The effect of electrophoretic convection in the packed column is presented. When an electric field is applied, the conformation of polyelectrolyte quickly orients in the field direction. The convective velocity of polyelectrolyte inside a porous gel particle is accelerated. The dependence of the transport in the gel particle upon field intensity and molecular size aids in understanding the transport of polyelectrolyte in the packed column. To date, Few dynamic studies of polyelectrolyte in a porous gel particle and transient concentration profiles in the column have been attempted for the separation of polyelectrolytes in the packed column. The convective-diffusive transport of DNA is analyzed using Peclet number described by experimentally measured electrophoretic mobility and the diffusion coefficient. The separation criterion of two different DNAs in the packed column is based on the variation of Pe(f)/Pe(g) of two different DNAs. The purpose of this study is to show how the variation of physicochemical properties in the gel particle affects the separation of DNAs from a mixture in the packed column. The spectral expansion is mathematically analyzed using the eigenvalue set of the transport operator. A theoretical model using the characteristic method is used to calculate the separation point in the packed column.