Fig. 7.

A tectosquare built out of MD states of four kissing loop models and one MD state of the L-shaped monomer used four times. (A) The KL states come from the following points in their respective trajectories: A1D2 – 4.0 ns, A2B1 – 4.5 ns, B2C1 – 18.9 ns, and C2D1 – 1.8 ns. Listed under each KL label are the actual KL torsion angles measured for each of them. The MD state of the L-shaped monomer comes from the 3.2 ns point in its trajectory. The color-coded KL fragments were truncated for display purposes to include only the two base pairs closest to the interacting hairpin loops, which were used as reference points in a chain-fitting of the building blocks together. The last KL in this procedure, C2D1, was fit to the monomer C and the gap between the KL and the D monomer was used as a measure of the overall closure quality. The gap distances were measured for the corresponding KL complex’s and L-shaped monomer’s 5′ and 3′-side P atoms of the second base pairs from the KL’s H-loops (L-KL interface points). A perfect fit would measure 0 Å for both gaps. The RMSD values of each fit in the chain assembly are listed next to each side of every KL. (B) A plot of the KL bending angle (red) and the KL torsion angle (black) in the MD simulation of the KL complex B2C1. A point in the trajectory corresponding to 18.917 ns is marked with the blue vertical line for which the KL bending angle is 177.9° and the KL torsion angle is 17.4°. This MD state was used as one of the kissing loops yielding the closed full tectosquare shown in (A).