DNA polymerase ß uses its lyase domain in a processive search for DNA damage.

ABSTRACT

DNA polymerase (Pol) ß maintains genome fidelity by catalyzing DNA synthesis and removal of a reactive DNA repair intermediate during base excision repair (BER). Situated within the middle of the BER pathway, Pol ß must efficiently locate its substrates before damage is exacerbated. The mechanisms of damage search and location by Pol ß are largely unknown, but are critical for understanding the fundamental features of the BER pathway. We developed a processive search assay to determine if Pol ß has evolved a mechanism for efficient DNA damage location. These assays revealed that Pol ß scans DNA using a processive hopping mechanism and has a mean search footprint of ∼24 bp at predicted physiological ionic strength. Lysines within the lyase domain are required for processive searching, revealing a novel function for the lyase domain of Pol ß. Application of our processive search assay into nucleosome core particles revealed that Pol ß is not processive in the context of a nucleosome, and its single-turnover activity is reduced ∼500-fold, as compared to free DNA. These data suggest that the repair footprint of Pol ß mainly resides within accessible regions of the genome and that these regions can be scanned for damage by Pol ß.