Zn ions improve the fidelity of metal-mediated primer extension while suppressing intrinsic and Mn-induced mutagenic effects by DNA polymerases.

While Mn ions are well-established for reducing the fidelity of DNA polymerases, leading to the misincorporation of nucleotides, our investigation of the effects of metal ions revealed a contrasting role of Zn. Here, we demonstrate that Zn ions enhance the fidelity of DNA polymerases (the 3' → 5' exonuclease-deficient Klenow fragment and Taq DNA polymerase) by suppressing misincorporation during primer extension reactions. Remarkably, Zn ions inhibit both intrinsic misincorporation and Mn-induced misincorporation of nucleotides. Furthermore, Zn ions also effectively suppressed misincorporation during metal-mediated primer extension reactions, which involved forming Ag and Hg ion-mediated base pairs. These findings suggest that Zn ions inhibit both intrinsic and Mn-induced mismatched base pair formation. Consequently, the combined use of Mn and Zn ions may offer a strategy for precisely regulating the fidelity of DNA polymerases. Remarkably, Zn ions even suppress misincorporation in primer extension reactions that rely on metal-mediated base pairs, and conversely, this suggests that DNA polymerases recognize metal-mediated base pairs such as T-Hg-T, C-Ag-A, and C-Ag-T as relatively stable base pairs. These results imply that Zn ions may also enhance the fidelity of DNA polymerases when incorporating non-canonical nucleobases, potentially paving the way for the expansion of the genetic alphabet.