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A nanomechanical device based on the B–Z transition of DNA

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Abstract

The assembly of synthetic, controllable molecular mechanical systems1,2,3,4,5,6,7 is one of the goals of nanotechnology. Protein-based molecular machines, often driven by an energy source such as ATP, are abundant in biology8,9. It has been shown previously that branched motifs of DNA can provide components for the assembly of nanoscale objects10, links11 and arrays12. Here we show that such structures can also provide the basis for dynamic assemblies: switchable molecular machines. We have constructed a supramolecular device consisting of two rigid DNA ‘double-crossover’ (DX) molecules connected by 4.5 double-helical turns. One domain of each DX molecule is attached to the connecting helix. To effect switchable motion in this assembly, we use the transition between the B and Z13,14 forms of DNA. In conditions that favour B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix. In Z-DNA-promoting conditions, however, these domains switch to opposite sides of the helix. This relative repositioning is detected by means of fluorescence resonance energy transfer spectroscopy, which measures the relative proximity of two dye molecules attached to the free ends of the DX molecules. The switching event induces atomic displacements of 20–60 Å.

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Figure 1: Design of the nanomechanical device.
Figure 2: FRET demonstration of nanomechanical motion.

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Acknowledgements

We thank S. Zhang for work done on previous systems, and D. Millar, N. Geacintov and R. Sheardy for advice and for the use of equipment. This work was supported by the Office of Naval Research, the National Institute of General Medical Sciences, the National Science Foundation/DARPA and the Information Directorate of the Air Force Research Laboratory (Rome, NY).

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  1. Department of Chemistry, New York University, New York, 10003, New York, USA

    Chengde Mao, Weiqiong Sun, Zhiyong Shen & Nadrian C. Seeman

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  1. Chengde Mao
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  2. Weiqiong Sun
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  3. Zhiyong Shen
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  4. Nadrian C. Seeman
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Correspondence to Nadrian C. Seeman.

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Mao, C., Sun, W., Shen, Z. et al. A nanomechanical device based on the B–Z transition of DNA. Nature 397, 144–146 (1999). https://doi.org/10.1038/16437

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