Nanotechnology can be thought of as the science of well-structured materials and their components. DNA nanotechnology employs branched motifs to these ends. This effort has been quite successful, because the sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of B-DNA. The use of stable branched DNA molecules permits one to make stick-figures and topological targets. We have used this strategy to construct covalently closed DNA polyhedra, knots and Borromean rings.
We have constructed a DNA nanomechanical device by combining left-handed Z-DNA with right-handed B-DNA. The device consists of two DNA double crossover (DX) molecules connected by a piece of DNA that can be converted to Z-DNA. DX molecules contain two DNA double helices with parallel axes linked by Holliday-like crossovers. Atoms move between 20 and 60 Å when the device undergoes the transition.
A central goal of DNA nanotechnology is the self-assembly of periodic matter. We have constructed micron-sized 2-dimensional DNA arrays in three different motifs. In the first motif, we have used DX molecules that have been designed to tile the plane. We decorate the simple DX molecule with DNA hairpins that protrude from the plane of the 2-D array; these hairpins act as topographic labels that are visible when the array is visualized by atomic force microscopy (AFM). We can change the pattern by changing the components, and by modification after assembly. We have used triple crossover (TX) molecules decorated similarly to produce patterns in 2D crystals. TX molecules contain three coplanar helical domains linked in the same fashion as DX molecules. Rotation of TX molecules leads to different patterns in the AFM. In addition, we have generated arrays from parallelograms predicated on Holliday junction analogs. These parallelograms contain cavities whose sizes can be tuned by design. Although these arrays are periodic, it is also possible to program aperiodic assemblies that represent the results of logical operations. In contrast to periodic arrays, the competition to occupy a given site involves not only one correct tile and a number of completely incorrect tiles; rather some of the competitors are partially correct. We have performed two cumulative XOR operations, with very high fidelity.
This research has been supported by grants from NIGMS, ONR, NSF/DARPA and USAF.