Experimental and theoretical works were performed for the separation of large polyelectrolytes such as DNA in the column packed with gel particles under an electric field. This paper shows how intraparticle convection effects the separation of DNAs in the column because DNAs quickly oriented through the pores in the field direction. Dimensionless transient mass balance equations were derived considering diffusion and electrophoretic convection. The separation criteria is theoretically studied using two different Peclet numbers in the fluid and solid phases and these criteria were verified uing two different DNAs by electrophoretic mobilities measured experimentally, showing how the separation position of DNAs varies in the column according to values of Pe(sub)f/Pe(sub)g of individual DNA. Governing equations are simultaneously solved by operator theoretic and characteristic methods to yield the column response.