DNA ORIGAMI DEVICES · Single-molecule studies of protein-protein and protein-DNA interactions, enabled by DNA origami

Adhesive interactions between macromolecules are ubiquitously found in biology. Regulatory processes in biology depend on temporary physical inter-biomolecular interactions whose strengths are regulated by the internal state of the cell. Obtaining quantitative insight the dynamic strength of interactions between biomolecules has remained a difficult task. Single-molecule approaches can provide detailed insight into intra-molecular interactions in biomolecules. Yet, protein-protein and protein-DNA interactions have remained largely inaccessible. We propose to enable the single-molecule study of protein and protein-DNA interactions by taking advantage of the fine positional control afforded by DNA origami to overcome critical experimental challenges. As a first case study we plan to employ the DNA origami devices to study the single-molecule mechanics protein-protein and protein-DNA interactions that are relevant in the regulation of the galactose metabolism in yeast. We also seek to take steps towards a high-throughput single-molecule protein-DNA and protein-protein interaction assay to open access to a quantitative and combinatorial study of many different inter-macromolecular interactions, as well as to study the effects exerted by additional inhibiting or activating ligands. The proposed project will open up novel opportunities for a systematic study of macromolecular interactions in biology and is likely to deepen our understanding of regulatory processes in biology. Lessons that will be learned may suggest new ways to the rational design or identification of compounds that can prevent disease-causing interactions.