Chirality modifies the interaction between knots

TL;DR

This study uses molecular dynamics simulations to show that the interaction between knots in a double-knotted DNA filament under tension depends on their relative chirality, affecting the free energy landscape.

Contribution

It reveals how chirality influences knot interactions in DNA, a novel insight into the role of chirality in biopolymer physics.

Findings

Double-knotted DNA has a free energy minimum when knots are intertwined.

The depth of the free energy minimum depends on the relative chirality of the knots.

Chirality affects the balance between entropy and bending energy in knot interactions.

Abstract

In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under strong stretching. Using exhaustive Molecular Dynamics simulations we show that not only does a double-knotted dsDNA filament under tension possess a free energy minimum when the two knots are intertwined, but also that the depth of this minimum depends on the relative chirality of the two knots. We rationalize this dependence of the effective interaction on the chirality in terms of a competition between chain entropy and bending energy.