The Havranek group seeks to understand the determinants of specificity in DNA-binding proteins. Our long-term goal is to develop a quantitative model for describing the interactions between proteins and their DNA binding sites, with applications in prediction and engineering.
We are currently studying DNA-binding specificity across a family of bacterial transcription factors. Computationally, we are using sequence analysis and structural modeling to assess the differences and similarities of the binding profiles for these proteins. Experimentally, we are combining high-throughput sequencing of binding sites selected from randomized DNA libraries with fluorescence-based binding assays to characterize relative and absolute binding preferences within this family of transcription factors.