Session 3A Lectures by Fellows/Associates

Understanding protein transport on DNA track

DNA metabolic processes, such as transcription, repression, replication, and DNA damage repair elicit movement of proteins from one subnuclear location to another. Transport of these DNA binding proteins (DBPs) is amazingly fast and their specific binding to short DNA target sequences in an enormous genomic background containing many alternative sites of similar sequences to that of the specific target site is extremely accurate. The fast association between proteins and DNA is governed by nonspecific interactions that allow protein transport (sliding) on DNA track, where the protein binds to DNA nonspecifically and performs a helical motion along the DNA major groove. We have explored using various computational approaches how the molecular characteristics of the interacting molecules and the in-vivo conditions (for example, crowding in the cell or coverage of DNA by nucleosomes) affect the transport efficiency of proteins on DNA. In my presentation, I shall discuss the molecular features of proteins and of the nucleic acids that allow fast dynamics and high-affinity binding on both single- and double-stranded DNA.