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Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat

Nature Nanotechnology volume 13, pages 723–729 (2018)Cite this article

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Abstract

Dynamic DNA nanotechnology has yielded nontrivial autonomous behaviours such as stimulus-guided locomotion, computation and programmable molecular assembly. Despite these successes, DNA-based nanomachines suffer from slow kinetics, requiring several minutes or longer to carry out a handful of operations. Here, we pursue the speed limit of an important class of reactions in DNA nanotechnology—toehold exchange—through the single-molecule optimization of a novel class of DNA walker that undergoes cartwheeling movements over a field of complementary oligonucleotides. After optimizing this DNA ‘acrobat’ for rapid movement, we measure a stepping rate constant approaching 1 s−1, which is 10- to 100-fold faster than prior DNA walkers. Finally, we use single-particle tracking to demonstrate movement of the walker over hundreds of nanometres within 10 min, in quantitative agreement with predictions from stepping kinetics. These results suggest that substantial improvements in the operating rates of broad classes of DNA nanomachines utilizing strand displacement are possible.

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Fig. 1: Principle and mechanism of a cartwheeling DNA walker.
Fig. 2: Single-molecule FRET characterization of walkers with varying toehold lengths.
Fig. 3: Characterization of 2D foothold arrays and long-range walker movement.

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Acknowledgements

This work was supported primarily by the US Department of Defense Army Research Office MURI award W911NF-12-1-0420 to N.G.W. and H.Y. The authors thank J. Damon Hoff for technical support, Z. R. Li for graphic design support, and B. Nijholt, E. Krieg, A. M. Bergman and W. Benjamin Rogers for discussions about DNA origami design.

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Author notes

  1. These authors contributed equally: Jieming Li, Alexander Johnson-Buck.

Authors and Affiliations

  1. Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA

    Jieming Li, Alexander Johnson-Buck & Nils G. Walter

  2. Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA

    Alexander Johnson-Buck & William M. Shih

  3. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA

    Alexander Johnson-Buck & William M. Shih

  4. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA

    Alexander Johnson-Buck & William M. Shih

  5. Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA

    Yuhe Renee Yang & Hao Yan

  6. School of Molecular Sciences, Arizona State University, Tempe, AZ, USA

    Yuhe Renee Yang & Hao Yan

Authors
  1. Jieming Li
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  2. Alexander Johnson-Buck
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  4. William M. Shih
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  6. Nils G. Walter
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Contributions

A.J.-B. conceived the ideas. Y.R.Y. designed, fabricated and characterized the DNA tile samples. W.M.S. and A.J.-B. designed, fabricated and characterized the DNA origami samples. J.L. and A.J.-B. performed smFRET and single-particle tracking measurements. J.L., A.J.-B., and N.G.W. analysed and interpreted the data. J.L. and A.J.-B. co-wrote the paper, and all authors discussed the results and edited the manuscript.

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Correspondence to Nils G. Walter.

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Supplementary Information

Supplementary Text, Supplementary Figures 1–34, Supplementary Tables 1–5 and Supplementary References

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Li, J., Johnson-Buck, A., Yang, Y.R. et al. Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat. Nature Nanotech 13, 723–729 (2018). https://doi.org/10.1038/s41565-018-0130-2

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