Deoxyribonucleic acid, commonly known as DNA, serves as the fundamental genetic material within living organisms. This molecule carries the instructions necessary for development, functioning, growth, and reproduction of all life. Before a cell can divide, its entire DNA must be copied precisely, a process known as DNA replication. This ensures that each new daughter cell receives a complete and accurate set of genetic instructions.
DNA’s Antiparallel Structure
DNA exists as a double helix, a structure resembling a twisted ladder composed of two long strands coiled around each other. Each strand has distinct directionality, defined by its chemical ends, referred to as the 5′ (five prime) and 3′ (three prime) ends. The 5′ end terminates with a phosphate group, while the 3′ end concludes with a hydroxyl group attached to the deoxyribose sugar.
These two strands are arranged in an antiparallel fashion. This means one strand runs 5′ to 3′, while its complementary partner runs in the opposite, 3′ to 5′ direction. This specific orientation plays a crucial role in how DNA is read and replicated within the cell.
The Directional Constraint of DNA Polymerase
DNA replication relies on enzymes called DNA polymerases, which are responsible for synthesizing new DNA strands. A significant characteristic of DNA polymerases is their limitation: they can only add new nucleotides to the 3′ end of a growing DNA strand. This means DNA synthesis always proceeds in a strict 5′ to 3′ direction along the newly forming strand.
This directional constraint poses a challenge during DNA replication due to the antiparallel nature of the DNA double helix. When DNA unwinds to form a replication fork, exposing two template strands, one is oriented 3′ to 5′ and the other is 5′ to 3′. DNA polymerase can continuously synthesize a new strand on the 3′ to 5′ template by moving along in the direction of the unwinding DNA, creating the leading strand. However, on the 5′ to 3′ template, DNA polymerase cannot synthesize continuously in the direction of the replication fork’s movement because that would require synthesis in a 3′ to 5′ direction.
The Discontinuous Synthesis of the Lagging Strand
To overcome the directional constraint of DNA polymerase on the 5′ to 3′ template strand, the cell employs a discontinuous synthesis mechanism, resulting in the formation of the lagging strand. As the replication fork opens, an enzyme called primase first synthesizes short RNA primers at intervals along this template strand. These primers provide the necessary 3′ hydroxyl ends for DNA polymerase to begin adding deoxyribonucleotides.
DNA polymerase III then extends these RNA primers by synthesizing short DNA segments known as Okazaki fragments. In eukaryotes, these fragments are approximately 100 to 200 base pairs long, while in bacteria, they can range from 1000 to 2000 nucleotides. Because DNA polymerase III synthesizes these fragments away from the replication fork, it must repeatedly stop and restart closer to the fork as more template DNA becomes available.
Once the Okazaki fragments are synthesized, DNA polymerase I removes the RNA primers and replaces them with DNA nucleotides. Finally, DNA ligase seals the small gaps between adjacent DNA fragments, creating a continuous lagging strand. This coordinated action of multiple enzymes ensures that both strands of the DNA helix are fully and accurately replicated, despite the limitations of DNA polymerase.