Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A robust DNA mechanical device controlled by hybridization topology

Abstract

Controlled mechanical movement in molecular-scale devices has been realized in a variety of systems—catenanes and rotaxanes1,2,3, chiroptical molecular switches4, molecular ratchets5 and DNA6—by exploiting conformational changes triggered by changes in redox potential or temperature, reversible binding of small molecules or ions, or irradiation. The incorporation of such devices into arrays7,8 could in principle lead to complex structural states suitable for nanorobotic applications, provided that individual devices can be addressed separately. But because the triggers commonly used tend to act equally on all the devices that are present, they will need to be localized very tightly. This could be readily achieved with devices that are controlled individually by separate and device-specific reagents. A trigger mechanism that allows such specific control is the reversible binding of DNA strands, thereby ‘fuelling’ conformational changes in a DNA machine9. Here we improve upon the initial prototype system that uses this mechanism but generates by-products9, by demonstrating a robust sequence-dependent rotary DNA device operating in a four-step cycle. We show that DNA strands control and fuel our device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA10,11 and its topoisomer JX2 DNA, in which one strand end is rotated relative to the other by 180°. We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Schematic drawings of the device.
Figure 2: Gel evidence for the operation of the device.
Figure 3: A highly simplified representation of the system used.
Figure 4: Evidence for the operation of the device, obtained from atomic force microscopy (AFM).

References

  1. Pease, A. R. et al. Switching devices based on interlocked molecules. Acc. Chem. Res. 34, 433–444 (2001).

    CAS  Article  Google Scholar 

  2. Jimenez, M. C., Dietrich-Buchecker, C. & Sauvage, J.-P. Towards synthetic molecular muscles: contraction and stretching of a linear-rotaxane dimer. Angew. Chem. Int. Edn Engl. 39, 3284–3287 (2000).

    CAS  Article  Google Scholar 

  3. Brouwer, A. M. et al. Photoinduction of fast, reversible translational motion in a hydrogen-bonded molecular shuttle. Science 291, 2124–2128 (2001).

    ADS  CAS  Article  Google Scholar 

  4. Koumura, N., Zijlstra, R. W. J., van Delden, R. A., Harada, N. & Feringa, B. L. Light-driven monodirectional molecular rotor. Nature 401, 152–155 (1999).

    ADS  CAS  Article  Google Scholar 

  5. Kelly, T. R., De Silva, H. & Silva, R. A. Unidirectional rotary motion in a molecular system. Nature 401, 150–152 (1999).

    ADS  CAS  Article  Google Scholar 

  6. Mao, C., Sun, W., Shen, Z. & Seeman, N. C. A DNA nanomechanical device based on the B-Z transition. Nature 397, 144–146 (1999).

    ADS  CAS  Article  Google Scholar 

  7. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).

    ADS  CAS  Article  Google Scholar 

  8. LaBean, T. H. et al. The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000).

    CAS  Article  Google Scholar 

  9. 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).

    ADS  CAS  Article  Google Scholar 

  10. Seeman, N. C. DNA nicks and nodes and nanotechnology. Nano Lett. 1, 22–26 (2001).

    ADS  CAS  Article  Google Scholar 

  11. Shen, Z. DNA Polycrossover Molecules and their Applications in Homology Recognition. Thesis, New York Univ. (1999).

    Google Scholar 

  12. Fu, T.-J. & Seeman, N. C. DNA double crossover structures. Biochemistry 32, 3211–3220 (1993).

    CAS  Article  Google Scholar 

  13. Seeman, N. C. De novo design of sequences for nucleic acid structure engineering. J. Biomol. Struct. Dyn. 8, 573–581 (1990).

    CAS  Article  Google Scholar 

  14. Caruthers, M. H. Gene synthesis machines: DNA chemistry and its uses. Science 230, 281–285 (1985).

    ADS  CAS  Article  Google Scholar 

  15. Sun, W., Mao, C., Iwasaki, H., Kemper, B. & Seeman, N. C. No braiding of Holliday junctions in positively supercoiled DNA molecules. J. Mol. Biol. 294, 683–699 (1999).

    CAS  Article  Google Scholar 

  16. Yang, X., Wenzler, L. A., Qi, J., Li, X. & Seeman, N. C. Ligation of DNA triangles containing double crossover molecules. J. Am. Chem. Soc. 120, 9779–9786 (1998).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank R. Sha for discussions. This work was supported by the Office of Naval Research, the National Institute of General Medical Sciences, the National Science Foundation/DARPA, the Information Directorate of the Air Force Research Laboratory located at Rome, New York, and the National Science Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nadrian C. Seeman.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Yan, H., Zhang, X., Shen, Z. et al. A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002). https://doi.org/10.1038/415062a

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/415062a

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing