Skip to main content
SpringerLink
Log in

Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy

  • Review Article
  • Published:

From Nature Structural Biology

View current issue Submit your manuscript

Abstract

Dynamic structural changes of macromolecules undergoing biochemical reactions can be studied using novel single molecule spectroscopy tools. Recent advances in applying such distance and orientation molecular rulers to biological systems are reviewed, and future prospects and challenges are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1: Energy landscape for the folding reaction.
Figure 2: Single molecule protein folding.
Figure 3: Single molecule ribozyme folding.
Figure 4: Single molecule dipole rotation.
Figure 5: Single pair FRET in a living cell.

Similar content being viewed by others

References

  1. Xie, X.S. Acc. Chem. Res. 29, 598–606 (1996).

    Article  CAS  Google Scholar 

  2. Basché, T., Moerner, W.E., Orrit, M. & Wild, U.P. Single-molecule optical detection, imaging and spectroscopy (WILEY-VCH, Weinheim, Cambridge; 1997).

    Google Scholar 

  3. Xie, X.S. In Focus on multidimensional microscopy (eds., Chen, P.C., Hwang, P.P., Wu, J.L., Wang, G. & Kim, H.) (World Scientific, Singapore; 1997).

    Google Scholar 

  4. Nie, S.M. & Zare, R.N. Annu. Rev. Biophys. Biomol. Struct. 26, 567–596 (1997).

    Article  CAS  PubMed  Google Scholar 

  5. Xie, X.S. & Trautman, J.K. Annu. Rev. Phys. Chem. 49, 441–480 (1998).

    Article  CAS  PubMed  Google Scholar 

  6. Moerner, W.E. & Orrit, M. Science 283, 1670–1676 (1999).

    Article  CAS  PubMed  Google Scholar 

  7. Weiss, S. Science 283, 1676–1683 (1999).

    Article  CAS  PubMed  Google Scholar 

  8. Ambrose, W.P. et al. Chem. Rev. 99, 2929–2956 (1999).

    Article  CAS  PubMed  Google Scholar 

  9. Tamarat, P., Maali, A., Lounis, B. & Orrit, M. J. Phys. Chem. A 104, 1–16 (2000).

    Article  CAS  Google Scholar 

  10. Förster, T. Ann. Phys. 2, 55–75 (1948).

    Article  Google Scholar 

  11. Stryer, L. & Haugland, R.P. Proc. Natl. Acad. Sci. USA 58, 719–730 (1967).

    Article  CAS  PubMed  Google Scholar 

  12. Selvin, P.R. Methods. Enzymol. 246, 300–333 (1995).

    Article  CAS  PubMed  Google Scholar 

  13. Selvin, P.R. Nature Struct. Biol. 7, 730–734 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Ha, T. et al. Proc. Natl. Acad. Sci. USA 93, 6264–6268 (1996).

    Article  CAS  PubMed  Google Scholar 

  15. Ha, T., Enderle, T., Chemla, D.S. & Weiss, S. IEEE J. Select. Top. Quant. Electron. 2, 1115–1128 (1996).

    Article  CAS  Google Scholar 

  16. Schütz, G.J., Trabesinger, W. & Schmidt, T. Biophys. J. 74, 2223–2226 (1998).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Ha, T. et al. Proc. Natl. Acad. Sci. USA 96, 893–898 (1999).

    Article  CAS  PubMed  Google Scholar 

  18. Ha, T. et al. Chem. Phys. 247, 107–118 (1999).

    Article  CAS  Google Scholar 

  19. Ishii, Y., Yoshida, T., Funatsu, T., Wazawa, T. & Yanagida, T. Chem. Phys. 247, 163–173 (1999).

    Article  CAS  Google Scholar 

  20. Deniz, A.A. et al. Proc. Natl. Acad. Sci. USA 96, 3670–3675 (1999).

    Article  CAS  PubMed  Google Scholar 

  21. Dahan, M. et al. Chem. Phys. 47, 85–106 (1999).

    Article  Google Scholar 

  22. Bonnet, G., Krichevsky, O. & Libchaber, A. Proc. Natl. Acad. Sci. USA 95, 8602–8606 (1998).

    Article  CAS  PubMed  Google Scholar 

  23. Brasselet, S., Peterman, E.J.G., Miyawaki, A. & Moerner, W.E. J. Phys. Chem. B 104, 3676–3682 (2000).

    Article  CAS  Google Scholar 

  24. Miyawaki, A. et al. Nature 388, 882–887 (1997).

    Article  CAS  PubMed  Google Scholar 

  25. Ha, T. et al. Proc. Natl. Acad. Sci. USA 96, 9077–9082 (1999).

    Article  CAS  PubMed  Google Scholar 

  26. Jia, Y. et al. Chem. Phys. 247, 69–83 (1999).

    Article  CAS  Google Scholar 

  27. Deniz, A.A. et al. Proc. Natl. Acad. Sci. USA. 97, 5179–5184 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Zhuang, X. et al. Science 288, 2048–2051 (2000).

    Article  CAS  PubMed  Google Scholar 

  29. Cantor, C.R. & Schimmel, P.R. Biophysical Chemistry (W.H. Freeman and Co., San Francisco; 1980).

    Google Scholar 

  30. Betzig, E. & Chichester, R.J. Science 262, 1422–1425 (1993).

    Article  CAS  PubMed  Google Scholar 

  31. Guttler, F. et al. J. Luminescence 56, 29–38 (1993).

    Article  Google Scholar 

  32. Ha, T., Enderle, T., Chemla, D.S., Selvin, P.R. & Weiss, S. Phys. Rev. Lett. 77, 3979–3982 (1996).

    Article  CAS  PubMed  Google Scholar 

  33. Ha, T., Glass, J., Enderle, T., Chemla, D.S. & Weiss, S. Phys. Rev. Lett. 80, 2093–2096 (1998).

    Article  CAS  Google Scholar 

  34. Ha, T., Laurence, T.A., Chemla, D.S. & Weiss, S. J. Phys. Chem. B 103, 6839–6850 (1999).

    Article  CAS  Google Scholar 

  35. Corrie, J.E., Craik, J.S. & Munasinghe, V.R.A Bioconjugate Chem. 9, 160–167 (1998).

    Article  CAS  Google Scholar 

  36. Griffin, B.A., Adams, S.R. & Tsien, R.Y. Science 281, 269–272 (1998).

    Article  CAS  PubMed  Google Scholar 

  37. van Oijen, A.M., Ketelaars, M., Kohler, J., Aartsma, T.J. & Schmidt, J. Science 285, 400–402 (1999).

    Article  CAS  PubMed  Google Scholar 

  38. Bopp, M.A., Sytnik, A., Howard, T.D., Cogdell, R.J. & Hochstrasser, R.M. Proc. Natl. Acad. Sci. USA 96, 11271–11276 (1999).

    Article  CAS  PubMed  Google Scholar 

  39. Sase, I., Miyata, H., Ishiwata, S. & Kinosita, K. Proc. Natl. Acad. Sci. USA 94, 5646–5650 (1997).

    Article  CAS  PubMed  Google Scholar 

  40. Warshaw, D.M. et al. Proc. Natl. Acad. Sci. USA 95, 8034–8039 (1998).

    Article  CAS  PubMed  Google Scholar 

  41. Hopkins, S.C., Sabido-David, C., Corrie, J.E., Irving, M. & Goldman, Y.E. Biophys. J. 74, 3093–3110 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Corrie, J.E. et al. Nature 400, 425–430 (1999).

    Article  CAS  PubMed  Google Scholar 

  43. Boyer, P.D. Annu. Rev. Biochem. 66, 717–49 (1997).

    Article  CAS  PubMed  Google Scholar 

  44. Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. Nature 386, 299–302 (1997).

    Article  CAS  PubMed  Google Scholar 

  45. Yasuda, R., Noji, H., Kinosita, K., Jr. & Yoshida, M. Cell 93, 1117–1124 (1998).

    Article  CAS  PubMed  Google Scholar 

  46. Sambongi, Y. et al. Science 286, 1722–1724 (1999).

    Article  CAS  PubMed  Google Scholar 

  47. Häsler, K., Engelbrecht, S. & Junge, W. FEBS Lett. 426, 301–304 (1998).

    Article  PubMed  Google Scholar 

  48. Adachi, K. et al. Proc. Natl. Acad. Sci. USA 97, 7243–7247 (2000).

    Article  CAS  PubMed  Google Scholar 

  49. Schütz, G.J., Kada, G., Pastushenko, V.P. & Schindler, H. EMBO J. 19, 892–901 (2000).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Schütz, G.J. et al. Single Molecules 1, 25–31 (2000).

    Article  Google Scholar 

  51. Sako, Y., Minoguchi, S. & Yanagida, T. Nature Cell Biol. 2, 168–172 (2000).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The author is indebted to A.P. Alivisatos, U. Banin, M. Bruchez, D.S. Chemla, M. Dahan, A.A. Deniz, Th. Enderle, J. Glass, J. Grunwell, T. Ha, T. Her, Th. Lacoste, T. Laurence, J. Liang, S. Licht, A. B. Martin, X. Michalet, F. Pinaud, P.G. Schultz, P.R. Selvin, A. Sonnleitner, and A.Y. Ting for their contributions to the single molecule spectroscopy effort in Berkeley and to A.A. Deniz, T. Her and X. Michalet for critical reading of the manuscript. This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory and the Director, Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy and the Office of Naval Research.

Author information

Authors and Affiliations

  1. Materials Sciences and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    Shimon Weiss

Authors
  1. Shimon Weiss
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shimon Weiss.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Weiss, S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat Struct Mol Biol 7, 724–729 (2000). https://doi.org/10.1038/78941

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/78941

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation