Electrophoresis of DNA molecules through entangled polymer solutions in both capillaries and microchips continues to be an invaluable tool for genetic analysis and is used in many genotyping and forensics applications as well as DNA and genomic sequencing. The transfer of most of these separation methods fully to microchips has already been accomplished or is in the process of being implemented. The design of the cross injector in microchips has greatly increased the efficiency of these separations, therefore reducing the required separation distance for many of these assays. To fully optimize the resolution of these separations, the polymer matrix and wall coating must be designed in such a way that both improves the peak spacing while also reducing the widths of the peaks. Separation mechanism models have been developed to describe the size-based mobility of DNA in the matrices. However, these models, as well as most experimental studies, generally ignore band broadening effects, which actually limit resolution for most separations. The narrow injection zones in microchips improve upon the broad injection plugs found in capillary-based separations. While injection plug widths dominate peak widths during capillary separations, microchips tend to be limited by analyte-wall interactions and electric field induced dispersion. Interestingly, different polymer matrix chemistries give rise to vastly different band broadening properties in the system. For example, we have shown that peaks are generally much wider in linear polyacrylamide based matrices (which are used ubiquitously in the literature) than in poly(N,N-dimethylacrylamide) matrices. In this report, we discuss both the physical and chemical properties of the polymer matrix along with the electrophoresis conditions that affect the widths of the analyte peaks during separation. Specifically, we show the quantitative effect of polymer and matrix physical properties on the DNA dispersion coefficients. Additionally, we explore the effect of wall coating chemistry on the peak widths as well and discuss the design of a DNA separation system to minimize band widths and maximize resolution for DNA separations.