Identifying the Features of Purine dNTPs that Allow Accurate and Efficient DNA Replication by Herpes Simplex Virus I DNA Polymerase

To accurately replicate its viral genome, the Herpes Simplex Virus 1 (HSV-1) DNA polymerase usually polymerizes the correct natural 2'-deoxy-5'-triphosphate (dNTP) opposite the template base being replicated. We employed a series of purine-dNTP analogues to determine the chemical features of the base necessary for the herpes polymerase to avoid polymerizing incorrect dNTPs. The enzyme uses N-3 to prevent misincorporation of purine dNTPs but does not require N-3 for correct polymerization. A free pair of electrons on N-1 also helps prevent misincorporation opposite A, C, and G and strongly drives polymerization opposite T. N-6 contributes a small amount both for preventing misincorporation and for correct polymerization. Within the context of guanine in either the incoming dNTP or the template base being replicated, N-2 prevents misincorporation opposite adenine but plays at most a minor role for incorporation opposite C. In contrast, adding N-2 to the dNTPs of either adenine, purine, 6-chloropurine, or 1-deazapurine greatly enhances incorporation opposite C, likely via the formation of a hydrogen bond between N-2 of the purine and O-2 of the pyrimidine. Herpes polymerase is very sensitive to the structure of the base pair at the primer 3'-terminus since eliminating N-1, N-3, or N-6 from a purine nucleotide at the primer 3'-terminus interfered with polymerization of the next two dNTPs. The biological and evolutionary implications of these data are discussed.