%0 Journal Article %1 allison98a %A Allison, S. A. %A Mazur, S. %D 1998 %J Biopolymers %K BIREFRINGENCE; CIRCULAR-CYLINDERS; DILUTE-SOLUTION; ELECTRIC ELECTROLYTE EQUATION; FRICTION; LENGTH; MACROMOLECULES; NUMERICAL-METHOD; PERSISTENCE POISSON-BOLTZMANN POLY-ELECTROLYTES; POLYIONS RIGID SYMMETRIC TOP %N 6 %P 359--373 %T Modeling the free solution electrophoretic mobility of short DNA fragments %V 46 %X Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stent 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 an lysozyme are reexamined in view of the presentfindings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter Gamma is briefly considered. (C) 1998 John Wiley & Sons, Inc.

@article{allison98a, abstract = {Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stent 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 an lysozyme are reexamined in view of the presentfindings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter Gamma is briefly considered. (C) 1998 John Wiley & Sons, Inc.}, added-at = {2007-06-15T17:33:15.000+0200}, author = {Allison, S. A. and Mazur, S.}, biburl = {https://www.bibsonomy.org/bibtex/224d938a56913fffadc0bb7efd92577bf/kaigrass}, de = {boundary element method; DNA electrophoresis; electrophoretic mobilityEOLEOLof DNA; free solution electrophoretic mobility of DNA; ion relaxation;EOLEOLDNA electrophoresis; modeling electrophoresis of polyions}, interhash = {6c69c7504a22cefb81513ed788495165}, intrahash = {24d938a56913fffadc0bb7efd92577bf}, journal = {Biopolymers}, keywords = {BIREFRINGENCE; CIRCULAR-CYLINDERS; DILUTE-SOLUTION; ELECTRIC ELECTROLYTE EQUATION; FRICTION; LENGTH; MACROMOLECULES; NUMERICAL-METHOD; PERSISTENCE POISSON-BOLTZMANN POLY-ELECTROLYTES; POLYIONS RIGID SYMMETRIC TOP}, month = {November}, number = 6, owner = {grass}, pages = {359--373}, sn = {0006-3525}, timestamp = {2007-06-15T17:33:16.000+0200}, title = {Modeling the free solution electrophoretic mobility of short DNA fragments}, ut = {ISI:000076534300002}, volume = 46, year = 1998 }