European Biophysics Journal

, Volume 29, Issue 8, pp 597–606

Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy

  • Giuseppe Chirico
  • Maddalena Collini
  • Katalin Tóth
  • Nathalie Brun
  • Jörg Langowski
Article

DOI: 10.1007/s002490000110

Cite this article as:
Chirico, G., Collini, M., Tóth, K. et al. Eur Biophys J (2001) 29: 597. doi:10.1007/s002490000110

Abstract.

The rotational dynamics of short DNA fragments with or without intrinsic curvature were studied using time-resolved phase fluorimetry of intercalated ethidium with detection of the anisotropy. Parameters determined were the spinning diffusion coefficient of the DNA fragments about the long axis and the zero-time ethidium fluorescence anisotropy. We find a significant decrease in the spinning diffusion coefficient for all curved fragments compared to the straight controls. This decrease is likewise evident in rotational diffusion coefficients computed from DNA structures obtained by a curvature prediction program for these sequences. Using a hinged-cylinder model, we can identify the change in rotational diffusion coefficient with a permanent bend of 13–16° per helix turn for the sequences studied. Moreover, for some of the curved fragments an increased flexibility has to be assumed in addition to the permanent bend in order to explain the data.

DNA torsional rigidity DNA bending Phase fluorimetry Curvature prediction 

Copyright information

© Springer-Verlag 2000

Authors and Affiliations

  • Giuseppe Chirico
    • 2
  • Maddalena Collini
    • 2
  • Katalin Tóth
    • 1
  • Nathalie Brun
    • 1
  • Jörg Langowski
    • 1
  1. 1.Deutsches Krebsforschungszentrum, Division Biophysics of Macromolecules, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
  2. 2.Istituto Nazionale di Fisica per la Materia, Università degli Studi di Milano Bicocca, Via Celoria 16, 20133 Milan, Italy

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