Atomistic Simulations of Supercoiled Linear DNA Under Tension

DNA in living beings is constantly subject to torsional stress as a result of processes such as transcription and replication, as well as the action of nucleosomes and nucleiod-associated proteins. This stress is relieved through DNA supercoiling; a process by which turns are added to or taken away from DNA, forming higher-order structures known as plectonemes. These structures are the result of the DNA duplex wrapping around itself in three dimensions, and act to bundle DNA together, compacting it. DNA supercoiling also plays a role in protein recognition and gene regulation, promoting the binding of transcription factors, and forming topological barriers. This thesis presents the results of all-atom molecular dynamics simulations of supercoiled DNA under tension, with the aim of understanding the dynamics of structure formation, as well as the role of sequence in dictating their behaviour.

These simulations re-create the experimental ‘hat-curve’, displaying clear asymmetry between positive and negative supercoiling, and revealing the presence of denaturation bubbles in negatively supercoiled systems. Showing high levels of co-localisation with the tips of plectonemes, these denatured regions confirm the existence of the ‘tip-bubbles’ observed previously in coarse grained simulations. Simulations also unveil the existence of ’tip-bubbles’ in positive supercoiling, which show high levels of curvature.

Also demonstrated is the possible role of sequence in structure formation, with regions of bubble formation clearly identified by predictive methods, but with probability landscapes perturbed by sharply bent plectoneme tips. Results also indicate that plectoneme nucleation locations are influenced by the inherent curvature of the DNA, with highly curved regions of DNA predicting the locations of plectoneme formation.

Finally, a simple model in which both size and ground path curvature is used to predict plectoneme position in positive supercoiling is formulated, with preliminary results from magneto-optical tweezers appearing to be predicted by these two factors.