In this paper we study the large scale transport of the DNA particles through a heterogeneous micro array in the framework of homogenization theory. We derive the macro scale particle transport equation and show that for transport of particles in a divergence free electric field as proposed by Duke and Austin [Du98] and Ertas [Er98] separation according to particle mass or size cannot been achieved. Our results explain the experimental findings of Duke and Austin [Du98] and Ertas [Er98] and thus close the gap between theory and experiment.