Our field is biophysical chemistry of protein-DNA interactions. The research in our lab focuses on the dynamic processes whereby transcription factors and DNA-modifying enzymes scan DNA and recognize their target sites. Our current major projects are as follows.
1. Ion-pair dynamics and their role in protein-DNA association
Ion-pair formation is one of the most fundamental chemical interactions for life. Despite their potential importance in molecular recognition and enzymatic catalysis, the dynamics of ion pairs of biological macromolecules are not well understood. Recently our group has developed unique NMR methods for investigating dynamics of ion pairs involving protein side chains. Using these methods, we are elucidating the role of ion-pair dynamics in protein-DNA interactions.
2. Mechanisms of DNA scanning by proteins
When transcription factors and DNA repair/modifying enzymes perform their function, these molecules must first locate their specific target sites in the vast presence of nonspecific but structurally similar sites on DNA. How do proteins scan DNA? Using NMR spectroscopy, stopped flow fluorescence spectroscopy, and other biophysical / biochemical methods along with mutagenesis, we are investigating how proteins scan DNA and locate their target sites.