Abstract: Described herein is a 3D nanoscale building platform. The platform is based on cube-shaped DNA nanostructures that are rigid enough to preserve cubic shape. Different cubes are connected together through complementary overhangs. We have developed a computational design algorithm that finds the smallest number of different cube types required to self-assemble target 3D shape. Each cube can be functionalized by attaching a cargo inside of it or adjacent to it (e.g., gold nanoparticles, carbon nanotubes, proteins, etc.) and can thus be used as a “scaffold” to construct arbitrary shapes in 3D from individual nanoscale building blocks. The final assembly can be a 3D periodic lattice, or a finite-sized object. From our simulation-designed cubes, we export to an experimental blueprint, where the strands and interactions between them are designed to self-assemble into a target shape.

Abstract: A computer-implemented system uses multiscale modeling and optimization algorithms to design DNA nanostructures that self-assemble into a target structure, such as a tetrastack lattice. The system converts a target structure into a Boolean Satisfiability problem and models nanostructure units as “patchy” nanostructure models, where patches encode kinetic properties that affect how each nanostructure model connects with other nanostructure models. The system iteratively simulates self-assembly of a plurality of nanostructure models into a nanostructure assembly model, and compares the nanostructure assembly model with the target structure to determine a set of optimal parameters (such as patch type assignments) for the nanostructure units that reliably result in self-assembly into the target structure.