Biology Department Seminar

A central mystery in the function of site-specific DNA-binding proteins is the detailed mechanism for rapid location and binding of target sites in DNA. DNA repair proteins, such as DNA glycosylases, must search out and initiate repair of rare lesions to prevent mutations and chromosomal defects. Rapid target search is thought to occur through ‘facilitated diffusion,’ a combination of diffusion through solution (three-dimensional) and diffusion along DNA (one-dimensional). We have characterized the one-dimensional pathway using high-speed imaging of single fluorescently-labeled protein molecules diffusing along DNA stretched by shear flow. Salt concentration-dependent measurements reveal that the proteins slide in persistent contact with DNA. The fast sliding suggests that DNA glycosylases locate lesion bases by a massively redundant search in which the enzyme selectively binds lesion bases under kinetic control. Ongoing work includes efforts to understand the effect of molecular crowding on sliding and the diversity of biological systems that take advantage of DNA-mediated facilitated diffusion.