Physical determinants of DNA recognition and genome organization in crowded environments

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Abstract The proposed research program seeks to understand how genomic information is organized and accessed. At the core of my proposal is an effort to develop a framework that bridges in vitro experiments to their counterparts in vivo. We will do this by employing novel in vitro experimental platforms that are uniquely poised to work with mesoscale materials. (1) DNA and chromatin curtains, which are a high-resolution, high-throughput single- molecule tool for imaging interactions on long extended DNA and chromatin fibers. (2) Optical tweezers, which measure forces on DNA or chromatin to exceptionally high resolution. And (3) droplet experiments, which allow us to measure key biophysical parameters, like free energies, partition coefficients, and relative mobilities. Using these assays, research in my lab is aimed at understanding how chromatin condenses into compact structures and the role that compaction plays in biology. In addition, we are investigating how epigenetic information is propagated along chromatin fibers and how chromatin dynamically partitions into regions of similar function in the nucleus. The proposed research program seeks to connect in vivo measurements into mechanistic frameworks of individual protein actions by tracing reactions across scales. Specifically, our approaches afford us the opportunity to increase the complexity of a particular reaction from isolated molecules in a test tube, to one dimensional reactions on extended molecules, to the disordered three dimensional environment of condensates, and finally to the nucleus. We feel that stepping across scales in our investigations, stopping at these intermediate levels of observation, which up to now have been missing, will allow us to successfully attack important questions in chromatin biology about regulation and domain formation, which have remained elusive. And ultimately, will drive us toward a cohesive model of how our genetic information is accessed, managed, and packaged.