Conventional methods for separating biomolecules are based on steric interactions between the biomolecules and randomly oriented gel fibers. The recently developed artificial molecular sieves also rely on steric interactions for separation. In this work, we present an experimental investigation of a method that can be used in these sieves to increase separation selectivity and resolution. This method exploits the electrostatic repulsion between the charged molecules and the charged nanofluidic structure. Although this method has been mentioned in the previous work, it has not been examined in detail. We characterize this method by comparing the selectivity with that achieved in devices with different dimensions. The results of this study are relevant to the optimization of chip-based gel-free biomolecule separation and analysis.