Prior to MD production runs, structures were first minimized then allowed to heat up from 0 K to 300 K for 40 ps. Production runs were done with the NPT ensemble at 300 K. We ran three 50 ns simulations with different starting trajectories for a total simulation time of 150 ns. Snapshots from these simulations were taken every 2 ps, and all atoms were stripped away apart from the central two base pairs (Fig. ). Dangling bonds were capped with hydrogens. To ensure representative sampling of the DNA configurational space, snapshots were processed using K-means clustering with a cluster size of five and a metric of distance-RMSD. The samples closest to the cluster centers were included in the training data. Given that there are four DNA bases (A, C, G, and T) and taking directionality into account, there are a total of ten unique combinations of base pair steps, requiring ten independent 12-mer molecular dynamics runs.