CRM: Centro De Giorgi
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Numerical Knots: Models and Simulations

Structure and dynamics of supercoiled knots and catenanes

speaker: Guillaume Witz (EPFL - Laboratory of Physics of Living Matter)

abstract: Circular DNA molecules in vivo form catenanes and knots during processes like replication or recombination. In addition, DNA molecules are often subjected to a torsional tension, which results in their supercoiling. The interplay between catenation, knotting and supercoiling leads to unexpected conformational changes of the DNA molecules, with interesting physical and biological consequences. In particular, the behavior of DNA molecules in the widely used technique of gel electrophoresis depends on these structural changes, which have therefore to be thoroughly understood. Using numerical simulation techniques where DNA is modeled as a semi-flexible ribbon, and where hydrodynamic interactions can be taken into account, we analyzed both the conformation and the sedimentation behavior of supercoiled molecules with complex topologies. The results that will be presented especially highlight the importance of the chirality of knots and catenanes in the structural changes induced by DNA supercoiling. For example, strongly linked right-handed toroidal DNA catenanes undergo a specific folding that can be reversed by the introduction of negative supercoiling in each chain, and the shape of negatively supercoiled DNA trefoil knots depends on their chirality. Comparison with experimental data, and biological consequences of the observe phenomena will also be presented.

Thu 9 Jun, 15:00 - 15:30, Aula Dini
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