Unraveling DNA translocation mechanisms through data-driven atomistic simulations

DNA replication is an essential and tightly regulated process that ensures the faithful transmission of genetic information in all living organisms. This mechanism relies on the coordinated action of numerous proteins that guarantee both the accuracy and efficiency of DNA synthesis. Among them, DNA polymerases (Pols) play a central role by catalyzing the addition of nucleotides to the growing DNA strand, using the complementary template as a guide. Replicative polymerases are responsible for most genome duplication and are characterized by high fidelity, proofreading activity, and remarkable processivity, ensuring correct copying of the genome. Mutations or dysregulation in these enzymes can compromise genomic stability, leading to replication errors and mutagenesis. In contrast, specialized translesion synthesis (TLS) Pols can bypass DNA lesions that would stall replication. These Y-family polymerases have flexible active sites that accommodate damaged or distorted DNA templates. For instance, ultraviolet (UV) radiation induces cyclobutane pyrimidine dimers (CPD), substrates for TLS polymerases. While protective by preventing replication fork collapse, their low fidelity can promote mutagenesis if misregulated. Both replicative and TLS Pols are targets for small-molecule modulation in cancer therapy. DNA polymerases are metalloenzymes that copy single-stranded DNA through a two-metal-ion mechanism. During the catalytic cycle, Pols incorporate an incoming deoxynucleotide triphosphate (dNTP) at the 3’ end of the primer. After each event, the DNA translocates by one base pair, repositioning the primer terminus for the next binding. While the chemical step is well-characterized, the atomistic details of translocation remain unclear. Recent computational studies show that replicative Pols use an open-to-close transition of a structural helix above the DNA to facilitate movement. TLS Pols lack this element and show no major conformational changes, raising questions on how they maintain catalytic efficiency despite structural differences.