Human DNA polymerase κ uses template–primer misalignment as a novel means for extending mispaired termini and for generating single-base deletions

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Abstract
Human DNA polymerase κ (hPolκ) is a proficient extender of mispaired primer termini on undamaged DNA, wherein it extends directly by incorporating the next correct nucleotide, generating single-base substitutions in the process. Biochemical and genetic studies, however, have indicated that, in addition to single-base substitutions, Polκ generates single-base deletions. Here we show that hPolκ is very adept at using template–primer misalignment as a novel means for extending mispaired termini and for generating single-base deletions. The proficient ability of hPolκ to extend mispaired primer termini either directly or by misalignment could be important for the continued and efficient progression of the replication fork when mismatches introduced by the replicative polymerase are not proofread. In extending from nucleotides opposite DNA lesions, hPolκ uses the direct and misalignment modes of mispair extension to different extents, depending on whether the template base is present or not at the primer terminus; thus, although hPolκ can extend directly from nucleotides opposite damaged bases, it can use only the misalignment mechanism to extend from nucleotides opposite an abasic site. A particularly unconstrained active site at the template–primer junction could afford hPolκ the ability to tolerate the geometric distortions of mismatched base pairs or those resulting from template–primer misalignment, thereby enabling it to use both of these modes of mispair extension.