DNA Replication Mechanisms and Primase-Polymerase Dynamics

DNA replication is the fundamental process by which cells duplicate their genetic material before division. Initiation occurs at defined origins where a hexameric helicase unwinds the double helix, generating a replication fork. On the leading strand, synthesis proceeds continuously, while on the lagging strand short RNA primers must be laid down at intervals to initiate Okazaki fragments. Classical primases generate these primers and hand them off to high-fidelity polymerases for extension. In contrast, primase-polymerases are multifunctional enzymes capable of both de novo primer synthesis and DNA polymerisation. These dual-function agents can reprime DNA synthesis downstream of impediments, bypass lesions via translesion synthesis and interact with single-stranded DNA-binding proteins and checkpoint kinases. Structural and biochemical studies have begun to reveal how conformational switching, protein–protein contacts and post-translational modifications coordinate primer initiation, transfer and elongation. Understanding these dynamics is critical for illuminating mechanisms of genome stability, informing strategies to modulate replication stress in cancer and advancing technologies such as single-cell genome amplification.

Research from Nature Portfolio

Recent studies have shown that activation of a DNA damage response kinase pathway enhances cell tolerance to oncogene-induced replication stress by modulating primase-polymerase activity. Phosphorylation of the primase-polymerase at a key residue promotes repriming of stalled forks in an ATR-dependent manner, maintaining fork progression but also generating single-stranded gaps that can lead to genomic instability. Another investigation has elucidated how replication protein A (RPA) recruits the primase-polymerase to stalled forks. Two distinct RPA-binding motifs on the enzyme were identified, and their interaction stimulates primer synthesis in vitro and is essential for fork restart in vivo, providing a molecular basis for targeted recruitment under stress conditions.

DNA Replication Mechanisms and Primase-Polymerase Dynamics publication trend

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

Technical terms

Replication fork: The Y-shaped junction where parental DNA strands are separated and new strands are synthesised.

Primase: An enzyme that synthesises short RNA primers needed for DNA polymerase to begin synthesis.

DNA polymerase: An enzyme that extends a primer by adding deoxynucleotides complementary to the template strand.

Primase-polymerase (PrimPol): A dual-function enzyme that both synthesises primers de novo and extends DNA strands, enabling repriming and lesion bypass.

Repriming: The process of laying down a new primer downstream of a replication impediment to restart DNA synthesis.

Translesion synthesis (TLS): A damage-tolerance mechanism in which specialised polymerases replicate past DNA lesions.

ATR: A protein kinase that senses replication stress and phosphorylates substrates to stabilise forks and coordinate repair.

Replication protein A (RPA): A heterotrimeric complex that binds single-stranded DNA, protecting it and recruiting replication and repair factors.

References

1. An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress. Nature Communications (2023).
2. Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy. Journal of the American Chemical Society (2024).
3. How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Molecular Cell (2023).
4. Mechanism of primer synthesis by Primase-Polymerases. Current Opinion in Structural Biology (2023).
5. Molecular basis for PrimPol recruitment to replication forks by RPA. Nature Communications (2017).
6. Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes. Nucleic Acids Research (2015).