Proteins at the Y-shaped DNA replication fork

Focusing on the schematic illustration in a, two DNA polymerase molecules are active at the fork at any one time. One moves continuously to produce the new daughter DNA molecule on the leading strand, whereas the other produces a long series of short Okazaki DNA fragments on the lagging strand. Both polymerases are anchored to their template by polymerase accessory proteins, in the form of a sliding clamp and a clamp loader. A DNA helicase, powered by ATP hydrolysis, propels itself rapidly along one of the template DNA strands (here the lagging strand), forcing open the DNA helix ahead of the replication fork. The helicase exposes the bases of the DNA helix for the leading-strand polymerase to copy. DNA topoisomerase enzymes facilitate DNA helix unwinding. In addition to the template, DNA polymerases need a pre-existing DNA or RNA chain end (a primer) onto which to add each nucleotide. For this reason, the lagging strand polymerase requires the action of a DNA primase enzyme before it can start each Okazaki fragment. The primase produces a very short RNA molecule (an RNA primer) at the 58 end of each Okazaki fragment onto which the DNA polymerase adds nucleotides. Finally, the single-stranded regions of DNA at the fork are covered by multiple copies of a single-strand DNA-binding protein, which hold the DNA template strands open with their bases exposed. In the folded fork structure shown in the inset, the lagging-strand DNA polymerase remains tied to the leading-strand DNA polymerase. This allows the lagging-strand polymerase to remain at the fork after it finishes the synthesis of each Okazaki fragment. As a result, this polymerase can be used over and over again to synthesize the large number of Okazaki fragments that are needed to produce a new DNA chain on the lagging strand. In addition to the above group of core proteins, other proteins (not shown) are needed for DNA replication. These include a set of initiator proteins to begin each new replication fork at