Several recent studies have demonstrated that small pore size ultrafiltration membranes can be used for purification of supercoiled plasmid DNA for therapeutic applications, but the performance of these membrane systems is severely limited by membrane fouling. The objective of this work was to examine the potential of pre-conditioning, in this case accomplished by pre-elongating the DNA by passage through a region with large pore size, to minimize fouling and enhance DNA separations. Data were obtained using both asymmetric hollow fiber membranes, with flow in either the normal or reverse orientation, and with composite membrane structures made by placing a larger pore size flat sheet microfiltration membrane in series with an ultrafiltration membrane. In all cases, flow through the larger pore size region pre-stretched the plasmid, leading to an increase in plasmid transmission and a significant reduction in fouling. This pre-conditioning also provided a significant increase in selectivity for separation of the linear and supercoiled isoforms. These results clearly demonstrate the potential for dramatically increasing the performance of membrane systems for plasmid DNA separations by controlling the pore morphology to pre-stretch the DNA before passing through the narrow pores of an ultrafiltration membrane. (C) 2015 Elsevier B.V. All rights reserved.