2022/11/14 by Sarah Wettermann, Wettermann, Sarah, Ranajay Datta +3
Biochemistry, Genetics and Molecular Biology · Computer Science · Environmental Science · #Algorithms and Data Compression #Bacteriophages and microbial interactions #FOS: Physical sciences #RNA and protein synthesis mechanisms #Soft Condensed Matter (cond-mat.soft)
paper · pdf · doi:10.48550/arxiv.2211.07326
openalex publication_date 2022/11/14 · openalex created_date 2022/11/23 · openalex updated_date 2026/07/28
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.