The huge efforts for the achievement of highly purified biomolecules are growing every day. A great number of efficient techniques, such as chromatography, are already available in laboratory for separation processes. However, membrane‐based technologies are the best match to assure simplicity, efficiency and easy scale‐up procedures. Herein we report the modification of a commercial microfiltration membrane for plasmid DNA purification by agarose gel impregnation. The membrane was characterized by SEM, ATR‐FTIR, EDS, contact angle, and porosity measurements. Additionally, the membrane pore radius was estimated from observed rejections of different proteins and with that information the rejection of a 6050 bp plasmid DNA (pDNA) molecule was estimated for different values of flux using a theoretical model of large flexible molecules in membranes with parallel cylindrical pores, which is applicable to pDNA ultrafiltration in conventional membranes, as recently shown in the literature. The experimental results show that the modified membrane has higher pDNA rejections than the predicted by the model, suggesting that the different type of porous structure that a hydrogel has, may have a positive effect on pDNA rejections as compared to other biomolecules with more rigid structures, making this type of modified membranes potential better candidates to be used for the selective recovery of pDNA in this type of bioprocesses. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41610.