Nanofluidic lab-on-chip technology offers the unique capability of free-flow separation, identification, and manipulation of biomolecules, with the potential of leading to breakthrough medical diagnostic devices. In this work, we present an experimental study in flat nanochannels on the effects of ionic strength on ss (single stranded) and ds (double stranded) DNA electrophoretic separations, towards optimizing resolution and accuracy of this technique. While the origin of nanoscale electrophoretic separations is not fully understood, it is clear that hybridization and separation behavior of DNA is influenced by a number of parameters including: buffer ionic strength, channel size, strand length, and strand conformation. By conducting a systematic set of experiments, we expose their relative importance and contribution, and propose an explanation of the origin of the observed behavior.