Structural Basis for C2′-methoxy Recognition by DNA Polymerases and Function Improvement

DNA modified with C2′-methoxy (C2′-OMe) greatly enhances its resistance to nucleases, which is beneficial for the half-life of aptamers and DNA nanomaterials. Although the unnatural DNA polymerases capable of incorporating C2′-OMe modified nucleoside monophosphates (C2′-OMe-NMPs) were engineered via directed evolution, the detailed molecular mechanism by which an evolved DNA polymerase recognizes C2′-OMe-NTPs remains poorly understood. Here, we present the crystal structures of the evolved Stoffel fragment of Taq DNA polymerase SFM4-3 processing the C2′-OMe-GTP in different states. Our results reveal the structural basis for recognition of C2′-methoxy by SFM4-3. Based on the analysis of other mutated residues in SFM4-3, a new Stoffel fragment variant with faster catalytic rate and stronger inhibitor-resistance was obtained. In addition, the capture of a novel pre-insertion co-existing with template 5′-overhang stacking conformation provides insight into the catalytic mechanism of Taq DNA polymerase.