Düşük çözünürlüklü bir DNA modeli ve süpersarmallanma dinamikleri

DNA polymers are the primary containers of information in all living organisms. In addition to its fundamental role as a biomolecule, DNA has technological applications as a building block for nanostructures. Even though molecular structure of DNA was established as a double helix in 1953, very little about its dynamical properties were discovered during the following decades. With the advent of single molecule experiments, probing dynamical processes in single DNA molecules has been possible in the last decades. Although recent experiments provide unprecedented insight, they have limited resolution in both time and length domains. Molecular simulations, on the other hand, provide complete knowledge of the system but are limited by computational cost. Coarse grained models aim to decrease the cost of molecular simulations while preserving most of the resolution. In this work, we built a coarse grained model to represent both single and double stranded DNA strands with high enough performance to simulate biologically relevant time and length scales. Supercoiling is a mechanism where a twist storing polymer such as DNA expresses torsional stress through conformational changes. Supercoiling is of interest from a biological point of view as it is readily observed in genome packing schemes and presumably affects gene expression patterns. A recent single molecule experiment provided indirect observations on the supercoil dynamics of overwound DNA. In this experiment, supercoiled regions along the length of DNA demonstrated fast hopping behaviour in addition to diffusive motion. In this work, we reproduced this experimental scenario in silico using a coarse grained model. We simulated up to 1 kilobase long overwound DNA strands under tension and observed time evolution of the conformation of the molecule. We produced supercoiled conformations associated with local density peaks observed in the experiment and time evolution of curvature along the length. We varied the degree of overwinding (?) and the amount of tension and observed a buckling transition at different threshold ? values. We reproduced the experimentally observed hopping behaviour in addition to diffusive motion near the threshold ? values.