DNA Polymerase Mechanisms in Replication Fidelity

Accurate duplication of the genome is fundamental to cellular viability and prevention of disease. Replicative DNA polymerases achieve high fidelity through three interconnected mechanisms: intrinsic nucleotide selectivity, exonucleolytic proofreading and post-replicative mismatch repair. During synthesis, the polymerase active site discriminates correct from incorrect nucleotides by subtle steric and hydrogen-bonding interactions. Occasionally, a mispaired terminus is transferred to an associated 3′–5′ exonuclease site, where incorrect nucleotides are excised before resynthesis. Processivity factors such as the sliding clamp (PCNA in eukaryotes) tether polymerases to DNA, balancing speed with error surveillance. After synthesis, residual mismatches can be recognised and removed by the mismatch repair machinery, further boosting overall fidelity. Distinct B-family polymerases (Pol ε and Pol δ) specialise in leading- and lagging-strand synthesis, respectively, yet demonstrate dynamic division of labour at initiation and termination. Defects in any component of this fidelity network predispose to mutagenesis and disease, from fungal pathogenesis to cancer, while detailed mechanistic insights guide drug development and biotechnological innovation.

Research from Nature Portfolio

High-resolution cryo-electron microscopy has delineated human Pol ε interactions with PCNA and DNA in both nucleotide-binding and nucleotide-exchange conformations, revealing a three-point interface that secures the holoenzyme and prevents competition from other PCNA-binding partners. Complementary structures capture mismatched primer termini bound to Pol ε, showing how the finger domain pivots around a [4Fe-4S] cluster to relay the primer between polymerase and exonuclease active sites. Together, these studies elucidate an intramolecular switching mechanism that underlies proofreading and establish the structural basis for ultra-high fidelity of leading-strand synthesis.

DNA Polymerase Mechanisms in Replication Fidelity publication trend

The graph below shows the total number of articles in dna polymerase mechanisms in replication fidelity across all publications each year (not limited to Nature Index journals).

Technical terms

DNA polymerase: Enzyme that catalyses template-directed synthesis of DNA strands.

Processivity: Ability of a polymerase to synthesise DNA without dissociating from the template.

Proofreading (3′–5′ exonuclease activity): Removal of misincorporated nucleotides from the nascent strand.

PCNA (proliferating cell nuclear antigen): Ring-shaped sliding clamp that tethers polymerases to DNA.

Holoenzyme: Multi-protein complex comprising polymerase and accessory factors for replication.

Mismatch repair: Post-replicative pathway that recognises and corrects base mispairings.

References

1. Structures of the human leading strand Polε–PCNA holoenzyme. Nature Communications (2024).
2. Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε. Nature Structural & Molecular Biology (2024).
3. Critical roles of Dpb3-Dpb4 sub-complex of DNA polymerase epsilon in DNA replication, genome stability, and pathogenesis of Candida albicans. mBio (2024).
4. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics (2024).
5. Roles for DNA polymerase δ in initiating and terminating leading strand DNA replication. Nature Communications (2019).