DNA Polymerase α has Cyclobutane Pyrimidine Dimer Translesion Activity that is Suppressed During Normal Replication.

To ensure rapid and accurate DNA replication during S-phase, the cell uses DNA damage tolerance (DDT) pathways, leaving lesions to be repaired after completion of replication. One established DDT pathway is Translesion Synthesis (TLS), in which lesions are bypassed by specialized TLS Polymerases that work in conjunction with the replisome. Here we demonstrate that DNA Polymerase alpha (Pol α), the replicative primase/polymerase, can also unexpectedly replicate through a bulky lesion in vitro. We use biochemical and single-molecule fluorescence assays to characterize cyclobutane pyrimidine dimer (CPD) TLS activity of Pol α. We find that Pol α overexpression does not alter UV sensitivity in TLS-null cells. Consistent with this, we observe that Pol ε, the leading strand replicative polymerase, strongly inhibits Pol α CPD TLS activity via proofreading, even with Pol α present at much higher relative concentrations. We further show that RPA, a single-stranded DNA binding protein complex, strongly inhibits CPD TLS activity of Pol α. In contrast, Pol η, the canonical TLS Pol for pyrimidine dimers, is unaffected by Pol ε and is conversely stimulated by RPA. Finally, we demonstrate with single-molecule Fluorescence Resonance Energy Transfer (FRET) that the DNA binding cleft of Pol α must remain in the open state to accommodate a bulky CPD lesion during TLS, possibly accounting for the relatively slow kinetics of CPD bypass that we observe. The results suggest that the intrinsic bulky TLS activity of Pol α is likely suppressed at the replication fork by the replisome itself during normal replication.