Modeling the free solution electrophoretic mobility of short DNA fragments

✍ Scribed by Stuart A. Allison; Suzann Mazur

• Publisher: Wiley (John Wiley & Sons)
• Year: 1998
• Tongue: English
• Weight: 201 KB
• Volume: 46
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/(sici)1097-0282(199811)46:6<359::aid-bip2>3.0.co;2-#

✦ Synopsis

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 solventaccessible 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 Å 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 G is briefly considered.