DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoilingdensity are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoilingpermits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNAshapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.