Replication of a cis–syn thymine dimer at atomic resolution

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cis–syn cyclobutane pyrimidine dimers (CPDs) as the most common lesion1. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol η2,3. Mutations in POLH encoding pol η are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer4,5,6. Here we have determined two crystal structures of Dpo4, an archaeal pol η homologue, complexed with CPD-containing DNA, where the 3′ and 5′ thymine of the CPD separately serves as a templating base. The 3′ thymine of the CPD forms a Watson–Crick base pair with the incoming dideoxyATP, but the 5′ thymine forms a Hoogsteen base pair with the dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site for catalysis. A model of the pol η–CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol η and the Dpo4–CPD complex suggests unique features that allow pol η to efficiently bypass CPDs.