Visualizing ion relaxation in the transport of short DNA fragments

Ion relaxation plays an important role in a wide range of phenomena involvi ng the transport of charged biomolecules. ion relaxation is responsible for reducing sedimentation and diffusion constants, reducing electrophoretic m obilities, increasing intrinsic viscosities, and, for biomolecules that lac k a permanent electric dipole moment, provides a mechanism for orienting th em in an external electric field. Recently, a numerical boundary element me thod was developed to solve the coupled Navier-Stokes, Poisson, and ion tra nsport equations for a polyion modeled as a rigid body of arbitrary size, s hape, and charge distribution. This method has subsequently been used to co mpute the electrophoretic mobilities and intrinsic viscosities of a number of model proteins and DNA fragments. The primary purpose of the present wor k is to examine the effect of ion relaxation on the ion density and fluid v elocity fields around short DNA fragments (20 and 40 bp). Contour density a s well as vector field diagrams of the various scalar and vector fields are presented and discussed at monovalent salt concentrations of 0.03 and 0.11 M. In addition, the net charge current fluxes in the vicinity of the DNA f ragments at low and high salt concentrations are briefly examined and discu ssed.