DNA NANOTECHNOLOGY AS A ROUTE TO ENGINEERING MOLECULAR MECHANICAL DEVICES

Nadrian C. Seeman, Xiaoping Yang and Chengde Mao
Department of Chemistry, New York University, New York, NY 10003

Molecular mechanical devices have at least two requirements: 1) Component parts and 2) Mechanisms to get them to change their spatial relationship to one another. In recent years, we have spent a great deal of effort to construct potential components from unusual DNA motifs. DNA is an extremely favorable construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of B-DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct covalently closed DNA molecule whose helix axes have the connectivity of a cube, and a second molecule, whose helix axes have the connectivity of a truncated octahedron. In addition to branching topology, DNA also affords control of linking topology, because double helical half-turns of B-DNA or Z-DNA can be equated, respectively, with negative or positive crossings in topological objects. Consequently, we have been able to use DNA to make trefoil knots of both signs, figure-8 knots, and Borromean rings.

There are two prominent controllable isomerizations of the DNA molecule that can re-orient its component parts. One of these entails relocation of the branch point of the Holliday junction. We have demonstrated recently in a synthetic system that changing the torsional stress on two opposite arms of a Holliday-like junction can be used to control the position of the branch point. The other isomerization is the B-->Z transition. A simple device has been constructed using two rigid antiparallel double crossover molecules. We have preliminary evidence that we can use the B-->Z transition to change the distance between two pendent probes on this device, thus enabling a nanomechanical switch.

This research has been supported by grants from the National Institute of General Medical Sciences and the Office of Naval Research.