DNA nanotechnology uses reciprocal exchange between DNA double helices or hairpins to produce branched DNA motifs or related structures. Some of these motifs are simple branched junctions, but other motifs represent more complex strand topologies, with greater structural integrity. In addition to branched junctions, we have found double crossover (DX), triple crossover (TX), paranemic crossover (PX) and parallelogram motifs to be of great utility. The sequences of these unusual motifs are designed by an algorithm that attempts to minimize sequence symmetry. We combine DNA motifs by sticky-ended cohesion, an interaction of DNA that occurs with high specificity, and that results in the formation of B-DNA; these properties make sticky-ended cohesion an outstanding means of exploiting molecular recognition, because not only is affinity guaranteed, but the local product structure is also known at the joining point. From simple branched junctions, we have constructed DNA stick-polyhedra, such as a cube and a truncated octahedron, a series of knots, and Borromean rings. 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 and a variant, JX2 DNA have been used to produce a robust sequence-dependent device (illustrated); sequence-dependent devices can provide the diversity of structures necessary for nanorobotics.
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 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 of the components after assembly. In addition, we have generated 2D arrays from DNA parallelograms. These arrays contain cavities whose sizes can be tuned by design. We have generated DNA 6-helix bundles that cohere readily to form 1D constructs over a micron long. In addition to specific periodic self-assembly, we have performed algorithmic constructions, corresponding to XOR operations.
This research has been supported by grants from the NIGMS, ONR, DARPA, NSF and USAF.