Base-pair step configurations are sampled from all-atom molecular dynamics (MD) simulations run with Amber 20 using the BSC1 force field . Ten initial B-DNA 12-mer structures representing the ten unique combinations of base-pair steps were each placed in a periodic truncated octahedral box with a 10 Å buffer and solvated with flexible SPC/E water . Note that flexible SPC/E water was used instead of TIP3P water to more realistically sample interacting DNA-solvent geometries.