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Fractal Dimension and Localization of DNA Knots

Erika Ercolini, Francesco Valle, Jozef Adamcik, Guillaume Witz, Ralf Metzler, Paolo De Los Rios, Joaquim Roca, and Giovanni Dietler
Phys. Rev. Lett. 98, 058102 – Published 29 January 2007

Abstract

The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic trapping of the three-dimensional (3D) configuration, and of (ii) weak binding, that permits (partial) relaxation on the surface. In (i) the radius of gyration of the adsorbed DNA knot scales with the 3D Flory exponent ν0.60 within error. In (ii), we find ν0.66, a value between the 3D and 2D (ν=3/4) exponents. Evidence is also presented for the localization of knot crossings in 2D under weak adsorption conditions.

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  • Received 13 July 2006

DOI:https://doi.org/10.1103/PhysRevLett.98.058102

©2007 American Physical Society

Authors & Affiliations

Erika Ercolini1, Francesco Valle1,*, Jozef Adamcik1, Guillaume Witz1, Ralf Metzler2,†, Paolo De Los Rios3, Joaquim Roca4, and Giovanni Dietler1

  • 1Laboratory of Physics of Living Matter, IPMC, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
  • 2Nordic Institute for Theoretical Physics (NORDITA), Blegdamsvej 17, 2100 København Ø, Denmark
  • 3Laboratory of Statistical Biophysics, ITP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
  • 4Instituto de Biologia Molecular de Barcelona, CID-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain

  • *Present address: Department of Biochemistry “G. Moruzzi,” University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
  • Present address: Physics Department, University of Ottawa, ON, K1N 6N5, Canada.

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Issue

Vol. 98, Iss. 5 — 2 February 2007

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