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Tying a molecular knot with optical tweezers

Nature volume 399, pages 446–448 (1999)Cite this article

Abstract

Filamentous structures are abundant in cells. Relatively rigid filaments, such as microtubules and actin, serve as intracellular scaffolds that support movement and force, and their mechanical properties are crucial to their function in the cell. Some aspects of the behaviour of DNA, meanwhile, depend critically on its flexibility—for example, DNA-binding proteins can induce sharp bends in the helix1. The mechanical characterization of such filaments has generally been conducted without controlling the filament shape, by the observation of thermal motions2,3,4,5 or of the response to external forces6,7,8,9 or flows10,11,12. Controlled buckling of a microtubule has been reported13, but the analysis of the buckled shape was complicated. Here we report the continuous control of the radius of curvature of a molecular strand by tying a knot in it, using optical tweezers to manipulate the strand's ends. We find that actin filaments break at the knot when the knot diameter falls below 0.4 µm. The pulling force at breakage is around 1 pN, two orders of magnitude smaller than the tensile stress of a straight filament. The flexural rigidity of the filament remained unchanged down to this diameter. We have also knotted a single DNA molecule, opening up the possibility of studying curvature-dependent interactions with associated proteins. We find that the knotted DNA is stronger than actin.

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Figure 1: Tying a knot in an actin filament.
Figure 2: Relation between the tension (T) and knot diameter (D).
Figure 3: Breakage parameters of a knotted actin filament.
Figure 4: Knotting a single DNA molecule.

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References

  1. Schultz, S. C., Shields, G. C. & Steitz, T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253, 1001–1007 (1991).

    Article  ADS  CAS  Google Scholar 

  2. Yanagida, M., Hiraoka, Y. & Katsura, I. Dynamic behaviors of DNA molecules in solution studied by fluorescence microscopy. Cold Spring Harbor Symp. Quant. Biol. 47, 177–187 (1983).

    Article  Google Scholar 

  3. Yanagida, T., Nakase, M., Nishiyama, K. & Oosawa, F. Direct observation of motion of single F-actin filaments in the presence of myosin. Nature 307, 58–60 (1984).

    Article  ADS  CAS  Google Scholar 

  4. Gittes, F., Mickey, B., Nettleton, J. & Howard, J. Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. J. Cell Biol. 120, 923–934 (1993).

    Article  CAS  Google Scholar 

  5. Yasuda, R., Miyata, H. & Kinosita, K. J Direct measurement of the torsional rigidity of single actin filaments. J. Mol. Biol. 263, 227–236 (1996).

    Article  CAS  Google Scholar 

  6. Cluzel, P.et al. DNA: an extensible molecule. Science 271, 792–794 (1996).

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  8. Dupuis, D. E., Guilford, W. H., Wu, J. & Warshaw, D. M. Actin filament mechanics in the laser trap. J. Muscle Res. Cell Motil. 18, 17–30 (1997).

    Article  CAS  Google Scholar 

  9. Tsuda, Y., Yasutake, H., Ishijima, A. & Yanagida, T. Torsional rigidity of single actin filaments and actin-actin bond breaking force under torsion measured directly by in vitro micromanipulation. Proc. Natl Acad. Sci. USA 93, 12937–12942 (1996).

    Article  ADS  CAS  Google Scholar 

  10. Perkins, T. T., Quake, S. R., Smith, D. E. & Chu, S. Relaxation of a single DNA molecule observed by optical microscopy. Science 264, 822–826 (1994).

    Article  ADS  CAS  Google Scholar 

  11. Bensimon, D., Simon, A. J., Croquette, V. & Bensimon, A. Stretching DNA with a receding meniscus: experiments and models. Phys. Rev. Lett. 74, 4754–4757 (1995).

    Article  ADS  CAS  Google Scholar 

  12. Smith, D. E. & Chu, S. Response of flexible polymers to a sudden elongational flow. Science 281, 1335–1340 (1998).

    Article  ADS  CAS  Google Scholar 

  13. Kurachi, M., Hoshi, M. & Tashiro, H. Buckling of a single microtubule by optical trapping forces: direct measurement of microtubule rigidity. Cell Motil. Cytoskel. 30, 221–228 (1995).

    Article  CAS  Google Scholar 

  14. Miyata, H.et al. Mechanical measurements of single actomyosin motor force. Biophys. J. 68, 286S–290S (1995).

    Google Scholar 

  15. Landau, L. D. & Lifshitz, E. M. Theory of Elasticity 2nd edn(Pergamon, Oxford, (1970).

    Google Scholar 

  16. Oosawa, F., Fujime, S., Ishiwata, S. & Mihashi, K. Dynamic property of F-actin and thin filament. Cold Spring Harbor Symp. Quant. Biol. 37, 277–285 (1973).

    Article  CAS  Google Scholar 

  17. Saitta, A. M., Soper, P. D., Wasserman, E. & Klein, M. L. Influence of a knot on the strength of a polymer strand. Nature 399, 46–48 (1999).

    Article  ADS  CAS  Google Scholar 

  18. Nishizaka, T., Miyata, H., Yoshikawa, H., Ishiwata, S. & Kinosita, K. J Unbinding force of a single motor molecule of muscle measured using optical tweezers. Nature 377, 251–254 (1995).

    Article  ADS  CAS  Google Scholar 

  19. Miyata, H., Yasuda, R. & Kinosita, K. J Strength and lifetime of the bond between actin and skeletal muscle α-actinin studied with an optical trapping technique. Biochim. Biophys. Acta 1290, 83–88 (1996).

    Article  Google Scholar 

  20. Holmes, K. C., Popp, D., Gebhard, W. & Kabsch, W. Atomic model of the actin filament. Nature 347, 44–49 (1990).

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  22. Harada, Y.et al. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76, 709–715 (1999).

    Article  ADS  CAS  Google Scholar 

  23. Suzuki, N., Miyata, H., Ishiwata, S. & Kinosita, K. J Preparation of bead-tailed actin filaments: estimation of the torque produced by the sliding force in an in vitro motility assay. Biophys. J. 70, 401–408 (1996).

    Article  CAS  Google Scholar 

  24. Yasuda, R., Noji, H., Kinosita, K. J & Yoshida, M. F1-ATPase is a highly efficient molecular motor that rotates with discrete 120° steps. Cell 93, 1117–1124 (1998).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank K. Adachi and Y. Hada for technical support and advice, S. Ishiwata for critically reading the manuscript, M. Hosoda for image processing, and H. Umezawa for laboratory management. This work was supported in part by Grants-in-Aid from Ministry of Education, Science, Sports and Culture of Japan, an Academic Frontier Promotional Project, and a Keio University Special Grant-in-Aid. R.Y. was a Research Fellow of the JSPS.

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Author notes

  1. Hidetake Miyata

    Present address: Physics Department, Graduate School, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan

Authors and Affiliations

  1. Department of Physics, Faculty of Science and Technology, Keio Univeristy, Hiyoshi 3-14-1, Kohoku-ku, 223-8522, Yokohama, Japan

    Yasuharu Arai, Ryohei Yasuda, Ken-ichirou Akashi, Yoshie Harada, Hidetake Miyata & Kazuhiko Kinosita Jr

  2. CREST (Core Research for Evolutional Science and Technology) Genetic Programming Team 13, Nogawa 907, Miyamae-ku, 216-0001, Kawasaki, Japan

    Yasuharu Arai, Ryohei Yasuda, Yoshie Harada, Kazuhiko Kinosita Jr & Hiroyasu Itoh

  3. Tsukuba Research Laboratory, Hamamatsu Photonics KK, Tokodai, 3002635, Tsukuba, Japan

    Hiroyasu Itoh

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Arai, Y., Yasuda, R., Akashi, Ki. et al. Tying a molecular knot with optical tweezers. Nature 399, 446–448 (1999). https://doi.org/10.1038/20894

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