The goal of this 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 investigators will use several DNA constructs (long and short double-stranded and single-stranded DNA molecules) 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. This project involves three specific aims: 1. To probe the structural dynamics of DNA-small molecule interactions using single molecule force spectroscopy. 2. To probe dynamic protein-DNA interactions important for LINE1 retrotransposition. 3. To probe the protein-protein and protein-DNA binding interactions that participate in the management of DNA polymerase switching in E. coli. The PIs will develop methods for understanding multiple protein interactions with DNA and use these methods to probe interactions involved in DNA polymerase management, which is critical for cellular responses to DNA damage.
The PI has developed innovative biophysical methods for examining DNA binding using single molecule manipulation. The PI integrates his research into teaching experimental methods, and he has a strong track record of training graduate and undergraduate students in interdisciplinary research at the interface of physics, chemistry, and biology. In addition to regularly hiring full-time 6-month physics co-op undergraduate students, he has hosted undergraduates from several other undergraduate institutions. The PI is hosting a professor and three of his students from a regional university with a majority of first-generation college students. This experience will be used to expand biophysics research and introduce biophysics into the university's curriculum. The co-PI is a Professor at a liberal arts college for women with a historical tradition of training undergraduate women scientists. She will involve multiple students in synthesizing DNA constructs and small molecule complexes that they will bring to Northeastern and characterize by single molecule force spectroscopy. This project is jointly supported by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences and the Physics of Living Systems Program in the Physics Division.
