Nanotechnology is the science of well-structured materials and their components. To this end, DNA nanotechnology uses reciprocal exchange between DNA double helices or hairpins to produce branched DNA motifs or related structures. Some of these motifs are straightforward branched junctions, but other motifs represent more complex strand topologies, whose structural integrity is greater than that of simple branches. In addition to conventional and Bowtie branched junctions, we have found double crossover (DX), triple crossover (TX), paranemic crossover (PX) and parallelogram motifs to be of great utility. We have combined these motifs by sticky-ended cohesion, an interaction of DNA molecules that occurs with high specificity, and that results in the formation of B-DNA.
From simple branched junctions, we have constructed DNA stick-polyhedra, knots and Borromean rings. We have used two DX molecules to construct a DNA nanomechanical device by linking them a segment that can be switched between left-handed Z-DNA with right-handed B-DNA. PX DNA also leads to a functional mechanical devices that are sequence-dependent.
A central goal of DNA nanotechnology is the self-assembly of periodic matter. We have produced 1D arrays from DNA triangles and from six-helix bundles based on DX molecules. 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 after assembly. In addition, we have generated both 1D and 2D arrays from conventional and Bowtie parallelograms. These arrays contain cavities whose sizes can be tuned by design. These arrays can be used analytically to measure flexible angles between helical domains. In addition to specific periodic self-assembly, recently we have performed algorithmic constructions, corresponding to XOR operations.