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Biophys. J. BioFAST: First Published March 18, 2005. doi:10.1529/biophysj.104.056945
© 2005 by the Biophysical Society.

A more recent version of this article appeared on June 1, 2005.
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Gilles Charvin
Alexander V Vologodskii
Vincent Croquette
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NUCLEIC ACIDS

Braiding DNA : experiments, simulations and models

Gilles Charvin 1*, Alexander V Vologodskii 2, Vincent Croquette 1 and David Bensimon 1

1 Ecole Normale Superieure
2 NYU

* To whom correspondence should be addressed. E-mail: gilles.charvin{at}lps.ens.fr.

Submitted on November 30, 2004
Revised on February 3, 2005
Accepted on 14 March 2005


  Abstract
DNA encounters topological problems in vivo because of its extended double-helical structure. As a consequence, the semi-conservative mechanism of DNA replication leads to the formation of DNA braids or catenanes, which have to be removed in order to complete cell division. To get a better understanding of these structures, we have studied the elastic behavior of two braided nicked DNA molecules using a magnetic trap apparatus. The experimental data let us identify and characterize three regimes of braiding: a slightly twisted regime prior to the formation of the first crossing followed by genuine braids which at large braiding number buckle to form plectonemes. Two different approaches support and quantify this characterization of the data. First, Monte-Carlo (MC) simulations of braided DNAs yield a full description of the molecules' behaviour and their buckling transition. Second, modeling the braids as a twisted swing provides a good approximation of the elastic response of the molecules as they are intertwined. Comparisons of the experiments and the MC simulations with this analytical model allow for a measurement of the diameter of the braids and its dependence upon entropic and electrostatic repulsive interactions. The MC simulations allow for an estimate of the effective torsional constant of the braids (at a stretching force F = 2 pN): Cb {approx} 48 nm (as compared with C {approx} 100 nm for a single unnicked DNA). Finally, at low salt concentrations and for sufficiently large number of braids, the diameter of the braided molecules is observed to collapse to that of double stranded (ds)DNA. We suggest that this collapse is due to the partial melting and fraying of the two nicked molecules and the subsequent right or left-handed intertwining of the stretched single strands.

Key Words: DNA braids, DNA catenanes, DNA micromanipulation, Monte-Carlo Simulation, Single molecule




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[Abstract] [Full Text] [PDF]


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Copyright © 2005 by the Biophysical Society.