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 DNA-fuelled molecular machine made of DNA

Abstract

Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles1,2, and DNA templates can direct the growth of semiconductor nanocrystals3 and metal wires4. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles5, linked rings6 and polyhedra7. The construction of active devices is also possible—for example, a nanomechanical switch8, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption9, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes10,11,12,13. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as ‘fuel’. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of ‘fuel’ DNA; each cycle produces a duplex DNA waste product.

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: Oligonucleotide sequences.
Figure 2: Construction and operation of the molecular tweezers.
Figure 3: Cycling the molecular tweezers.
Figure 4: Analysis of tweezer formation by polyacrylamide gel electrophoresis.

References

  1. Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607– 609 (1996).

    ADS  CAS  Article  Google Scholar 

  2. Alivisatos, A. P. et al. Organization of ‘nanocrystal groups’ using DNA. Nature 382, 609–611 (1996).

    ADS  CAS  Article  Google Scholar 

  3. Coffer, J. L. et al. Dictation of the shape of mesoscale semiconductor nanoparticle assemblies by plasmid DNA. Appl. Phys. Lett. 69, 3851–3853 (1996).

    ADS  CAS  Article  Google Scholar 

  4. Braun, E., Eichen, Y., Sivan, U. & Ben-Yoseph, G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature 391, 775–778 ( 1998).

    ADS  CAS  Article  Google Scholar 

  5. 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 

  6. Mao, C., Sun, W. & Seeman, N. C. Assembly of Borromean rings from DNA. Nature 386, 137–138 ( 1997).

    ADS  CAS  Article  Google Scholar 

  7. Chen, J. & Seeman, N. C. Synthesis from DNA of a group with the connectivity of a cube. Nature 350, 631–633 (1991).

    ADS  CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  9. Asanuma, H., Ito, T., Yoshida, T., Liang, X. & Komiyama, M. Photoregulation of the formation and dissociation of a DNA duplex by using the cis-trans isomerization of azobenzene. Angew. Chem. Int. Edn Engl. 38, 2393– 2395 (1999).

    CAS  Article  Google Scholar 

  10. Porta, H. & Lizardi, P. M. An allosteric hammerhead ribozyme. Biotechnology 13, 161– 164 (1995).

    CAS  PubMed  Google Scholar 

  11. Tang, J. & Breaker, R. R. Rational design of allosteric ribozymes. Chem. Biol. 4, 453– 459 (1997).

    CAS  Article  Google Scholar 

  12. Araki, M., Okuno, O., Hara, Y. & Sugiura, Y. Allosteric regulation of a ribozyme activity through ligand-induced conformational change. Nucleic Acids Res. 26, 3379–3384 (1998).

    CAS  Article  Google Scholar 

  13. Robertson, M. P. & Ellington, A. D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nature Biotechnol. 17, 62– 66 (1999).

    CAS  Article  Google Scholar 

  14. Smith, S. B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA groups by using magnetic beads. Science 258, 1122–1126 (1992).

    ADS  CAS  Article  Google Scholar 

  15. Manning, G. S. A procedure for extracting persistence lengths from light-scattering data on intermediate molecular weight DNA. Biopolymers 20 , 1751–1755 (1981).

    CAS  Article  Google Scholar 

  16. Smith, S. B., Yujia, C. & Bustamante, C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA groups. Science 271, 795–799 (1996).

    ADS  CAS  Article  Google Scholar 

  17. Stryer, L. & Haugland, R. P. Energy transfer: a spectroscopic ruler. Proc. Natl Acad. Sci. USA 58, 719 –726 (1967).

    ADS  CAS  Article  Google Scholar 

  18. Heller, M. J. & Morrison, L. E. in Rapid Detection and Identification of Infectious Agents (eds Kingsbury, D. T. & Falkow, S.) 245 –256 (Academic, New York, 1985).

    Google Scholar 

  19. SantaLucia, J. Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95, 1460–1465 ( 1998).

    ADS  CAS  Article  Google Scholar 

  20. Record, M. T. Jr, Anderson, C. F. & Lohman, T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11, 103– 178 (1978).

    CAS  Article  Google Scholar 

  21. Bockelmann, U., Essevaz-Roulet, B. & Heslot, F. Molecular stick-slip motion revealed by opening DNA with piconewton forces. Phys. Rev. Lett. 79, 4489–4492 (1997).

    ADS  CAS  Article  Google Scholar 

  22. Svoboda, K., Schmidt, C. F., Schnapp, B. J. & Block, S. M. Direct observation of kinesin stepping by optical trapping interferometry. Nature 365, 721–727 (1993).

    ADS  CAS  Article  Google Scholar 

  23. Kuo, S. C. & Sheetz, M. P. Force of single kinesin groups measured with optical tweezers. Science 260, 232–234 (1993).

    ADS  CAS  Article  Google Scholar 

  24. Finer, J. T., Simmons, R. M. & Spudich, J. A. Single myosin group mechanics: piconewton forces and nanometre steps. Nature 368, 113– 119 (1994).

    ADS  CAS  Article  Google Scholar 

  25. Ishijima, A. et al. Single-group analysis of the actomyosin motor using nano-manipulation. Biochem. Biophys. Res. Commun. 199, 1057 –1063 (1994).

    CAS  Article  Google Scholar 

  26. Green, C. & Tibbetts, C. Reassociation rate limited displacement of DNA strands by branch migration. Nucleic Acids Res. 9, 1905–1918 (1981).

    CAS  Article  Google Scholar 

  27. Lee, C. S., Davis, R. W. & Davidson, N. A physical study by electron microscopy of the terminally repetitious, circularly permuted DNA from the coliphage particles of Escherichia coli 15. J. Mol. Biol. 48, 1– 22 (1970).

    CAS  Article  Google Scholar 

  28. Wetmur, J. G. & Davidson, N. Kinetics of renaturation of DNA. J. Mol. Biol. 31, 349– 370 (1968).

    CAS  Article  Google Scholar 

  29. Radding, C. M., Beattie, K. L., Holloman, W. K. & Wiegand, R. C. Uptake of homologous single-stranded fragments by superhelical DNA: IV branch migration. J. Mol. Biol. 116, 825– 839 (1977).

    CAS  Article  Google Scholar 

  30. Turberfield, A. J., Yurke, B. & Mills, A. P. Jr Coded self-assembly of DNA nanostructures. Bull. Am. Phys. Soc. 44, 1711 (1999).

    Google Scholar 

Download references

Acknowledgements

F.C.S. thanks the Alexander von Humboldt Foundation for support.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Andrew J. Turberfield.

Supplementary Information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Yurke, B., Turberfield, A., Mills, A. et al. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000). https://doi.org/10.1038/35020524

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/35020524

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