2020/09/21 by Jan Smrek, Davide Michieletto, Smrek, Jan +1
Engineering · Environmental Science · #Bacteriophages and microbial interactions #Biological Physics (physics.bio-ph) #FOS: Physical sciences #Microfluidic and Bio-sensing Technologies #Nanopore and Nanochannel Transport Studies #Soft Condensed Matter (cond-mat.soft)
paper · pdf · doi:10.48550/arxiv.2009.09742
openalex publication_date 2020/09/21 · openalex created_date 2022/07/24 · openalex updated_date 2026/07/28
DNA is increasingly employed for bio and nanotechnology thanks to its\nexquisite versatility and designability. Most of its use is limited to\nlinearised and torsionally relaxed DNA but non-trivial architectures and\ntorsionally constrained -- or supercoiled -- DNA plasmids are largely\nneglected; this is partly due to the limited understanding of how supercoiling\naffects the rheology of entangled DNA. To address this open question we perform\nlarge scale Molecular Dynamics (MD) simulations of entangled solutions of DNA\nplasmids modelled as twistable chains. We discover that, contrarily to what\ngenerally assumed in the literature, larger supercoiling increases the average\nsize of plasmids in the entangled regime. At the same time, we discover that\nthis is accompanied by an unexpected increase of diffusivity. We explain our\nfindings as due to a decrease in inter-plasmids threadings and entanglement\n