Eukaryotic cells must accurately and efficiently duplicate their genomes during each round of the cell cycle. Multiple linear chromosomes, a large number of regulatory elements, and chromosomal packaging are challenges that the eukaryotic DNA replication fork machinery must successfully overcome. The replication machinery, the “replisome” complex, is composed of many specialized proteins with functions to support replication by DNA polymerases.
Efficient replisome progression relies on close coordination between the various replisome factors. Furthermore, replisome progression must occur in less than ideal templates at various genomic loci. Here, we describe the functions of the main components of the replisome, as well as some of the obstacles to efficient DNA replication that the replisome faces. Taken together, this review summarizes the current understanding of the enormously complicated task of replicating eukaryotic DNA.
Keywords: DNA replication, replisome, replication fork, genome stability, checkpoint, hairpin barriers, hard-to-replicate sites
What is the replication fork?
Our DNA determines everything about us. And for this reason, a copy of our DNA is needed in every cell in our body, except for our red blood cells. A copy of DNA is made just before a cell divides to create two cells. For this DNA replication to take place, the DNA has to be in an orientation that allows the replication machinery to make a copy. Our DNA is double-stranded, and the strands are held together by hydrogen bonds.
The normal structure of our DNA when not copied is a double helix. This looks a lot like a spiral staircase. In this normal form, DNA cannot be copied. DNA helicase is needed to open the DNA and expose the nucleotide bases that are used as a template to replicate the DNA. The area of DNA that the DNA helicase opens is known as the replication fork because it looks a lot like a fork in the road.
The role of the replication fork
The replication fork is the area where DNA replication will actually take place. There are two strands of DNA that are exposed once the double helix opens. One strand is called the leading strand and the other strand is called the lagging strand. The leading strand is exposed in the 5′-3′ direction, while the lagging strand is exposed in the 3′-5′ direction. DNA is always copied in the 5′-3′ direction.
As the main strand is exposed, DNA polymerase will use the main strand as a template to create a continuous complementary strand of DNA. As the lagging strand is exposed, RNA primers are needed to start the replication process. The RNA primer will bind to the most 5′ end of the exposed part of the lagging strand. This primer then allows DNA polymerase to bind and add the complementary strand to the lagging strand in small segments known as Okazaki fragments.