larger. This indicates that there is an association between Tris + and DNA beyond the classical electrostatic interactions accounted for in modeling. For 18 bp DNA in 0.04 M Tris acetate, a model in which the phosphate charges of DNA are reduced from -1.0 to -0.45 gives good agreement with experiment. Alternatively, a model in which 40% of the DNA phosphates are neutralized by Tris + cations specifically bound to the fragment also gives a mobility consistent with experiment.

Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stern surfaces of the DNA fragments are modeled as plated cylinders that reproduce translational and rotational diffusion constants. The solvent‐accessible and ion‐accessible surfaces are taken to be coincident with the Stern surface. The mobilities are computed by solving simultaneously the coupled Navier–Stokes, Poisson, and ion‐transport equations. The equilibrium electrostatics are treated at the level of the full Poisson–Boltzmann equation and ion relaxation is included. For polyions as highly charged as short DNA fragments, ion relaxation is substantial. At .11 M KCl, the simulated mobilities of a 20 base pair DNA fragment are in excellent agreement with experiment. At .04 M Tris acetate, pH = 8.0, the simulated mobilities are about 10–15% higher than experimental values and this discrepancy is attributed to the relatively large size of the Tris counterion. The length dependence of the mobility at .11 M KCl is also investigated. Earlier mobility studies on lysozyme are reexamined in view of the present findings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter γgG is briefly considered. © 1998 John Wiley & Sons, Inc. Biopoly 46: 359–373, 1998

Brownian dynamics simulation is used to study the transient deformation of semiflexible polyions (specifically a 194 bp DNA fragment) in time varying electric fields. The polyion is represented as a string of beads, and the interaction of the polyion with the electric field is accounted for by placing effective charges on the subunits. Charge polarization effects are included by adapting the model of Szabo, Haleem, and Eden (J. Chem. Phys. 1986, 85, 7422), which also accounts for the response time of the ion atmosphere to a time varying field. Simulation results are in qualitative agreement with transient electric dichroism experiments on short DNA fragment which exhibit “amplitude inversion”. Amplitude inversion is a consequence of a bowing deformation which results from the electrophoretic migration of the polyion. The model studies also show that the bowing deformation can be eliminated by replacing a constant electric field pulse (of duration T) with a rapidly reversing square wave of period 2T‘, provided T‘ is short compared to the coil deformation time of the fragment but long compared to the ion atmosphere relaxation time.