Single-molecule view of coordination in a multi-functional DNA polymerase

Replication and repair of genomic DNA requires the action of multiple enzymatic functions that must be coordinated in order to ensure efficient and accurate product formation. Here we have used single-molecule FRET microscopy to investigate the physical basis of functional coordination in DNA polymerase I (Pol I) from E. coli, a key enzyme involved in lagging-strand replication and base excision repair. Pol I contains active sites for template-directed DNA polymerization and 5 flap processing in separate domains. We show that a DNA substrate can spontaneously transfer between polymerase (pol) and 5 nuclease (5 nuc) domains during a single encounter with Pol I. Additionally, we show that the flexibly tethered 5 nuc domain adopts different positions within Pol I-DNA complexes, depending on the nature of the DNA substrate. Our results reveal the structural dynamics that underlie functional coordination in Pol I and are likely relevant to other multi-functional DNA polymerases.