Human DNA polymerase κ forms nonproductive complexes with matched primer termini but not with mismatched primer termini

Human DNA polymerase kappa (pol κ) is a member of the Y family of DNA polymerases that function in translesion synthesis. It synthesizes DNA with moderate fidelity and does not efficiently incorporate nucleotides opposite DNA lesions. Pol κ has the unusual ability to efficiently extend from mismatched primer termini, and it extends readily from nucleotides inserted by other DNA polymerases opposite a variety of DNA lesions. All of this has suggested that pol κ functions during the extension step of translesion synthesis. Here, we have carried out pre-steady-state kinetic studies of pol κ using DNA with matched and mismatched primer termini. Interestingly, we find that mismatches present only a modest kinetic barrier to nucleotide incorporation by pol κ. Moreover, and quite surprisingly, active-site titrations revealed that the concentration of active pol κ is very low with matched DNA, and from DNA trapping experiments we determined that this was due to the formation of nonproductive protein-DNA complexes. In marked contrast, we found that the concentration of active pol κ was six-fold greater with mismatched DNA than with matched DNA. Thus, pol κ forms nonproductive complexes with matched but not with mismatched DNA. From these observations, we conclude that pol κ has evolved to specifically function on DNA substrates with aberrant primer-terminal base pairs, such as the ones it would encounter during the extension step of translesion synthesis.