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DNA topology in chromosomes: a quantitative survey and its physiological implications

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Abstract

Using a simple geometric model, we propose a general method for computing the linking number of the DNA embedded in chromatin fibers. The relevance of the method is reviewed through the single molecule experiments that have been performed in vitro with magnetic tweezers. We compute the linking number of the DNA in the manifold conformational states of the nucleosome which have been evidenced in these experiments and discuss the functional dynamics of chromosomes in the light of these manifold states.

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Notes

  1. The 2002 work of Starostin has been published in 2005 (Starostin 2005), but the preprint version contains more material than its published version, and in particular a whole section devoted to the writhe additivity, to which we refer in our paper.

  2. Compare with Eq. 16 in Starostin (2005). Incidentally, we point out an error in the round term of that formula, that should be rewritten as \(+round(aL/2\pi )\).

  3. We note that the same viewpoint \(F\) was introduced by Crick (1976).

  4. The fact that in the skeleton structure the tangent vector presents discontinuous points may appear as a limitation to the application of the theorem, but this problem may be easily solved by defining a correct limiting procedure (Starostin 2005)

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Authors and Affiliations

  1. Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, and CNRS GDR 3536, Université Pierre et Marie Curie, Case courrier 121, 4 place Jussieu, 75252 , Paris, France

    Maria Barbi, Julien Mozziconacci & Jean-Marc Victor

  2. Institut Pasteur, 25-28 rue du Docteur Roux, 75015 , Paris, France

    Hua Wong

  3. CNRS GDR 3536, Université Pierre et Marie Curie, Case Currier 121, 4 place Jussieu, 75252 , Paris, France

    Hua Wong

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  1. Maria Barbi
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  2. Julien Mozziconacci
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  3. Hua Wong
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  4. Jean-Marc Victor
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Correspondence to Maria Barbi.

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Barbi, M., Mozziconacci, J., Wong, H. et al. DNA topology in chromosomes: a quantitative survey and its physiological implications. J. Math. Biol. 68, 145–179 (2014). https://doi.org/10.1007/s00285-012-0621-y

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  • DOI: https://doi.org/10.1007/s00285-012-0621-y

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