Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

Significance Positive and negative supercoiling refers to the overwinding or underwinding, respectively, of a DNA double helix. Supercoiling is important ubiquitous, as all cells, from bacterial human, deploy proteins keep their genome negatively supercoiled facilitate transcription replication. Additionally, polymerase transcribes gene, its action generates twin domains supercoils opposite sign. Here we characterize, by simulations, three-dimensional geometry such domains, show that can be exploited act at distance on DNA-binding proteins, for instance, unwrapping nucleosome long before reaches it. We also quantify dynamics double-stranded supercoiling, striking timescale separation between diffusive relaxation twist writhe.