What Is an Okazaki Fragment in DNA Replication?
An Okazaki fragment is a short, newly synthesized segment of DNA that forms on one of the template strands during DNA replication. These segments are created in a discontinuous manner, and are later joined together to form a continuous strand. In eukaryotic cells, these fragments typically range from approximately 100 to 200 base pairs in length. In bacterial cells, they can be longer, around 1000 to 2000 nucleotides.
The Directional Problem of DNA Replication
DNA exists as a double helix. This structure consists of two individual strands that run in opposite directions, a characteristic known as antiparallel orientation. One strand is oriented from its 5′ (five-prime) end to its 3′ (three-prime) end, while its complementary partner runs from 3′ to 5′.
The process of copying DNA, known as replication, relies on an enzyme called DNA polymerase. This enzyme can only add new nucleotides to the 3′ end of a growing DNA strand. This means that DNA polymerase can only synthesize a new strand in the 5′ to 3′ direction. The antiparallel nature of the DNA double helix presents a challenge during replication because both template strands need to be copied simultaneously, but DNA polymerase can only move in one direction.
Forming Fragments on the Lagging Strand
During DNA replication, the double helix unwinds and separates, forming a Y-shaped structure known as a replication fork. One of the parental DNA strands is oriented from 3′ to 5′ in the direction of the replication fork’s movement. This strand is called the leading strand, and DNA polymerase can continuously add nucleotides to its new complementary strand in the 5′ to 3′ direction, following the unwinding fork.
The other parental strand, the lagging strand, runs from 5′ to 3′ in the direction of the replication fork. Because DNA polymerase can only synthesize in the 5′ to 3′ direction, it must work backward, away from the moving replication fork. As the fork opens more template DNA, the lagging strand is synthesized in short, separate pieces. These short pieces are the Okazaki fragments.
To begin each Okazaki fragment, a specialized enzyme called primase lays down a short RNA primer. This RNA primer provides a starting point with a free 3′-hydroxyl group, allowing DNA polymerase to then extend the primer by adding DNA nucleotides. This discontinuous synthesis ensures that both strands of DNA can be copied despite the directional limitation of DNA polymerase.
Joining Fragments into a Complete Strand
After the Okazaki fragments are synthesized on the lagging strand, they require further processing. The RNA primers that initiated each fragment must first be removed. A different type of DNA polymerase, such as DNA Polymerase I in bacteria, removes the RNA nucleotides of the primer and replaces them with DNA nucleotides.
After the RNA primers are replaced with DNA, small gaps or “nicks” remain between the newly synthesized DNA fragments. To seal these nicks and create a seamless DNA backbone, DNA ligase is required. DNA ligase forms the phosphodiester bond that connects the adjacent Okazaki fragments, completing the continuous lagging strand.
Discovery and Biological Significance
The existence of these short DNA fragments was first proposed and later confirmed by Japanese molecular biologists Reiji Okazaki and Tsuneko Okazaki, along with their colleagues, in the 1960s. Their experiments, using Escherichia coli bacteria, provided evidence that DNA replication was not continuous on both strands. They observed that newly synthesized DNA often appeared as small fragments before becoming part of larger, continuous strands.
The formation and subsequent joining of Okazaki fragments are a significant aspect of DNA replication in all living organisms. This mechanism is necessary for accurately copying an organism’s entire genetic material during cell division. It ensures that both antiparallel strands of the DNA double helix can be replicated, which is necessary for proper growth, cellular repair, and the transmission of genetic information from one generation to the next.