Dynamics of DNA Double Helices

  • Dietmar Porschke
Part of the NATO ASI Series book series (ASIC, volume 291)


First, a short survey is given on the time scale of various ‘elementary’ processes observed in nucleic acids. Then, the ‘self-organisation’ of long viral DNA molecules from voluminous, disordered wormlike coils to compact well ordered toroids is discussed with respect to its dynamics. Two limit cases of the reaction mechanism for the spermine induced toroid formation have been demonstrated by stopped flow and electric field jump measurements:
  1. 1)

    At low spermine concentrations the rate of toroid formation is limited by the rate of spermine association to the DNA chain. The observed induction periods and the overall reaction rates indicate that spermine molecules move along the DNA with a rate of ~ 200 residues/s.

  2. 2)

    In the limit of high spermine concentrations winding of DNA strands into the toroidal form is reflected by a spectrum of time constants ranging from 25µs to 2ms. This high rate is quite remarkable and suggests the analogy of a spring, which is kept under tension by electrostatic repulsion and which collapses immediately, when the repulsion is reduced by ligand binding.

Bending of DNA double helices has been analyzed in further detail by electrooptical measurements on restriction fragments. Bending amplitudes and bending time constants have been assigned as a function of the DNA chain length. An orientation function for weakly bent rods has been developed, which serves to explain the stationary dichroism and bending amplitudes. Most of the data are consistent with simple thermal bending, but deviations under special conditions suggest the existence of inherent curvature.

Finally, a simple model of toroid formation is proposed.


Electric Field Pulse Persistence Length Light Scattering Intensity Relaxation Time Constant Range Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    W. Saenger, Principles of Nucleic Acid Structure, Springer, Berlin (1984)CrossRefGoogle Scholar
  2. 2.
    V.A. Bloomfield, D. Crothers and I. Tinoco, jr., Physical Chemistry of Nucleic Acids, Harper & Row, NewYork (1974)Google Scholar
  3. 3.
    P.A. Mirau, R.W. Behling and D.R. Kearns, Biochemistry 24, 6200–6211 (1985)CrossRefGoogle Scholar
  4. 4.
    D.R. Kearns, CRC Crit. Rev. Biochem. 15, 237–290 (1984)CrossRefGoogle Scholar
  5. 5.
    J.H. Shibata, B.S. Fujimoto and J.M. Schurr, Biopolymers 24, 1909–1930 (1985)CrossRefGoogle Scholar
  6. 6.
    M. Hogan, J. Le Grange and B. Austin, Nature 304, 752–754 (1983)CrossRefGoogle Scholar
  7. 7.
    S.C. Kao and A.M. Bobst, Biochemistry 24, 5465–5469 (1985)CrossRefGoogle Scholar
  8. 8.
    T. Dorfmiller et al., this volumeGoogle Scholar
  9. 9.
    J. Langowski, Biophys. Chem. 27. 263–271 (1987)CrossRefGoogle Scholar
  10. 10.
    D. Porschke, Mol. Biol., Biochem. Biophys. 24, 191–218 (1977)Google Scholar
  11. 11.
    D. Porschke and F. Eggers, Eur. J. Biochem. 26, 490–498 (1972)CrossRefGoogle Scholar
  12. 12.
    D. Porschke, Biochemistry 15, 1495–1499 (1976)CrossRefGoogle Scholar
  13. 13.
    D. Porschke, Biopolymers 17, 315–323 (1978)CrossRefGoogle Scholar
  14. 14.
    G.G. Hammes and A.C. Park, J. Amer. Chem. Soc. 90, 4151–4156 (1968)CrossRefGoogle Scholar
  15. 15.
    D. Porschke, Biophys. Chem. 22, 237–247 (1985)CrossRefGoogle Scholar
  16. 16.
    D. Porschke, Nucleic Acids Res. 6, 883–898 (1979)CrossRefGoogle Scholar
  17. 17.
    D. Porschke, Biochemistry 23, 4821–4828 (1984)CrossRefGoogle Scholar
  18. 18.
    D. Porschke, Biophys. Chem. 2, 97–101 (1974)CrossRefGoogle Scholar
  19. 19.
    D. Porschke, Biophys. Chem. 72, 83–96 (1974)CrossRefGoogle Scholar
  20. 20.
    D. Porschke, O.C. Uhlenbeck and F.H. Martin, Biopolymers 72, 1313–1335 (1973)CrossRefGoogle Scholar
  21. 21.
    D. Porschke, J. Biomol. Structure and Dynamics 4, 373–389 (1986)Google Scholar
  22. 22.
    F.M. Pohl and T.M. Jovin, J. Mol. Biol. 67, 375–396 (1972)CrossRefGoogle Scholar
  23. 23.
    L.C. Gosule and J.A. Schellman, J. Mol. Biol. 121, 311–326 (1978)CrossRefGoogle Scholar
  24. 24.
    D.K. Chattoray, L.C. Gosule and J.A. Schellman, J. Mol. Biol. 121, 327–337 (1978)CrossRefGoogle Scholar
  25. 25.
    K.A. Marx and G.R. Ruben, Nucleic Acids Res. 11, 1839–1854 (1983)CrossRefGoogle Scholar
  26. 26.
    J. Widom and R.L. Baldwin, J. Mol. Biol. 144, 431–453 (1980)CrossRefGoogle Scholar
  27. 27.
    R.N. Wilson and V.A. Bloomfield, Biochemistry 18, 2192–2196 (1979)CrossRefGoogle Scholar
  28. 28.
    D. Porschke, Biochemistry 23, 4821–4828 (1984)CrossRefGoogle Scholar
  29. 29.
    D. Porschke, Biopolymers 24, 1981–1993 (1985)CrossRefGoogle Scholar
  30. 30.
    J.D. McGhee and P.H. von Hippel, J. Mol. Biol. 86, 469–489 (1974)CrossRefGoogle Scholar
  31. 31.
    I.R. Epstein, Biopolymers 18, 2037–2050 (1979)CrossRefGoogle Scholar
  32. 32.
    S. Diekmann, W. Hillen, B. Morgeneyer, R.D. Wells and D. Porschke, Biophys. Chem. 15, 263–270 (1982)CrossRefGoogle Scholar
  33. 33.
    S. Broersma, J. Chem. Phys. 32 1626–1631 (1960)CrossRefGoogle Scholar
  34. 34.
    D. Porschke, N. Geissler and W. Hillen, Nucleic Acids Res. 10, 3791–3802 (1982)CrossRefGoogle Scholar
  35. 35.
    J.E. Hearst, J. Chem. Phys. 38, 1062–1065 and personal communicationGoogle Scholar
  36. 36.
    D. Porschke, Biopolymers, in pressGoogle Scholar
  37. 37.
    S. Diekmann and D. Porschke, Biophys. Chem. 26, 207–216 (1987)CrossRefGoogle Scholar
  38. 38.
    G. Manning,Cell Biophysics 7, 57–89 (1985)Google Scholar

Copyright information

© Kluwer Academic Publishers 1989

Authors and Affiliations

  • Dietmar Porschke
    • 1
  1. 1.Max-Planck-Institut für biophysikalische ChemieGöttingenGermany

Personalised recommendations