Modeling the electrophoresis of short duplex DNA: Counterions K+ and Tris(+)

The electrophoretic mobility of short 18 and 20 bp duplex DNAs is modeled b y an iterative boundary element procedure that numerically solves the coupl ed 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 con cluded that this coupling has very little effect on either diffusion or ele ctrophoresis. When the buffer consists primarily of KCI, the calculated mob ility 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 betwe en Tris(+) and DNA beyond the classical electrostatic interactions accounte d for in modeling. For 18 bp DNA in 0.03 M Tris acetate, a model in which t he phosphate charges of DNA are reduced from -1.0 to -0.45 gives good agree ment with experiment. Alternatively, a model in which 40% of the DNA phosph ates are neutralized by Tris+ cations specifically bound to the fragment al so gives a mobility consistent with experiment.