Single molecule DNA interactions between the E. coli DNA polymerase III α subunit and the polymerase manager protein UmuD

Abstract

The E. coli replicative DNA polymerase III (Pol III) α stalls upon encountering DNA damage. Specialized translesion synthesis (TLS) DNA polymerases are required for efficient bypass of damaged DNA. Although the mechanism for exchanging Pol III α for a TLS polymerase is not yet well understood, the protein UmuD is extensively involved in modulating cellular responses to DNA damage. UmuD binds both the polymerase α and the β processivity clamp, which tethers α to the DNA template. This interaction releases α from β, which has been proposed to facilitate polymerase switching (Silva et al. in preparation). Furthermore, UmuD may bind α and disrupt its interaction with the single-stranded DNA (ssDNA) template in an effort to facilitate polymerase exchange. We use single molecule DNA stretching, a technique that was previously used to characterize the DNA binding properties of α (McCauley et al. ACS Chem. Biol. 3, 2008), to investigate the possibility that UmuD disrupts the binding of α and ssDNA. Although UmuD alone does not bind DNA, its presence with α weakens the binding of α to ssDNA.