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Problem Addressed

The field of DNA nanotechnology has been vastly expanded in recent years allowing target shapes to be programmed from the bottom-up using complementary Watson-Crick base pairing. For instance, scaffolded DNA origami is a powerful means of creating structured DNA assemblies, but it requires complex scaffold routing and staple design to realize a limited scope of target geometries. Furthermore, only one previous approach offers a solution to the inverse problem of sequence design based on specification of target geometry, but it is only semi-automated and relies on single duplex DNA arms and multi-junctions to represent polyhedral geometries, which may result in compliant and unstable assemblies that are unsuitable for many applications. This invention is a top-down design algorithm for programming arbitrary 3D geometries using DNA.