Supercoiling Enhances DNA Mobility by Reducing Threadings and Entanglements

TL;DR

This study uses large-scale MD simulations to reveal that supercoiling in DNA plasmids increases their size and diffusivity by reducing entanglements, challenging previous assumptions about DNA rheology.

Contribution

The paper demonstrates how supercoiling reduces entanglements in DNA solutions, leading to increased size and mobility, which was previously not well understood.

Findings

Supercoiling increases DNA plasmid size in entangled solutions.

Supercoiling enhances diffusivity of DNA plasmids.

Supercoiling reduces threadings and entanglements among DNA molecules.

Abstract

DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained -- or supercoiled -- DNA plasmids are largely neglected; this is partly due to the limited understanding of how supercoiling affects the rheology of entangled DNA. To address this open question we perform large scale Molecular Dynamics (MD) simulations of entangled solutions of DNA plasmids modelled as twistable chains. We discover that, contrarily to what generally assumed in the literature, larger supercoiling increases the average size of plasmids in the entangled regime. At the same time, we discover that this is accompanied by an unexpected increase of diffusivity. We explain our findings as due to a decrease in inter-plasmids threadings and entanglement