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. 2017 May 8;45(11):6284–6298. doi: 10.1093/nar/gkx378

Figure 3.

Figure 3.

Equilibrium structures of the polyhedral nanoparticles generated by the FE framework and the MD simulations. (A) Four aligned snapshots at 25, 50, 75, and 100 ns of the MD trajectory of the tetrahedron. (B) The snapshot at 25 ns of the tetrahedron with vertices with the absence and presence of interactions between unpaired bases termed as ‘open vertices’ and ‘closed vertices’, respectively. (C) Four snapshots at 25, 50, 75, and 100 ns of the MD trajectory of the octahedron are rendered in the same way as in (a). (D) The snapshot at 25 ns of the octahedron. (E) The distribution of the twist-angle, bow-angle, and radial vacancy during the MD simulations of the tetrahedral and octahedral nanoparticles. Each angle is averaged over the four vertices of the tetrahedron or the six vertices of the octahedron. Solid lines indicate the mean value during the MD trajectory and dashed lines indicate the value obtained from the ground-state FE model. (F–J) FE equilibrium structures, colored in blue, of (F) the tetrahedron, (G) the octahedron, (H) the icosahedron, (I) the cuboctahedron, and (J) the reinforced cube were fit into the reconstructed cryo-EM map using the software UCSF Chimera (91). All scale bars are 5 nm.