Complex phase transition of DNA condensation under crowding confinement conditions

Abstract

The mechanism underlying the crowding effects that assist the condensation process by multivalent cations under confinement is not yet reported. Based on the strong correlation model, Monte Carlo simulation was implemented to detect the crowding effects on DNA condensation within a capsule-like space, and its geometry controlled by the aspect ratio. With the addition of crowders, the condensed conformations confined within the spherical space (aspect ratio is 1) become more compact than those without crowders. The DNA-condensed conformations undergo a transition from the initial random coil structure to toroid structure, followed by the extended rod-like structure, and finally to totally compacted structure. The critical volume fraction corresponding to the transition from the rod-like structure to totally compacted structure pertained to the crowder size proportionally. Moreover, the critical volume fraction corresponding to the phase transition strongly depends on the confinement geometry, the critical volume fraction for the case with constant radius is inversely proportional to the aspect ratio. Conversely, the case with constant cylinder length showed that the critical volume fraction is proportional to the aspect ratio. These phenomena are consistent with their corresponding phase diagram re-expressed in the space of volume fraction and aspect ratio. The effects of confinement geometry and crowder size on the response of DNA condensation to crowding are elucidated and generalized into the space diagram in the space of aspect ratio and crowder size. When the aspect ratio less than 1.6 and the crowder size larger than 2.0 nm or when the aspect ratio ≥ 1.6 and the crowder size larger than the critical dc∗, the DNA conformation undergo the transition from the initial random coil structure to toroid structure, followed by totally compacted structure; when the aspect ratio ≥ 1.6 and the crowder size ≤dc∗, the DNA condensed conformations will be condensed further from the totally compacted structure to the extended rod-like structure. Furthermore, the transition from the totally compacted structure to the extended rod-like structure is entirely due to the crowder size and the confinement geometry between the de Gennes and Odijk regimes.