Dynamic basis for dG•dT misincorporation via tautomerization and ionization

Tautomeric and anionic Watson-Crick-like mismatches have important roles in replication and translation errors through mechanisms that are not fully understood. Here, using NMR relaxation dispersion, we resolve a sequence-dependent kinetic network connecting G•T/U wobbles with three distinct Watson-Crick mismatches: two rapidly exchanging tautomeric species (G^enol•T/UG•T^enol/U^enol; population less than 0.4%) and one anionic species (G•T^-/U^-; population around 0.001% at neutral pH). The sequence-dependent tautomerization or ionization step was inserted into a minimal kinetic mechanism for correct incorporation during replication after the initial binding of the nucleotide, leading to accurate predictions of the probability of dG•dT misincorporation across different polymerases and pH conditions and for a chemically modified nucleotide, and providing mechanisms for sequence-dependent misincorporation. Our results indicate that the energetic penalty for tautomerization and/or ionization accounts for an approximately 10^-2 to 10^-3-fold discrimination against misincorporation, which proceeds primarily via tautomeric dG^enol•dT and dG•dT^enol, with contributions from anionic dG•dT^- dominant at pH 8.4 and above or for some mutagenic nucleotides.