Structural DNA nanotechnology uses the concept of reciprocal exchange between DNA double helices or hairpins to produce branched DNA motifs, like Holliday junctions, or related structures, such as double crossover (DX), triple crossover (TX), paranemic crossover (PX) and DNA parallelogram motifs. We combine DNA motifs to produce specific structures by using sticky-ended cohesion or by other interactions, such as PX cohesion. The key strength of sticky-ended cohesion is that it produces predictable adhesion combined with known structure. From branched junctions, we have constructed DNA stick-polyhedra, whose edges are double helices, and whose vertices are the branch points of DNA branched junctions. These include a cube, a truncated octahedron, and an irregular graph. This approach has also rendered accessible several topological targets, such as deliberately designed knots and Borromean rings. Recently, we have begun to template the topology of industrial polymers, such as nylon with DNA-like scaffolds.
Nanorobotics are key to the success of nanotechnology. To move in this direction, we have used two DX molecules to construct a DNA nanomechanical device by linking them with a segment that can be switched between left-handed Z-DNA with right-handed B-DNA. PX DNA has been used to produce a robust sequence-dependent device that changes states by varied hybridization topology. The sequence-dependent nature of this device means that a variety of them attached to a motif can all be addressed individually. Recently, we have constructed a protein-activated device that can be used to measure the ability of the protein to do work. A bipedal walker has also been built. Other devices are under construction.
A central goal of DNA nanotechnology is the self-assembly of periodic matter. We have constructed micron-sized 2-dimensional DNA arrays from DX, TX and two kinds of parallelogram motifs. We can produce specific designed patterns visible in the AFM from DX and TX molecules. We can change the patterns by changing the components, and by modification after assembly. In addition, we have generated 2D arrays from DNA parallelograms. These arrays contain cavities whose sizes can be tuned by design. Recently, we have used new motifs to produce honeycomb-shaped arrays.
The key challenge in the area is the extension of the 2D results obtained so far to 3D systems with a high degree of ordering. Several motifs have been produced that can produce 2D arrays in each of the three directions normal to the vectors that span the 3D space. Crystals with dimensions as large as a millimeter, ordered to 10 Å resolution (as determined by X-ray diffraction) have been produced. Ultimately, we expect to be able to produce high resolution crystals of DNA host lattices with heterologous guests, leading to well-ordered bio-macromolecular systems amenable to diffraction analysis. Other challenges are to incorporate DNA nanomechanical devices in periodic and aperiodic lattices and to use the lattices to organize nanoelectronic components, such as metallic nanoparticles or carbon nanotubes.