Hydrodynamics of DNA loop extrusion

The compaction of chromosomal DNA during various stages of the cellular life cycle has been shown to involve a class of enzymatic molecular motors known as structural maintenance of chromosomes (SMC) complexes, of which condensin and cohesin are two important examples. These complexes are long ring shaped motors and have been observed to translocate along chromatin in a force-dependent directed manner to form loops via a process known as "loop extrusion" using the energy obtained from the hydrolysis of ATP. This loop formation has been studied in recent in vitro single-molecule experiments on lambda phage DNA under imposed shear flow, where the two ends of the DNA were tethered to a wall and loops were shown to nucleate and grow in the presence of active SMC complexes. Motivated by these experiments, we present a microscopic model for the dynamics of active loop extrusion that accounts for the structural features and dynamics of the motor proteins. Combining modeling and Brownian dynamics simulations, we demonstrate the roles played by hydrodynamic interactions, the active response of the motors and chain mechanics in assisting loop extrusion under different parameter regimes.