Seminar by Simone Pigolotti
Sequence-dependent effects in facilitated diffusion
It has been established that transcription factors find their target on DNA by "facilitated diffusion", i.e. by alternating 3D diffusion and 1D random walk along the DNA. I will briefly discuss why this dynamics speeds up target search and recent experimental evidences supporting the theory. This implies that the "genetic context", i.e. the DNA energy landscape around a specific target finding can have an important role for the transcription factor kinetics. In particular, by analyzing DNA sequences from E.Coli, I will show how genetic context can be used to speed-up target search. I will end up discussing the possible evolutionary implications of this finding.