Influence of ionic conditions on knotting in a coarse-grained model for DNA

TL;DR

This study uses a coarse-grained model to analyze how ionic conditions influence DNA knotting, revealing that salt levels significantly affect the formation and dissolution of knots, with implications for understanding DNA topology.

Contribution

The paper demonstrates that a coarse-grained Kratky-Porod model can quantitatively predict DNA knotting behavior under varying ionic conditions, aligning with experimental data.

Findings

High salt enhances DNA knotting

Low salt reduces knot formation

Model accurately predicts experimental topological features

Abstract

We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers. We find that the occurrence of knots in DNA can be reinforced considerably by high salt conditions and confinement between plates. Likewise, knots can almost be dissolved completely in a low salt scenario. Comparisons with recent experiments confirm that the coarse-grained model is able to capture and quantitatively predict topological features of DNA and can be used for guiding future experiments on DNA knots.