Adam Pollak Final Defense

Thursday, October 30, 2014
2:00 PM
Elings Hall, Room 1601



    Site specific DNA binding by proteins is critical for cellular function. Yet, how proteins move along the DNA maize to find their rare sites remains incompletely understood. We demonstrate that a bacterial DNA methyltransferase (Dam) uses a novel mechanism of movement – intersegmental hopping – where proteins “hop” between looped DNA segments, allowing for efficient long-range searches. This intersegmental hopping mechanism provides for protein movement in spite of the presence of various DNA binding proteins that compact genomic DNA in the cell. Additionally, an extreme sliding mechanism is demonstrated for a bacterial restriction endonuclease (EcoRI), involving rigorous, redundant searches of local DNA sequence space. The site finding mechanisms particular proteins utilize can be rationalized by considering their cellular roles.