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

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.

Automated summary

We investigate the probability of knotting in long double-stranded DNA strands using a coarse-grained Kratky-Porod model and Monte Carlo simulations. We manipulate the ionic conditions by adjusting the effective diameter of monomers. Our findings show that high salt conditions and confinement between plates significantly increase the occurrence of knots, while knots can be almost completely dissolved in low salt scenarios. Comparisons with recent experiments indicate that the coarse-grained model accurately captures and predicts topological features of DNA, making it a useful tool for guiding future experiments on DNA knots.