Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Poster Abstracts

3-POS Board 3 Modelling the Unknotting Functionof Topoisomerases and Knot Adjacency Agnese Barbensi 1 ; Dorothy Buck 2 ; Heather A Harrington 1 ; Daniele Celoria 1 1 University of Oxford, Oxford, United Kingdom 2 University of Bath, Bath, United Kingdom

Action of type II topoisomerases on covalently closed DNA molecules can change the topology, resulting in a range of different knot types. Here we model the configuration space of a knotted DNA molecule as a graph. The vertices are planar projections (i.e. shadows) of the molecule, which can be thought as a closed polymer in the space, and these are connected by edges representing local deformations and inter-segmental passages. This diagram focused approach is applied to investigate knot adjacency and the unknotting function of topoisomerases. We complement and synthesise earlier work by Stasiak and collaborators by looking at neighboring subspaces in the graph of the configurations, modeled as a network of grid diagrams with increasing complexity. We suggest a grid-based calculation as a new and computationally convenient method for investigating unbiased knotting probability biopolymers. Furthermore, in this setting we are able to emulate simulations by Zechiedrich and collaborators in the lattice model to investigate the role of local juxtaposition geometry for Topoisomerases action.

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