Importance of Many Body Interactions in DNA Synthesis Initiation

The synthesis of DNA primers, which are subsequently extended, is performed by DNA primases. This process is indispensable for DNA replication, and thus the understanding of the precise mechanism for this process is of great importance. In this contribution we will present the molecular basis for the primase synthesis mechanism of the CRISPR-associated primase-polymerase from Marinitoga piezophila (Mp). The crystal structure of a primer initiation complex reveals how the incoming nucleotides are positioned within the active site, adjacent to metal cofactors and paired with the templating single-stranded DNA strand, before synthesis of the first phosphodiester bond. Quantum mechanical energy decomposition analysis was used to reveal the inter-molecular interactions between different components of the active site to understand the basis of the stabilization of the two triphosphate nucleotides in the active site prior to phosphodiester bond formation. Polarizable molecular dynamics simulations provide additional insights on the stability of the enzyme/substrate complex. Results from these calculations and relevance of many-body effects in the stabilization of the system will be discussed.