PT  - JOURNAL ARTICLE
AU  - Barbensi, Agnese
AU  - Celoria, Daniele
AU  - Harrington, Heather A.
AU  - Stasiak, Andrzej
AU  - Buck, Dorothy
TI  - Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology
AID  - 10.1126/sciadv.aay1458
DP  - 2020 Feb 01
TA  - Science Advances
PG  - eaay1458
VI  - 6
IP  - 9
4099  - http://advances.sciencemag.org/content/6/9/eaay1458.short
4100  - http://advances.sciencemag.org/content/6/9/eaay1458.full
SO  - Sci Adv2020 Feb 01; 6
AB  - 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 modeling 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 the grid diagram–based approach provides an important, new, and computationally convenient framework for investigating entanglement in biopolymers.