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A stochastic DNA walker that traverses a microparticle surface

Nature Nanotechnology volume 11, pages 157–163 (2016)Cite this article

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Abstract

Molecular machines have previously been designed that are propelled by DNAzymes1,2,3, protein enzymes4,5,6 and strand displacement7,8,9. These engineered machines typically move along precisely defined one- and two-dimensional tracks. Here, we report a DNA walker that uses hybridization to drive walking on DNA-coated microparticle surfaces. Through purely DNA:DNA hybridization reactions, the nanoscale movements of the walker can lead to the generation of a single-stranded product and the subsequent immobilization of fluorescent labels on the microparticle surface. This suggests that the system could be of use in analytical and diagnostic applications, similar to how strand exchange reactions in solution have been used for transducing and quantifying signals from isothermal molecular amplification assays10,11. The walking behaviour is robust and the walker can take more than 30 continuous steps. The traversal of an unprogrammed, inhomogeneous surface is also due entirely to autonomous decisions made by the walker, behaviour analogous to amorphous chemical reaction network computations12,13, which have been shown to lead to pattern formation14,15,16,17.

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Figure 1: Schematic and proof-of-concept for CHA on microparticles.
Figure 2: Double catalyst walking behaviour detected with flow cytometry.
Figure 3: Interpretation of walking behaviour with numerical simulation.
Figure 4: Fluorescence microscopy of CHA on microparticles.
Figure 5: Amplification of miRNA detection using a walker.

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Acknowledgements

This work was funded by the National Institutes of Health (EUREKA, 1-R01-GM094933), The Welch Foundation (F-1654) and a National Security Science and Engineering Faculty Fellowship (FA9550-10-1-0169). The authors also acknowledge D. Stefanovic for his helpful discussion of the modelling system.

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  1. C. Jung and P. B. Allen: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, 78712, Texas, USA

    C. Jung, P. B. Allen & A. D. Ellington

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  1. C. Jung
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Contributions

C.J. and P.B.A. conceived the walker scheme. C.J. performed most of the experiments. P.B.A. carried out a fluorescence microscopy experiment and performed modelling and analysis. A.D.E. supervised the project. C.J., P.B.A. and A.D.E. wrote the manuscript.

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Correspondence to A. D. Ellington.

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The authors declare no competing financial interests.

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Jung, C., Allen, P. & Ellington, A. A stochastic DNA walker that traverses a microparticle surface. Nature Nanotech 11, 157–163 (2016). https://doi.org/10.1038/nnano.2015.246

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