The Replisome

The replisome is a highly coordinated multi-protein assembly that carries out DNA replication and significantly increases its efficiency. Core components include helicase, single-strand DNA binding proteins, DNA primase, sliding clamps, clamp loaders, and multiple DNA polymerases, all working together near the replication fork to enable rapid and accurate genome copying.

Sliding clamp proteins tether DNA polymerase to the template strand, dramatically increasing processivity from approximately 10 nucleotides to 1,000 nucleotides. The clamp loader uses ATP hydrolysis to open the clamp's ring-like structure around the primer-template complex. Once closed, the polymerase-clamp complex slides along DNA, enabling continuous synthesis on the leading strand.

The Trombone model describes how leading and lagging strands are synthesized simultaneously through DNA loop formation and collapse. When DNA polymerase initiates Okazaki fragment synthesis from an RNA primer, the lagging strand forms a loop that grows as helicase unwinds DNA. When polymerase encounters the next primer, the loop releases and the cycle repeats, allowing coordinated synthesis of both strands.

Prokaryotes use single hexamer helicases and single-subunit primase (DnaG), while eukaryotes employ double hexamer helicases requiring Cdc45 and GINS proteins, and multisubunit primase (DNA polymerase-α primase). Prokaryotes use one replicative polymerase (Pol III), whereas eukaryotes use two (Pol ε and Pol δ). Sliding clamps differ too: β-clamp in prokaryotes versus PCNA in eukaryotes.

Single-strand DNA binding proteins prevent separated DNA strands from reannealing after helicase unwinding. In prokaryotes, SSB proteins consist of a single subunit, while eukaryotic versions form a heterotrimeric complex called replication protein A (RPA). These proteins stabilize single-stranded regions, keeping template strands accessible for polymerase synthesis and primer synthesis.

Primase synthesizes short RNA primers that provide the 3'-OH group required for DNA polymerase to begin synthesis. In prokaryotes, DnaG primase creates approximately 12-nucleotide primers, while eukaryotic DNA polymerase-α primase generates around 25-nucleotide RNA-DNA hybrid primers. These primers are essential because DNA polymerases cannot initiate synthesis de novo.

Clamp loaders are pentameric AAA+ ATPase proteins that use ATP hydrolysis to load sliding clamps onto DNA. When ATP binds, the clamp loader opens the clamp's ring structure, allowing it to encircle the primer-template complex. ATP hydrolysis causes the clamp loader to dissociate and the clamp to close, securing the polymerase to the DNA template for processive synthesis.