Figure 8.

Two typical structures named ‘Stack’ and ‘Kink’ observed in the 30 lowest-energy structures. Two NCD molecules are shown as a sphere model (VDW scale is 0.8). DNA strands are shown by the line. The coloring of atoms is as follows; H = white, C = light green, N = blue, O = red. (A) The enlarged view of the state 1 structure, shown as a typical example of ‘Stack’ structure, where the base pairs are well stacked at the step between the G6-NP and NP-G17. (B) The enlarged view of state 2 structure, shown as an example of ‘Kink’ structure, where an apparent stacking defect is observed at the step between the G6-NP and NP-G17 pairs.