Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.

ABSTRACT: Measurements of protein-mediated DNA looping reveal that in vivo conditions favor the formation of loops shorter than those that occur in vitro, yet the precise physical mechanisms underlying this shift remain unclear. To understand the extent to which in vivo supercoiling may explain these shifts, we develop a theoretical model based on coarse-grained molecular simulation and analytical transition state theory, enabling us to map out looping energetics and kinetics as a function of two key biophysical parameters: superhelical density and loop length. We show that loops on the scale of a persistence length respond to supercoiling over a much wider range of superhelical densities and to a larger extent than longer loops. This effect arises from a tendency for loops to be centered on the ple

SUBMITTER: Starr CH 

PROVIDER: S-EPMC9199097 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature