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This method involves determining the structure’s geometry based on an inputted 3D polyhedral or 2D polygonal shape. Once the shape is inputted, the process continues by identifying a route for a single-stranded RNA scaffold to trace throughout the desired shape. The process concludes by generating the sequences of the scaffold strand and optionally the nucleic acid sequence of the “staple strands”—the short strands which guide the folding of the scaffold into the desired shape. Identifying the route of the scaffold requires a multi-step process involving creating a spanning tree, which establishes connectivity between each vertex in the nanostructure. This spanning tree can be used to calculate a Euler circuit (a trail in a graph which visits every edge exactly once) to represent the path the scaffold traces. Nanostructures produced through this process may also contain a molecule such as a peptide nucleic acid (PNA), protein, lipid, etc. bound to or encapsulated within the structure.