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DNA Knots

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Topological Polymer Chemistry

Abstract

Knotting is statistically inevitable in long polymer chains, especially under spatial confinement, and tightly packed genomic DNA filaments are no exception. Over several decades, ever more powerful experimental techniques have demonstrated the occurrence of knots and other forms of entanglements in DNA extracted from viruses, bacteria, and eukaryotes. The data have in turn prompted a broad range of theoretical and computational studies of the abundance and complexity of DNA knots, and especially: (i) how it depends on the length and degree of confinement of the filaments (ii) whether it can be used to infer the multiscale spatial organization of genomic DNA, and (iii) its impact on biological processes in vivo. Here, we present an overview and a personal perspective of such theoretical and experimental efforts, from the equilibrium knotting of DNA in bulk to the one observed in various organisms, and concluding with a comparison with RNAs and their entanglement properties.

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Acknowledgements

The material presented in this overview intersects the work of many colleagues and research groups that I had the pleasure to interact with during collaborations, visits, and exchanges and at conferences. For the topics touched here, I wish to recall, in particular, Lucia Coronel, Tetsuo Deguchi, Giovanni Dietler, Marco Di Stefano, Massimiliano Di Ventra, Alexander Grosberg, Davide Marenduzzo, Ken Millet, Henri Orland, Enzo Orlandini, Eric Rawdon, Joaquim Roca, Angelo Rosa, Andrzej Stasiak, Antonio Suma, De Witt Sumners, Erica Uehara, Yasuyuki Tezuka, and Luca Tubiana. I am indebted to many of them not only for having enriched me scientifically but also personally. I am also grateful to Prof. Yasuyuki Tezuka and Prof. Tetsuo Deguchi for the editing of this contribution.

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  1. SISSA, Via Bonomea 265, 34136, Trieste, Italy

    Cristian Micheletti

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  1. Cristian Micheletti
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Correspondence to Cristian Micheletti .

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  1. Tokyo Institute of Technology, Tokyo, Japan

    Yasuyuki Tezuka

  2. Ochanomizu University, Tokyo, Japan

    Tetsuo Deguchi

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Micheletti, C. (2022). DNA Knots. In: Tezuka, Y., Deguchi, T. (eds) Topological Polymer Chemistry. Springer, Singapore. https://doi.org/10.1007/978-981-16-6807-4_8

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