Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
DNA: Not Merely the Secret of Life
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. The sequence design of stable branched molecules is based on the notion of minimized sequence symmetry. 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 machine that prototypes the simplest features of the ribosome. Two protein-activated devices have been developed that can measure the ability of the protein to do work, and bipedal walkers, both clocked and autonomous have been built. We have also built a robust 3-state device that includes a state corresponding to a contraction.
One of the long-sought goals of nanotechnology has been the construction of molecular assembly lines. We have combined a DNA origami layer with three PX-based devices, so that there are eight different states represented by the arrangements of these 2-state devices; we have programmed a novel DNA walking device to pass these three stations. As a consequence of proximity, the devices add a cargo molecule to the walker. We have demonstrated that all eight products (including the null product) can be built from this system. More extensive origami systems could be used to make even more diverse and complex products. Most recently, we have used DNA origami in a diagnostic tool.
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 self-assembled a 3D crystalline array and have solved its crystal structure to 4 Å resolution, using traditional unbiased crystallographic methods. Nine other crystals have been designed following the same principles of sticky-ended cohesion. We can use crystals with two molecules in the crystallographic repeat to control the color of the crystals. Thus, structural DNA nanotechnology has fulfilled its initial goal of controlling the structure of matter in three dimensions. A new era in nanoscale control is beginning.
This research has been supported by grants GM-29554 from the National Institute of General Medical Sciences, CTS-0608889 and CCF-0726378 from the National Science Foundation, 48681-EL and W911NF-07-1-0439 from the Army Research Office, N000140910181 and N000140911118 from the Office of Naval Research and a grant from the W.M. Keck Foundation..
Nadrian C. Seeman
Department of Chemistry