From nature to nano: structure, dynamics and reactivity of DNA three-way junctions

The double helix is the iconic structure of DNA, but this unbranched form is not the active one in vivo. Considering that the structure and dynamics of duplex DNA still preoccupies experimentalists and theoreticians around the world, sixty years after the structure was announced by Watson and Crick, it is clear that the study of branched DNA is in its infancy. The aim of this proposal is to use cutting-edge single-molecule tools to understand the structure and dynamics of an important branched DNA molecule, the three-way junction, at the nanoscale. These branched species are present in vivo, they are implicated in neurological diseases, and they are used as building blocks in DNA-based nanoscience. The project will give otherwise inaccessible information on key biological processes, and could lead to potential drug targets, to new design strategies for synthetic biology and to the development of the next generation of programmable DNA nanoscale machines.

This project aims to understand the fundamental properties of an important class of branched DNA molecule, the three-way junction. These molecules are implicated in a range of neurological disorders. This work will provide underpinning knowledge for the development of new pharmaceuticals that target abhorrent DNA structures. This project will also provide increased understanding of how mutations arise when processes such as DNA replication is disrupted. This information will benefit clinicians by enhancing our knowledge about the links between DNA replication and the formation of mutations, providing opportunities for the development of new therapeutic and diagnostic tools for genetic diseases and cancer.

The field of synthetic biology will also benefit from this proposed research. Synthetic biology aims to generate partially or wholly synthetic cells optimised for use in energy production, chemical synthesis and other environmentally and economically important processes. Our programme will provide insight into what must be included in synthetic lifeforms to ensure accurate copying of their genetic blueprints. Those interested in using nucleic acids in a non-biological context, particularly for advanced nanoscience applications such as nanomachines and computation, will benefit from the fundamental structural aspects of this work and from the investigation into the reactivity of three-way junctions to oligonucleotides.

The public will be the ultimate beneficiaries of this work. Results from our experiments will provide potential new avenues for the development of pharmaceuticals related to health whilst enhanced design of synthetic cells has the potential to contribute new solutions to major environmental challenges. Thus our work will contribute to the health and well-being of the population and also enhancement of the UK economy. This research will also make a significant contribution to the provision of a scientifically-literate workforce and so will enhance the economic competitiveness of the UK. The project is interdisciplinary, using cutting-edge techniques to analyse complex biological molecules. The researcher employed on this project will therefore receive excellent training in a wide range of techniques, and will be well-placed to discuss the topical themes of nanoscience, single-molecule detection and synthetic biology at public engagement events.