Replication fork



The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching "prongs", each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands which will be created as DNA polymerase matches complementary nucleotides to the templates. The templates may be properly referred to as the leading strand template and the lagging strand template.

Replication
When replicating, the original DNA splits in two, forming two "prongs" which resemble a fork (hence the name "replication fork"). DNA has a ladder-like structure; imagine a ladder broken in half vertically, along the steps. Each half of the ladder now requires a new half to match it. Because DNA polymerase can only synthesize a new DNA strand in a 5' to 3' manner, the process of replication goes differently for the two strands comprising the DNA double helix.

Leading strand
The leading strand template is the strand of DNA being replicated continuously. It is the strand that is being continuously polymerized towards the replication fork. All DNA synthesis occurs 5'-3'. The original DNA strand must be read 3'-5' to produce a 5'-3' nascent strand.

The leading strand is formed as a polymerase "reads" the template DNA and continuously adds nucleotides to the 3' end of the elongating strand. This polymerase is DNA polymerase III (DNA Pol III) in prokaryotes and presumably Pol ε in eukaryotes.

Lagging strand
The lagging strand grows in the direction opposite to the movement of the growing fork. It grows away from the replication fork and it is synthesized discontinuously. Because the strand is growing away from the replication fork, it needs to be replicated in fragments because the Primase (that adds the RNA primer) has to wait until the fork opens to be able to put the primer. The RNA Polymerase reaches the origin of replication and stops replication until a new RNA primer is placed. These fragments of DNA produced on the lagging strand are called Okazaki fragments. The orientation of the original DNA on the lagging strand prevents continual synthesis. As a result, replication of the lagging strand is more complicated than replication of the leading strand.

On the lagging and leading strand templates, the primer is added by Primase that "reads" the template DNA and adds RNA to it in short, separated segments. In eukaryotes, primase is intrinsic to Pol α. DNA polymerase III or Pol δ lengthens the primed segments, forming Okazaki fragments. Primer removal in eukaryotes is also performed by Pol δ. In prokaryotes, DNA polymerase I "reads" the fragments, removes the RNA using its flap endonuclease domain, and replaces the RNA nucleotides with DNA nucleotides (this is necessary because RNA and DNA use slightly different kinds of nucleotides). DNA ligase joins the fragments together.