6.6: Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.

There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the opposite direction. 2) For leading strand synthesis, a single primer is needed, whereas multiple RNA primers are required for lagging strand synthesis. 3) After initial primer synthesis, the leading strand needs only DNA polymerase for replication to continue, whereas the lagging strand needs multiple enzymes, including DNA polymerase I, RNase H, and ligase. 4) The leading strand is synthesized as a continuous piece, whereas the lagging strand is synthesized as a series of shorter pieces called Okazaki fragments. Thus, lagging strand synthesis is a multistep process involving sophisticated coordination among different molecules.

Due to the different genome sizes of prokaryotes and eukaryotes, the process of lagging strand synthesis differs between them. The most prominent difference is the length of the Okazaki fragments. The average Okazaki fragment length is around 1000 to 2000 nucleotides in prokaryotes, but only 100 to 200 nucleotides in eukaryotes.

The complementary strands in double-stranded DNA replicate at different rates. On one strand, the replication process is continuous and fast; this newly formed daughter strand is called the leading strand. 

On the other strand, the replication process is discontinuous, relatively slower, and starts slightly later; this daughter strand is known as the lagging strand.

DNA polymerase can only synthesize DNA in the 5' to 3' direction. Because of this, the leading strand is synthesized continuously. 

However, DNA polymerase cannot synthesize DNA in a 3' to 5' direction on the lagging strand.

To deal with this problem, DNA synthesis is carried out discontinuously in a 5' to 3' direction.

The enzyme DNA primase, which is present close to the opening of the replication fork, will synthesize multiple RNA primers on the lagging strand as the DNA unwinds.

Then, DNA polymerase synthesizes DNA onto the end of the primer until it encounters the next primer.

This cycle of primer synthesis by primase and subsequent DNA elongation by polymerase continues along the lagging strand. The resultant short DNA fragments are known as Okazaki fragments.

The enzyme RNase H then removes the RNA primers interspersed between the Okazaki fragments.

Another DNA polymerase then fills the empty spaces left after the removal of the RNA primers.

However, the DNA polymerase cannot fill the nicks present between Okazaki fragments.

This final task is performed by the enzyme DNA ligase, which joins the 3’ end of one fragment with 5’ end of another in order to make the discontinuous lagging strand into a continuous one.