Exploration of DNA systems under internal and external forcing using coarse-grained modelling

Thesis

The profound simplicity and versatility of the molecule at the heart of all earth- bound life forms, DNA, continues to inspire new frontiers of scientific inquiry. Central to many of these, including the de novo design of novel DNA nanostructures and the use of DNA to probe the principles of biological self-assembly and the operation of cellular nanomachines, is the interaction of DNA with forces, both internal and external. This thesis comprises a survey of three key ways coarse- grained simulations using the oxDNA model can contribute to efforts to characterize these interactions. First, a non-equilibrium data analysis framework based on the Jarzynski equality from statistical physics is validated for use with oxDNA through the reconstruction of free energy landscapes for canonical DNA hairpin systems. We provide a framework for assessing errors in the method and apply it to study a system for which conventional equilibrium simulations would be impractical: DNA origami ‘handles’ proposed for use in force spectroscopy experiments. Next, we simulate the forcible unravelling of three DNA origami structures, the largest systems yet studied with simulated force spectroscopy. We combine these results with experimental AFM data to probe the mechanical response of origami in unprecedented detail, highlighting the effect of nanostructure design on unfolding behaviour. Lastly, we examine the validity of using widely-employed polymer elastic models to predict internal entropic forces in ssDNA. We develop a framework for measuring internal forces in the oxDNA coarse-grained model and apply it to analyze the pico-Newton range forces exerted by a recently proposed DNA origami force clamp, ultimately concluding that conventional means of estimating internal ssDNA forces are often inaccurate and should be supplemented with coarse-grained simulations. In addition to providing new insights about the DNA systems we present, our results highlight the significant fruits of complementing experimental studies with coarse-grained simulations.

Authors: Engel, M

• DOI: 10.5287/ora-obezv0vqk
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: DNA; single molecule force spectroscopy; force-extension curve; molecular dynamics; non-equilibrium physics; DNA nanotechnology; oxDNA
• Subjects: Computational physics; DNA nanotechnology; Non-equilibrium physics