Skip to main content
SpringerLink
Log in

Nonlinear mechanical response of DNA due to anisotropic bending elasticity

  • Published:
The European Physical Journal E Aims and scope Submit manuscript

Abstract.

The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend coupling that can lead to the formation of kinks and modulations in the curvature and/or in the twist, depending on the values of the elastic constants and the imposed deflection angle. The typical wavelength for the modulations, or the distance between the neighboring kinks is found to be set by half of the DNA pitch.

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

Similar content being viewed by others

References

  1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter, Molecular Biology of the Cell, 4th edn. (Garland, New York, 2002)

  2. L. Stryer, Biochemistry, 4th edn. (Freeman, 1995)

  3. S.A. Darst, E.W. Kubalek, R.D. Kornberg, Nature 340, 730 (1989); A. Polyakov, E. Severinova, S.A. Darst, Cell 83, 365 (1995); T.H. Tahirov, D. Temiakov, M. Anikin, V. Patlan, W.T. McAllister, D.G. Vassylyev, S. Yokoyama, Nature 420, 43 (2002)

    Article  Google Scholar 

  4. L.S. Beese, V. Derbyshire, T.A. Steitz, Science 260, 352 (1993); J.R. Kiefer, C. Mao, J.C. Braman, L.S. Beese, Nature 391, 304 (1998)

    Google Scholar 

  5. K. Luger, A.W. Mader, R.K. Richmond, D.F. Sargent, T.J. Richmond, Nature 389, 251 (1997)

    CAS  PubMed  Google Scholar 

  6. T.J. Richmond, C.A. Davey, Nature 423, 145 (2003)

    Article  Google Scholar 

  7. C.J. Benham, Biopolymers 22, 2477 (1983); M. Le Bret, Biopolymers 23, 1835 (1984); F. Tanaka, H. Takahash, J. Chem. Phys. 83, 6017 (1985); H. Tsuru, M. Wadati, Biopolymers 25, 2083 (1986)

    Google Scholar 

  8. B. Fain, J. Rudnick, S. Östlund, Phys. Rev. E 55, 7364 (1997); B. Fain, J. Rudnick, Phys. Rev. E 60, 7239 (1999); R. Zandi, J. Rudnick, Phys. Rev. E 64, 051918 (2001)

    Article  Google Scholar 

  9. J.F. Marko, E.D. Siggia, Phys. Rev. E 52, 2912 (1995)

    Article  Google Scholar 

  10. C. Bouchiat, M. Mézard, Phys. Rev. Lett. 80, 1556 (1998); Eur. Phys. J. E 2, 377 (2000)

    Article  Google Scholar 

  11. S. Panyukov, Y. Rabin, Phys. Rev. Lett. 85, 2404 (2000); Phys. Rev. E 62, 7135 (2000); Europhys. Lett. 57, 512 (2002)

    Article  Google Scholar 

  12. T. Schlick, W.K. Olson, Science 257, 1110 (1992); W.K. Olson, Curr. Opin. Struc. Biol. 6, 242 (1996); P. Auffinger, E. Westhof, Curr. Opin. Struc. Biol. 8, 227 (1998)

    Google Scholar 

  13. A. Balaeff, L. Mahadevan, K. Schulten, Phys. Rev. Lett. 83, 4900 (1999)

    Article  Google Scholar 

  14. J.F. Marko, E.D. Siggia, Macromolecules 27, 981 (1994); 29, 4820(E) (1996)

    Google Scholar 

  15. R.D. Kamien, T.C. Lubensky, P. Nelson, C.S. O’Hern, Europhys. Lett. 38, 237 (1997)

    Article  Google Scholar 

  16. T.B. Liverpool, R. Golestanian, K. Kremer, Phys. Rev. Lett. 80, 405 (1998); R. Golestanian, T.B. Liverpool, Phys. Rev. E 62, 5488 (2000); A. de Col, T.B. Liverpool, e-print cond-mat/0203561

    Article  Google Scholar 

  17. L. Landau, E. Lifshitz, Theory of elasticity, 3rd edn. (Pergamon, 1986)

  18. A.V. Vologodskii, S.D. Levene, K.V. Klenin, M. Frankkamenetskii, N.R. Cozzarelli, J. Mol. Biol. 227, 1224 (1992)

    Google Scholar 

  19. W.K. Olson, N.L. Marky, R.L. Jernigan, V.B. Zhurkin, J. Mol. Biol. 232, 530 (1993)

    Article  Google Scholar 

  20. F. Mohammad-Rafiee, R. Golestanian, work in progress

  21. For a similar argument in the case of force-extension curve for inhomogeneous DNA see: D. Bensimon, D. Dohm, M. Mezard, Europhys. Lett. 42, 97 (1998); P. Nelson, Phys. Rev. Lett. 80, 5810 (1998)

    Article  Google Scholar 

  22. C.S. O’Hern, R.D. Kamien, T.C. Lubensky, P. Nelson, Eur. Phys. J. B 1, 95 (1998)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute for Advanced Studies in Basic Sciences, 45195-159, Zanjan, Iran

    F. Mohammad-Rafiee & R. Golestanian

Authors
  1. F. Mohammad-Rafiee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. Golestanian
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to F. Mohammad-Rafiee.

Additional information

Received: 7 September 2003, Published online: 5 February 2004

PACS:

87.15.-v Biomolecules: structure and physical properties - 87.15.La Mechanical properties of biomolecules - 87.14.Gg DNA, RNA

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mohammad-Rafiee, F., Golestanian, R. Nonlinear mechanical response of DNA due to anisotropic bending elasticity. Eur. Phys. J. E 12, 599–604 (2003). https://doi.org/10.1140/epje/e2004-00032-5

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1140/epje/e2004-00032-5

Keywords

Search

Navigation