DNA dynamics and organization in sub-micron scale: Bacterial chromosomes and plasmids in vivo and in vitro

Decades of research have witnessed that the mechanical properties of DNA and the associated protein interactions are crucial to the structural organizations and dynamic behaviors of bacterial DNA molecules. Packaged in a restricted cellular space and respective compositions, the entropic force due to confinement is a major factor driving the basal structural formation of the bacterial chromosome and the distribution of plasmids. The dynamic responses of the DNA-protein interactions also modulate the DNA organization when the cellular functions proceed. In this review, we survey the in-vivo and in-vitro evidence and the current understandings of the cellular phenomena of DNA molecules in the sub-micron scale of the bacterial cellular environment. The physical nature and constraints of DNA in cells and the related biological factors, especially the effects induced by gene expressions, are also discussed. We anticipate that by the methodological advances in vivo and in vitro as well as their combinations, the fundamental insights of the coupling from the physical environment and DNA-protein interactions on bacterial DNA dynamics and organization may be revealed.