Modeling the Electrophoresis of Short Duplex DNA:  Counterions K+ and Tris+

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.