(A) CopA–CopT sequence and the dot-bracket representation (interaction in orange) of the constrained 2D path (full 2D path in Supplemental Fig. S1). (B) Two representative starting clusters with very different 3D conformations. CopA is shown in green, CopT in blue, and the interaction region in orange. (C) Summary of simulation results for nstep = 5000: Each column of the heatmap represents one extension step (defined by the length of the interaction constraint). Each column shows the histogram of observed interaction lengths (blue color gradient). In the first two extension steps, most structures retain the initial interaction length of 3 bp; 6 bp interactions become prevalent in the last extension step. The last row (purple) reports, for every extension step, the percentage of the (originally) 50 runs that successfully extended in all previous steps (i.e., passed checkpoint [e3]) and are still active. Thus, in the second extension step (constraint length 5), only 44% of runs manage to extend the interaction and proceed to the next extension step (7 bp). Only 18% of the runs reach the final extension step (9 bp), and none of these extends even further.
