Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology

Agnese Barbensi, Daniele Celoria, Heather A. Harrington, Andrzej Stasiak, Dorothy Buck

Research output: Contribution to journalArticle


Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process such as the topoisomerase-mediated preferential unknotting of DNA molecules. We model here topoisomerase-mediated passages of double-stranded DNA segments through each other using the formalism of grid diagrams. We show that this grid diagram-based modelling approach captures the essence of the preferential unknotting mechanism, based on topoisomerase selectivity of hooked DNA juxtapositions as the sites of intersegmental passages. We show that grid diagram-based approach provide an important, new and computationally convenient framework for investigating entanglement in biopolymers.
Original languageUndefined/Unknown
JournalPreprint on arXiv
Publication statusPublished - 12 Sep 2019


  • q-bio.BM

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