DNA Replication and Repair Mechanisms in Eukaryotic Systems

Eukaryotic DNA replication is initiated at multiple origins through a tightly regulated sequence of events: origin licensing, helicase activation and assembly of the replisome. The replicative polymerases α, δ and ε are recruited to synthesise leading and lagging strands, aided by the sliding clamp, proliferating cell nuclear antigen (PCNA), loaded onto DNA by replication factor C. Nascent lagging strands are processed into Okazaki fragments by flap endonuclease and ligated to form a continuous strand. Throughout this process, a network of repair pathways safeguards genome integrity. Base excision repair corrects small lesions, nucleotide excision repair removes bulky adducts, and mismatch repair rectifies replication errors. When replication forks encounter obstacles, PCNA is monoubiquitinated to trigger translesion synthesis, allowing specialised polymerases to bypass lesions. Double-strand breaks are addressed by homologous recombination or non-homologous end joining. Coordination between replication and repair is essential to prevent mutagenesis, chromosomal rearrangements and cellular senescence. Dysregulation underlies ageing, cancer and developmental disorders, while insights into clamp dynamics, polymerase switching and post-translational modifications of repair factors inform novel therapeutic strategies and biomolecular engineering.

Research from Nature Portfolio

Recent studies have elucidated the structural basis for clamp–DNA interactions and regulatory co-factors. High-resolution analyses reveal that PCNA recognises the DNA backbone via a spiral arrangement of basic residues within its ring channel, enabling a cogwheel-like sliding mechanism that maintains a fixed orientation relative to the helix. Mutation of key interface residues impairs replication-competent holoenzyme assembly, underlining the importance of precise clamp positioning for polymerase δ function. Complementary work on the intrinsically disordered regulator p15PAF shows that its PIP-box motif binds to the front face of PCNA while its termini thread through the ring interior. This dual interaction stabilises the clamp on DNA and modulates transitions between replicative and translesion polymerases, suggesting a flexible drag model that fine-tunes fork progression and lesion bypass.

DNA Replication and Repair Mechanisms in Eukaryotic Systems publication trend

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

Technical terms

Proliferating Cell Nuclear Antigen (PCNA): A homotrimeric sliding clamp that encircles DNA to enhance polymerase processivity and recruit repair factors.

Clamp Loader (Replication Factor C): An ATP-dependent complex that opens and places PCNA onto primer–template junctions.

PIP-box: A short linear motif in client proteins that mediates binding to the front face of PCNA.

Ubiquitination: Covalent attachment of ubiquitin to PCNA or other proteins, regulating protein interactions and lesion bypass.

Translesion Synthesis (TLS): Bypass of DNA lesions by specialised low-fidelity polymerases, often triggered by PCNA monoubiquitination.

References

1. Structural basis of human PCNA sliding on DNA. Nature Communications (2017).
2. Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair. Nature Communications (2015).
3. Proliferating cell nuclear antigen inhibitors block distinct stages of herpes simplex virus infection. PLOS Pathogens (2023).
4. A FRET-Based Assay for the Identification of PCNA Inhibitors. International Journal of Molecular Sciences (2023).
5. The potential of PCNA inhibition as a therapeutic strategy in cervical cancer. Journal of Medical Virology (2023).