Abstract
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 supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.
Highlights
Numerous theoretical, computer simulation and experimental studies have shown that as the concentration of long circular polymers increases their equilibrium shapes change from swollen, spread out configurations to compressed globules [1,2,3,4,5,6,7,8,9]
Using Brownian dynamics simulations and atomic force microsopy we have investigated how the shape of circular supercoiled and non-supercoiled DNA molecules is affected by topological exclusion caused by high concentration of circular DNA molecules
We have shown that self-crowding of supercoiled DNA molecules acts in a similar way as increasing effective density of supercoiling in non-crowded DNA molecules
Summary
Computer simulation and experimental studies have shown that as the concentration of long circular polymers increases their equilibrium shapes change from swollen, spread out configurations to compressed globules [1,2,3,4,5,6,7,8,9]. This contrasts with the properties of highly crowded linear polymers, which at equilibrium, can freely spread in the available volume [8]. This well-characterized structure may be significantly different from the biologically relevant structure of supercoiled DNA at the physiological self-crowding conditions
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