Theory and simulation of twisted DNA duplexes

Thesis

We use basic statistical mechanics and computer simulations with coarse-grained models to investigate the response of (inhomogeneous) DNA duplexes to linear and torsional mechanical stress. While the response of homogeneous DNA to more modest external stresses has been studied in detail, much less is know about DNA response to very strong over or under twisting, or about the biologically relevant case of inhomogeneous DNA under external torsion. By simulating geometries that resemble single-molecule molecular tweezers experiments previously reported in the literature, we validate our basic models, and measure the end-to-end duplex extension, torque, and the denaturation states of individual base-pairs, as well as the position of plectonemes when present in the post-buckling state. We generalise previous observations that plectonemes are preferentially localised (i.e. pinned) on sequence mismatches to predict that any sequence that is either significantly more bent or more flexible than the rest of the duplex should present a similar effect. We develop a simple theory to quantify this preference and test it in simulations, observing a semi-quantitative agreement. We also propose a general protocol to extend the popular oxDNA coarse-grained model of DNA to treat such bent/flexible sequences, and apply it to model thymine dimers, the most common DNA photoproducts. The theory provides almost quantitative agreement with simulations; in particular, the prediction that the pinning is dependent only on the bending angle and flexibility of the sequence, but not on the detail of how these are generated, is confirmed. Some consequences of the presence of a thymine dimer in biological DNA are also proposed. Finally, we use oxDNA to investigate the boundaries between the pre-buckling, post-buckling, and torsionally melted states, as well as the features of torsionally-melted underwound and overwound DNA, respectively called L-DNA and P-DNA. Unexpectedly, we observe that both torsionally-melted forms preferentially relax writhe by forming solenoids, rather than plectonemes. We compare our results with previous experimental and theoretical work and propose some experiments to confirm or deny this peculiar feature.

Authors: Randisi, F

• Alternative title: The impact of flexible, bent, or damaged DNA sequences in molecular tweezers experiments on DNA duplexes, and nucleotide-level molecular simulations of P-DNA and L-DNA
• DOI: 10.5287/ora-qxmnrpkaj
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: thymine dimers; DNA modelling; P-DNA; Supercoiling; DNA damage; L-DNA; coarse-grained modelling
• Subjects: Molecular biology; Biochemistry; Computational physics; Computational chemistry