Modeling the free solution electrophoretic mobility of short DNA fragments

Abstract

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

Electrophoretic mobility and primary electroviscous effect of dilute “hard” prolate ellipsoids

“…The outermost shell is placed at a distance of 12/κ or 16/κ from S p , where κ is the Debye-Hückel screening parameter. The outermost shell should be placed sufficiently far from S p to insure that the equilibrium charge density and gradient in equilibrium electrostatic potential are negligible [26]. The approximation is made that field quantities are constant over each of the N surface plates of S p as well as all volume elements in the surrounding fluid.…”

“…The approximation is made that field quantities are constant over each of the N surface plates of S p as well as all volume elements in the surrounding fluid. This "discretization approximation" leads to small systematic error that can be accounted for by considering a series of models in which N is varied and extrapolating computed transport properties to the 1/N → 0 limit [26,27]. The disadvantage of this approach is that computation time varies roughly as N 2 , which limits N to a maximum value of about 500.…”

The free solution mobility of DNA in Tris‐acetate‐EDTA buffers of different concentrations, with and without added NaCl

“…More recent theories of electrophoretic mobility have included ion atmosphere relaxation and electrophoretic effects, at least to some degree [16][17][18][19][20]. However, most of these theories also include one or more adjustable parameters to bring the calculated mobilities into agreement with experiment.…”

Formulation of a new and simple nonuniform size‐modified poisson–boltzmann description

“…PB-based electrostatics descriptions are also useful in modeling colloidal stability and electrokinetic effects such as electrophoresis and electro-osmosis 18, 19 with applications to paper-manufacturing and water purification.…”