A Course-Grained Model for DNA Loop Extrusion

Abstract

We craft a coarse-grained model which captures the statics and dynamics of loop extrusion experiments performed at the Max Planck Institute of Biophysics quantitatively. After getting a working model for extrusion, we parameterize our model to the experimental results of Biswajit et al. and attempt to uncover the physical mechanisms behind the observations. In the experiments, the DNA is grafted at two ends and exposed to ATP along with the loop extruding protein SMC 5/6, where the extrusion stalls at a particular loop size. Using our parameterized values, we have managed to map the loop sizes of our simulation with those of the experiment, and explain the origin for stalling of the extrusion. We also conduct detailed analyses of the model dynamics employing principles of statistical physics, elucidating the underlying mechanisms driving the observed simulation outcomes. Additionally, we propose a model for generating torsional strain and producing coiled structures within the polymer. This is done to generate physically relevant structures called plectonemes, which are formed in DNA.