Structural DNA nanotechnology is based on using stable branched DNA motifs, like the 4-arm Holliday junction, or related structures, such as double crossover (DX), triple crossover (TX), and paranemic crossover (PX) motifs. We have been working since the early 1980's to combine these DNA motifs to produce target species. From branched junctions, we have used ligation to construct DNA stick-polyhedra and topological targets, such as Borromean rings. Branched junctions with up to 12 arms have been produced. We have also built DNA nanotubes with lateral interactions.

Nanorobotics is a key area of application. PX DNA has been used to produce a robust 2-state sequence-dependent device that changes states by varied hybridization topology. We have used this device to make a translational device that prototypes the simplest features of the ribosome. A protein-activated device that can be used to measure the ability of the protein to do work, and a bipedal walker have both been built. We have also built a robust 3-state device.

A central goal of DNA nanotechnology is the self-assembly of periodic matter. We have constructed 2-dimensional DNA arrays from many different motifs. We can produce specific designed patterns visible in the AFM. We can change the patterns by changing the components, and by modification after assembly. Recently, we have used DNA scaffolding to organize active DNA components, as well as other materials. Active DNA components include DNAzymes and DNA nanomechanical devices; both are active when incorporated in 2D DNA lattices.