Writhe formulas and antipodal points in plectonemic DNA configurations

Sébastien Neukirch and Eugene L. Starostin
Phys. Rev. E 78, 041912 – Published 20 October 2008

Abstract

The linking and writhing numbers are key quantities when characterizing the structure of a piece of supercoiled DNA. Defined as double integrals over the shape of the double helix, these numbers are not always straightforward to compute, though a simplified formula was established in a theorem by Fuller [Proc. Natl. Acad. Sci. U.S.A. 75, 3557 (1978)]. We examine the range of applicability of this widely used simplified formula, and show that it cannot be employed for plectonemic DNA. We show that inapplicability is due to a hypothesis of Fuller theorem that is not met. The hypothesis seems to have been overlooked in many works.

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  • Received 30 May 2008

DOI:https://doi.org/10.1103/PhysRevE.78.041912

©2008 American Physical Society

Authors & Affiliations

Sébastien Neukirch

  • Institut Jean le Rond d’Alembert, CNRS and UPMC Univ. Paris 6, 4 Place Jussieu (case 162), 75005 Paris, France

Eugene L. Starostin

  • Centre for Nonlinear Dynamics, Department of Civil, Environmental and Geomatic Engineering, University College London, London, United Kingdom

Comments & Replies

Reply to “Comment on ‘Writhe formulas and antipodal points in plectonemic DNA configurations’ ”

Sébastien Neukirch and Eugene L. Starostin
Phys. Rev. E 80, 063902 (2009)

Comment on “Writhe formulas and antipodal points in plectonemic DNA configurations”

Joseph Samuel, Supurna Sinha, and Abhijit Ghosh
Phys. Rev. E 80, 063901 (2009)

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Vol. 78, Iss. 4 — October 2008

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