Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection

Abstract

We designed and created nanofabricated quartz cylinders well suited for torque application and detection in an angular optical trap. We made the cylinder axis perpendicular to the extraordinary axis of the quartz crystal and chemically functionalized only one end of each cylinder for attachment to a DNA molecule. We directly measured the torque on a single DNA molecule as it underwent a phase transition from B-form to supercoiled P-form.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Illustration of the angular optical trapping configuration.
Figure 2: Nanofabrication of quartz cylinders.
Figure 3: Measurements during DNA supercoiling.

References

  1. 1

    Charvin, G., Strick, T.R., Bensimon, D. & Croquette, V. Annu. Rev. Biophys. Biomol. Struct. 34, 201–219 (2005).

    CAS  Article  Google Scholar 

  2. 2

    Bryant, Z. et al. Nature 424, 338–341 (2003).

    CAS  Article  Google Scholar 

  3. 3

    Oroszi, L., Galajda, P., Kire, H., Bottka, S. & Ormos, P. Phys. Rev. Lett. 97, 058301 (2006).

    Article  Google Scholar 

  4. 4

    Friese, M.E.J., Nieminen, T.A., Heckenberg, N.R. & Rubinsztein-Dunlop, H. Nature 394, 348–350 (1998).

    CAS  Article  Google Scholar 

  5. 5

    Bishop, A.I., Nieminen, T.A., Heckenberg, N.R. & Rubinsztein-Dunlop, H. Phys. Rev. A. 68, 033802 (2003).

    Article  Google Scholar 

  6. 6

    La Porta, A. & Wang, M.D. Phys. Rev. Lett. 92, 190801 (2004).

    Article  Google Scholar 

  7. 7

    Bishop, A.I., Nieminen, T.A., Heckenberg, N.R. & Rubinsztein-Dunlop, H. Phys. Rev. Lett. 92, 198104 (2004).

    Article  Google Scholar 

  8. 8

    Singer, W., Nieminen, T.A., Gibson, U.J., Heckenberg, N.R. & Rubinsztein-Dunlop, H. Phys. Rev. E 73, 021911 (2006).

    Article  Google Scholar 

  9. 9

    Ashkin, A., Dziedzic, J.M. & Yamane, T. Nature 330, 769–771 (1987).

    CAS  Article  Google Scholar 

  10. 10

    Kleinfeld, D., Kahler, K.H. & Hockberger, P.E. J. Neurosci. 8, 4098–4120 (1988).

    CAS  Article  Google Scholar 

  11. 11

    Volkmuth, W.D. & Austin, R.H. Nature 358, 600–602 (1992).

    CAS  Article  Google Scholar 

  12. 12

    Deufel, C. & Wang, M.D. Biophys. J. 90, 657–667 (2006).

    CAS  Article  Google Scholar 

  13. 13

    Strick, T.R., Allemand, J-F., Bensimon, D. & Croquette, V. Biophys. J. 74, 2016–2028 (1998).

    CAS  Article  Google Scholar 

  14. 14

    Lionnet, T., Joubaud, S., Lavery, R., Bensimon, D. & Croquette, V. Phys. Rev. Lett. 96, 178102 (2006).

    Article  Google Scholar 

  15. 15

    Gore, J. et al. Nature 442, 836–839 (2006).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank B. Brower-Toland and L. Bai for help with DNA template preparation, C.K. Ober, U. Wiesner, H. Ow and A. La Porta for discussions on particle design considerations, and members of the Wang lab for helpful discussions and critical reading of the manuscript. This work was performed in part at the Cornell NanoScale Facility, a member of the National Nanotechnology Infrastructure Network, which is supported by the US National Science Foundation (grant ECS 03-35765). This work was supported by the Keck Foundation to M.D.W. and a Molecular Biophysics Training Grant to Cornell University.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Michelle D Wang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Deufel, C., Forth, S., Simmons, C. et al. Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection. Nat Methods 4, 223–225 (2007). https://doi.org/10.1038/nmeth1013

Download citation

Further reading

Search

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