Figure 1: 3D structure-prediction procedure for two exemplary designs.
From: Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
(a) Topological routing of DNA strands shown in different colors with arrowheads representing the 3′ ends. (b) The topological routing is subsequently divided into interconnected four-way junctions. (c) These junctions are input as the initial configuration of the finite element model generated. Connectivities between junctions are shown as dashed lines. For example, duplex end A connects A′, and B connects B′. Initial junction configurations are parameterized by a scissor-like interhelical angle Jtwist and junction twist angle stiffness ktwist. (d) Final solution structures computed from their initial, stress-free configurations. Finite element models are visualized using corresponding atomic models generated using DNA strands colored the same as in their topological representations. Scale bars are 2 nm.
