Dynamic DNA nanotechnology using strand-displacement reactions

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Abstract

The specificity and predictability of Watson–Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnology is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous molecular motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.

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Figure 1: DNA switches.
Figure 2: Logic gates and cascaded circuits64.
Figure 3: Complex dynamics (in this case, a limit cycle oscillator) with DNA strand-displacement reaction networks.
Figure 4: Controlling the self-assembly of DNA nanostructures with strand displacement74.
Figure 5: DNA amplification by non-covalent catalysis88.
Figure 6: An autonomous, processive and directional DNA walker based on strand displacement95.

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Acknowledgements

We thank E. Klavins, N. Pierce, N. Seeman, D. Soloveichik, E. Winfree and P. Yin for discussions. D.Y.Z. was supported by the Fannie and John Hertz Foundation, and is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation. G.S. is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and NSF CAREER award No. 0954566.

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Correspondence to David Yu Zhang or Georg Seelig.

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Zhang, D., Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chem 3, 103–113 (2011) doi:10.1038/nchem.957

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