Rosalind Franklin's pioneering work to establish the atomic structure of DNA has underpinned much of our understanding of the 'molecule of life', however in the cell, DNA is tangled and twisted, adopts complex topologies and is frequently maintained under superhelical stress. The effect of coiling, twisting and knotting on complex genomic DNA affects its function and how it interacts with molecular machinery. However the complexity and flexibility of this molecule means that much about the structure and interactions of tangled and twisted DNA remains poorly defined. It is critical that we improve this understanding as complex DNA structures, which make up the majority of the genome, have a huge impact on our health: in aging, cancer and fighting infectious disease.

Despite its unique capabilities for observing individual molecules at high resolution in fluid, the widespread adoption of AFM has been limited by the complexity of the technique, and the limited analysis of the powerful data produced. Traditionally, the majority of AFM analysis has been carried out by hand, relying on a highly trained and experienced researcher. When coupled with data acquisition that is highly dependent on the expertise of the operator, this has meant that AFM has not been adopted as the tool that can solve problems currently inaccessible to other tools of structural biology, which operate at this length scale. I will pioneer the use of high-resolution AFM and automated analysis to overcome these limitations and uncover the effect of DNA structure and conformation on DNA-protein interactions.

To achieve this I will work in collaboration with industry to combine state-of-the-art atomic force microscopy developments, with new automated analysis tools that facilitate tracing and quantification of the topology, structure and conformation of DNA substrates, using multiple machine learning approaches. I will work with the AFM community to ensure that these tools are available to researchers at all levels, improving the reproducibility of their analysis, and lowering the activation energy for this method of imaging, currently a considerable barrier to entry. Using these tools I will determine how the structural heterogeneity of DNA impacts its interactions with key antibiotic and anti-cancer targets: topoisomerases; the gene editing tool CRISPR-Cas9; and G-quadruplexes, alternative DNA structures with potential as new anti-cancer targets. This programme is focussed on systems with translational potential, to enable me to impact pharmaceutical development.