The goal of this new project is to develop single molecule methods for the quantitative study of DNA interactions with small molecules and proteins and to use these methods to investigate specific biologically important systems. The CIRCS Associate Director Mark Williams and co-PI Megan Nunez from Mount Holyoke College will use several DNA constructs and data analysis methods to probe the thermodynamics and kinetics of DNA-ligand interactions and determine the time-dependent changes of DNA structure as proteins and small molecules bind. In addition to method development, this work will shed light on the fundamental biophysics of DNA-small molecule interactions as well as the biophysical and biochemical mechanisms of multiple protein interactions involved in retrotransposon replication and DNA damage response. The three specific aims of this project include probing the structural dynamics of DNA-small molecule interactions using single molecule force spectroscopy, studying dynamic protein-DNA interactions important for LINE1 retrotransposition, and investigating the protein-protein and protein-DNA binding interactions that participate in the management of DNA polymerase switching in E. coli. The total grant amount is $950,000 over 5 years, beginning March 1, 2013.