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High-speed DNA-based rolling motors powered by RNase H

Nature Nanotechnology volume 11, pages 184–190 (2016)Cite this article

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Abstract

DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next-generation sensors, drug-delivery platforms and biological computing. Despite their exquisite programmability, DNA-based walkers are challenging to work with because of their low fidelity and slow rates (∼1 nm min–1). Here we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three orders of magnitude greater than the maximum for conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridize to a surface modified with complementary RNA; the motion is achieved through the addition of RNase H, which selectively hydrolyses the hybridized RNA. The spherical motors can move in a self-avoiding manner, and anisotropic particles, such as dimerized or rod-shaped particles, can travel linearly without a track or external force. We also show that the motors can be used to detect single nucleotide polymorphism by measuring particle displacement using a smartphone camera.

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Figure 1: Approach used to generate RNA-fuelled, enzyme-catalysed autonomous DNA motors.
Figure 2: Characterization of particle motion driven by RNase H.
Figure 3: Elucidating the mechanism of particle motion and determining factors that influence particle velocity.
Figure 4: Directional motor translocation from self-avoiding to ballistic.
Figure 5: SNP detection with a smartphone microscope.

Change history

  • 10 December 2015

    In this Article, the wrong version of Fig. 1a was used. This error has now been corrected in all versions of the Article.

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Acknowledgements

K.S. is grateful for support from the National Institutes of Health through R01-GM097399, the Alfred P. Sloan Research Fellowship, the Camille–Dreyfus Teacher–Scholar Award and the National Science Foundation (NSF) CAREER Award (1350829). K.Y. thanks the ARCS Foundation for their support and V. Pui-Yan Ma for generating Fig. 1. We also thank S. Urazhdin for access to the thermal evaporator and M. Grover and D. Stabley for helpful discussions. E.R.W. was funded by the NSF (CMMI-1250235) and S.V. was funded by Emory University. This research project was supported in part by the Emory University Integrated Cellular Imaging Microscopy Core.

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Authors and Affiliations

  1. Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, 30322, Georgia, USA

    Kevin Yehl, Yang Liu, Yun Zhang, Mengzhen Fan & Khalid Salaita

  2. Department of Physics, Emory University, 400 Dowman Drive, Atlanta, 30322, Georgia, USA

    Andrew Mugler, Skanda Vivek & Eric R. Weeks

  3. Department of Physics, Purdue University, West Lafayette, 47907, Indiana, USA

    Andrew Mugler

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Contributions

K.Y. conducted all the experiments and analysis, A.M. performed the simulations and theoretical validation, S.V. helped in the data analysis and validation of the theoretical model, Y.Z. helped with particle functionalization, Y.L. collected SIM data, M.F. assisted with SNP detection, K.S. and K.Y. wrote the manuscript with input from A.M. and E.R.W., K.S. oversaw all the aspects of the work and E.R.W. supervised and discussed the experiments with S.V.

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Correspondence to Khalid Salaita.

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The authors declare no competing financial interests.

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Yehl, K., Mugler, A., Vivek, S. et al. High-speed DNA-based rolling motors powered by RNase H. Nature Nanotech 11, 184–190 (2016). https://doi.org/10.1038/nnano.2015.259

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