Figure 14.

An example of melting for a 2-base toehold. As before, the blue strand is the substrate, the red is the incumbent and the green is the invading strand. (A) Both base pairs of the toehold (shown in gold) are formed. (B) One base pair (shown in black) is broken, and one (gold) remains. (C) Both base pairs (black) are broken. (D) Plots of hydrogen bonding and stacking site separation during this detachment, demonstrating the relatively minor disruption of interstrand stacking (only the stacking between incumbent and invading strand is disrupted) and rearrangement of structure necessary, and the proximity of the transition state to the fully bound state. The relevant distances for the stacking interactions are shown in (A), and for the hydrogen-bonding in (B). (A), (B) and (C) correspond to times of 175, 204 and 210 ps on the trajectory shown in (D). In this case, the system first breaks the intrastrand stack ST4, followed by base pairs HB1 and HB2. Trajectories with different orders are also observed.