The Replisome

DNA replication is carried out by a highly coordinated multi-protein assembly known as the DNA replication machinery or the replisome, which increases the efficiency of DNA replication.

The core components of the machinery are helicase, single-strand DNA binding proteins, DNA primase, sliding clamps, a clamp loader, and multiple DNA polymerases, which are all associated with each other near the replication fork.

Replicative DNA polymerases have a processivity of around 10 nucleotides, which is the number of nucleotides it can add to the daughter strand before dissociating from the template strand. 

This is too inefficient to copy entire genomes in a reasonable timeframe and this problem is solved with the help of sliding clamp proteins.

When ATP associates with the clamp loader protein, they will bind to and open the sliding clamp so that its ring-like structure can surround the primer-template DNA complex.  Once bound, the clamp loader hydrolyzes the ATP to ADP, causing the clamp loader to disassociate and the clamp to close around the DNA.

Then, DNA polymerase binds to the clamp proteins and together they slide along the template DNA, tethering DNA polymerase to the strand and increasing its processivity up to 1000 nucleotides.  

This increased processivity allows the DNA polymerase to carry out continuous DNA replication on the leading strand.

However, on the lagging strand template, another DNA polymerase performs discontinuous DNA replication in a manner that allows the DNA polymerase molecules to synthesize the leading and lagging strands simultaneously. This process is sometimes described as the “Trombone model.”

The lagging strand and its template strand form a loop when DNA polymerase initiates Okazaki fragment synthesis from an RNA primer. 

The DNA loop grows from both directions as helicase unwinds DNA and the lagging strand is synthesized.

When the DNA polymerase encounters the next RNA primer, it detaches from the template strand.  Meanwhile, primase adds another primer to the lagging strand, and the growing DNA loop is released. 

The clamp and clamp loader proteins allow DNA polymerase to quickly reassociate with the primed DNA template.

The formation and subsequence collapse of the DNA loop repeats with the synthesis of each new Okazaki fragment.