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Direct observation of stepwise movement of a synthetic molecular transporter

Nature Nanotechnology volume 6, pages 166–169 (2011)Cite this article

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Abstract

Controlled motion at the nanoscale can be achieved by using Watson–Crick base-pairing to direct the assembly and operation of a molecular transport system consisting of a track, a motor1,2,3,4,5,6,7,8,9,10,11,12 and fuel13,14,15, all made from DNA. Here, we assemble a 100-nm-long DNA track on a two-dimensional scaffold16, and show that a DNA motor loaded at one end of the track moves autonomously and at a constant average speed along the full length of the track, a journey comprising 16 consecutive steps for the motor. Real-time atomic force microscopy allows direct observation of individual steps of a single motor, revealing mechanistic details of its operation. This precisely controlled, long-range transport could lead to the development of systems that could be programmed and routed by instructions encoded in the nucleotide sequences of the track and motor. Such systems might be used to create molecular assembly lines modelled on the ribosome.

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Figure 1: DNA motor and track.
Figure 2: Fluorescence measurements of movement on intact and broken tracks.
Figure 3: Observation of motor movement by AFM.
Figure 4: AFM observation of discrete steps of a single motor molecule.

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References

  1. Shin, J-S. & Pierce, N. A. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–10835 (2004).

    Article  CAS  Google Scholar 

  2. Sherman, W. B. & Seeman, N. C. A precisely controlled DNA biped walking device. Nano Lett. 4, 1203–1207 (2004).

    Article  CAS  Google Scholar 

  3. Tian, Y. & Mao, C. A pair of DNA circles continuously rolls against each other. J. Am. Chem. Soc. 126, 11410–11411 (2004).

    Article  CAS  Google Scholar 

  4. Yin, P., Yan, H., Daniell, X. G., Turberfield, A. J. & Reif, J. H. A unidirectional DNA walker that moves autonomously along a DNA track. Angew. Chem. Int. Ed. 43, 4906–4911 (2004).

    Article  CAS  Google Scholar 

  5. Tian, Y., He, Y., Peng, Y. & Mao, C. A DNA enzyme that walks processively and autonomously along a one-dimensional track. Angew. Chem. Int. Ed. 44, 4355–4358 (2005).

    Article  CAS  Google Scholar 

  6. Bath, J., Green, S. J. & Turberfield, A. J. A free-running DNA motor powered by a nicking enzyme. Angew. Chem. Int. Ed. 44, 4358–4361 (2005).

    Article  CAS  Google Scholar 

  7. Pei, R. et al. Behaviour of polycatalytic assemblies in a substrate-displaying matrix. J. Am. Chem. Soc. 128, 12693–12699 (2006).

    Article  CAS  Google Scholar 

  8. Venkataraman, S., Dirks, R. M., Rothemund, P. W. K., Winfree, E. & Pierce, N. A. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotech. 2, 490–494 (2007).

    Article  Google Scholar 

  9. Yin, P., Choi, H. M., Calvert, C. R. & Pierce, N. A. Programming biomolecular self-assembly pathways. Nature 451, 318–322 (2008).

    Article  CAS  Google Scholar 

  10. Green, S. J., Bath, J. & Turberfield, A. J. Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys. Rev. Lett. 101, 238101 (2008).

    Article  CAS  Google Scholar 

  11. Bath, J. Green, S. J., Allen, K. E. & Turberfield, A. J. Mechanism for a directional, processive and reversible DNA motor. Small 5, 1513–1516 (2009).

    Article  CAS  Google Scholar 

  12. Omabegho, T., Sha, R. & Seeman, N. C. A bipedal Brownian motor with coordinated legs. Science 324, 67–71 (2009).

    Article  CAS  Google Scholar 

  13. Turberfield, A. J. et al. DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003).

    Article  CAS  Google Scholar 

  14. Bois, J. S. et al. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res. 33, 4090–4095 (2005).

    Article  CAS  Google Scholar 

  15. Green, S. J., Lubrich, D. & Turberfield, A. J. DNA hairpins: fuel for autonomous DNA devices. Biophys. J. 91, 2966–2975 (2006).

    Article  CAS  Google Scholar 

  16. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  Google Scholar 

  17. Antal, T. & Krapivsky, P. L. Molecular spiders with memory. Phys. Rev. E 76, 021121 (2007).

    Article  Google Scholar 

  18. Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–210 (2010).

    Article  CAS  Google Scholar 

  19. Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009).

    Article  CAS  Google Scholar 

  20. Heiter, D., Lunnen, K. D. & Wilson, G. G. Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI. J. Mol. Biol. 348, 631–640 (2005).

    Article  CAS  Google Scholar 

  21. Yurke, B., Turberfield, A. J., Mills, A. P. Jr, Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    Article  CAS  Google Scholar 

  22. Yurke, B. & Mills, A. P. Jr. Using DNA to power nanostructures. Genet. Program. Evol. Mach. 4, 111–122 (2003).

    Article  Google Scholar 

  23. Ando, T. et al. High-speed atomic force microscope for studying biological macromolecules. Proc. Natl Acad. Sci. USA 98, 12468–12472 (2001).

    Article  CAS  Google Scholar 

  24. Endo, M., Katsuda, Y., Hidaka, K. & Sugiyama, H. Regulation of DNA methylation using different tensions in the double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 132, 1592–1597 (2010).

    Article  CAS  Google Scholar 

  25. Endo, M., Sugita, T., Katsuda, Y., Hidaka, K. & Sugiyama, H. Programmed-assembly system using DNA jigsaw pieces. Chem. Eur. J. 16, 5362–5368 (2010).

    Article  CAS  Google Scholar 

  26. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).

    Article  CAS  Google Scholar 

  27. Gu, H., Chao, J., Xiao, S. J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–205 (2010).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the Engineering and Physical Sciences Research Council (EP/G037930/1), the Clarendon Fund, the Oxford–Australia Scholarship Fund, the CREST of JST and a Grant-in-Aid for Science Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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Authors and Affiliations

  1. Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK

    Shelley F. J. Wickham, Jonathan Bath & Andrew J. Turberfield

  2. Institute for Integrated Cell–Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan

    Masayuki Endo & Hiroshi Sugiyama

  3. Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo, 102-0075, Japan

    Masayuki Endo & Hiroshi Sugiyama

  4. Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan

    Yousuke Katsuda, Kumi Hidaka & Hiroshi Sugiyama

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  1. Shelley F. J. Wickham
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  2. Masayuki Endo
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  3. Yousuke Katsuda
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Contributions

Experiments were designed by S.W. with input from J.B. and A.J.T. Ensemble fluorescence experiments were carried out by S.W in the laboratory of A.J.T. Real-time AFM experiments were done by S.W., M.E., Y.K. and K.H in the laboratory of H.S. The manuscript was written by S.W., J.B., H.S. and A.J.T.

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Correspondence to Hiroshi Sugiyama or Andrew J. Turberfield.

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The authors declare no competing financial interests.

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Wickham, S., Endo, M., Katsuda, Y. et al. Direct observation of stepwise movement of a synthetic molecular transporter. Nature Nanotech 6, 166–169 (2011). https://doi.org/10.1038/nnano.2010.284

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