Knotting of linear DNA in nano-slits and nano-channels: a numerical study

TL;DR

This study numerically investigates how spatial confinement in nano-slits and nano-channels influences DNA knotting, revealing confinement-dependent variations in knotting probability, knot length, and potential implications for biological and nanotechnological applications.

Contribution

It provides a comparative numerical analysis of DNA knotting in nano-slits versus nano-channels, highlighting how confinement geometry affects entanglement properties.

Findings

Knotting probability peaks at slit widths of 70-100nm.

Maximum knotting incidence is below 20% in slits, over 50% in channels.

Knot length decreases significantly below 100nm in channels, remains constant in slits.

Abstract

The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices, and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30nm- 1\mu m range and the confined DNA chains are 1 to 4\mu m long. It is found that the knotting probability is maximum for slit widths in the 70-100nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region which drops significantly below D ~100nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications.