Fig. 1. Design overview for A-form DX wireframe origami.

Starting with a target polyhedron and scaffold sequence as inputs, we algorithmically route the scaffold through the polyhedron and route and assign staple for I. edges with no scaffold crossover, II. edges with a scaffold crossover, III. vertices, and predict an atomic model structure. The basic routing scheme for edges with 4 helical turns is shown, scaffold in red and staples in grey. Using the calculated staple sequences, we can then fold the RNA scaffold into the target structure and characterize with gel mobility shift assays for preliminary folding evaluation, DMS-MaPseq or other RNA chemical probing method to evaluate base-pairing per nucleotide, and cryo-electron microscopy to evaluate overall structure formation.