Figure 2.

Multiresolution structural relaxation of a curved DNA origami object. (A) Cadnano (45) design of a curved six-helix bundle. A regular pattern of insertions (blue loops) in the two helices on the left and deletions (red crosses) in the two helices on the right induce the curvature (56). (B–D) Low-resolution CG simulation of the bundle. In just 40 nanoseconds, the bundle adopts a curved conformation. The bundle is shown using a bead-and-stick representation, where each bead represents 5 bp, on average. (E and F) High-resolution CG simulations of the bundle. A spline-based mapping procedure yields a high-resolution (2 beads per base pair) model by interpolation. The high-resolution model includes a local representation of each base pair’s orientation (teal beads). The twist dihedral angle potential between adjacent orientation beads is smoothly truncated to allow the linking number to relax during a brief, 10 ns simulation (E). A subsequent 10 ns simulation performed without the truncation of the twist potential allows complete relaxation of the bundle (F). (G) Resulting atomic model of the curved six-helix bundle. Canonical base pairs are placed throughout the structure using the spline-based mapping procedure. The images below each of the three CG simulation steps illustrate schematically how the model represents one turn of DNA.