DNA Structural analysis was performed with the CURVES+ software. This software package is designed to evaluate 41 key structural features of DNA systems including intrabase and interbase pair parameters as well as groove parameters among others. The analysis was performed in several parts using approximately 1000 frames sampled at equidistant time intervals from each of the classical trajectories of the reduced wild-type, defect region 1, and defect region 2 systems. A global analysis of 146-base pairs was compared to an analysis in which the first and last 20 base pairs were removed in order to assess the impact of tail flexibility. Then, differences in structural parameter distributions between wild-type and defect systems were assessed. Finally, when differences between wild-type and defect systems were visually observable in the resulting distributions, a side-by-side comparison for four, equally-sized sections of the NCP systems was performed to evaluate how structural differences were localized across the NCP. The four 21 base pair sections of the NCP systems started from the 32nd base pair to the 52nd (section 1), the 53rd to the 73rd (section 2 and the region 1 defect section), the 74th to 94th (section 3 and the region 2 defect section), and 95th to the 115th base pair (section 4). At the classical level, the oxidized and reduced simulations of the same system differ only by one counter ion within the entire simulation box making the reduced and oxidized runs almost equivalent from a classical perspective. With this in mind, we chose to perform the structural analysis on only one of classical trajectories per system, in this case we chose reduced systems.