DNA replication is the process cells use to copy their DNA before cell division. The result is two DNA molecules that carry the same genetic information as the original, with each new molecule containing one original strand and one newly synthesized strand.
Replication is remarkably accurate, but it is not a single-step event. It is a coordinated sequence involving DNA unwinding, primer formation, new-strand synthesis, removal of temporary primers, proofreading, and completion of the chromosome ends. Understanding the order of these events makes the entire process easier to follow.
What DNA replication accomplishes
DNA is made of two complementary strands twisted into a double helix. The strands are held together by hydrogen bonds between paired bases: adenine (A) pairs with thymine (T), while cytosine (C) pairs with guanine (G).
Because the two strands are complementary, each can serve as a template for building its partner. If a template contains the sequence A-C-G-T, for example, the complementary strand will contain T-G-C-A.
DNA replication takes advantage of this property. The original double-stranded DNA is separated, and each original strand guides the construction of a new complementary strand. This produces two DNA molecules, each consisting of one parental strand and one newly made strand. This arrangement is called semiconservative replication.
Replication also has an important directional constraint. DNA polymerases, the enzymes that add DNA nucleotides, can extend a strand only in the 5′ to 3′ direction. This restriction determines how the two new strands are made.
Step 1: Replication begins at an origin
Replication starts at specific DNA sequences called origins of replication. At an origin, the cell assembles the proteins needed to begin copying the DNA.
In bacteria, which typically have a single circular chromosome, replication generally begins at one origin. Eukaryotic chromosomes are much longer and contain many origins so that their DNA can be copied efficiently.
Once replication begins, the DNA around the origin opens, creating a region where the two strands can be copied. The active area is known as a replication fork because its structure resembles a fork with two diverging arms.
Step 2: Helicase separates the DNA strands
The first major physical step is opening the double helix.
An enzyme called helicase moves along the DNA and breaks the hydrogen bonds between complementary bases. This separates the two parental strands, exposing their bases so they can serve as templates.
The separated DNA would naturally tend to re-form the double helix. Other proteins help prevent this. Single-strand DNA-binding proteins attach to the exposed strands and keep them apart while replication proceeds.
Unwinding also creates twisting and tension in the DNA ahead of the replication fork. Enzymes called topoisomerases relieve this mechanical stress by temporarily cutting DNA, allowing it to relax, and then resealing it.
At this point, the templates are accessible, but DNA synthesis still cannot begin directly.
Step 3: Primase makes RNA primers
DNA polymerase cannot simply attach the first DNA nucleotide to an exposed template. It needs an existing strand with a free 3′ hydroxyl (3′-OH) group to extend.
The cell solves this problem with a short piece of RNA called a primer.
An enzyme called primase synthesizes the RNA primer using the exposed DNA strand as a template. The primer provides the starting point that DNA polymerase needs.
This temporary RNA segment is essential, but it will not remain as part of the finished DNA molecule.
Step 4: DNA polymerase begins adding DNA nucleotides
With a primer in place, a DNA polymerase can begin building the new DNA strand.
The polymerase reads the template strand and adds complementary DNA nucleotides. Because base pairing is specific, A in the template calls for T in the new strand, while C calls for G.
DNA polymerase adds each nucleotide to the growing strand’s 3′ end. As a result, the new DNA strand is always synthesized 5′ to 3′.
This directional rule creates a key difference between the two strands being copied.
Step 5: The leading strand is synthesized continuously
One new strand can be synthesized continuously as the replication fork advances. This is the leading strand.
Its template is oriented in a way that allows DNA polymerase to move toward the advancing replication fork while continuously adding nucleotides to the new strand.
After the initial primer is placed, synthesis of the leading strand can therefore proceed in a relatively uninterrupted manner.
Step 6: The lagging strand is synthesized in pieces
The other template strand runs in the opposite direction. Because DNA polymerase can synthesize DNA only 5′ to 3′, the cell cannot copy this template continuously toward the replication fork.
Instead, the lagging strand is made in short sections called Okazaki fragments.
Primase repeatedly creates RNA primers along the exposed template. DNA polymerase then extends each primer, producing a new DNA fragment. As the replication fork moves forward, additional primers are placed and additional fragments are synthesized.
The lagging strand is therefore not copied backward. Each individual fragment is still synthesized 5′ to 3′. The apparent difference comes from the orientation of the template and the repeated restarting of synthesis.
Step 7: RNA primers are removed and replaced with DNA
The RNA primers have served their purpose, but the finished chromosome needs DNA rather than RNA at these positions.
Cellular enzymes remove the RNA primers. The resulting gaps are then filled with DNA nucleotides.
Different organisms use somewhat different sets of enzymes for this task. In bacteria, DNA polymerase I has an important role in removing RNA primers and replacing them with DNA; in eukaryotes, primer removal involves other specialized proteins and nucleases.
The essential sequence is the same: remove the temporary RNA, fill the resulting gap with DNA, and prepare the neighboring DNA fragments for joining.
Step 8: DNA ligase joins the fragments
After the primers have been removed and the gaps filled, the newly synthesized DNA on the lagging strand still contains breaks in its sugar-phosphate backbone between adjacent fragments.
An enzyme called DNA ligase seals these breaks.
Ligase does not create the DNA sequence itself. Instead, it forms the final phosphodiester bond needed to connect neighboring DNA segments into one continuous strand.
After ligation, the lagging strand has been converted from a series of separate Okazaki fragments into a continuous DNA molecule.
Step 9: DNA polymerase proofreads the new DNA
Replication must be highly accurate because copying errors can change genetic information.
Many DNA polymerases have a proofreading function called 3′ to 5′ exonuclease activity. If the polymerase inserts an incorrect nucleotide, it can detect the mismatch, remove the incorrect nucleotide, and continue synthesis with the correct one.
This proofreading greatly improves replication accuracy.
Proofreading is not the only safeguard. Cells also have DNA repair systems that can detect and correct some errors that remain after replication. Together, polymerase proofreading and DNA repair keep the error rate of DNA copying very low.
Step 10: Replication finishes
Replication continues until the DNA in the region being copied has been duplicated and the replication machinery completes its work.
In a bacterial circular chromosome, replication forks eventually meet and the newly copied chromosomes are separated. Because bacterial chromosomes are circular, they do not have the same end-replication problem found in linear chromosomes.
Eukaryotic chromosomes are linear, which creates an additional challenge.
The problem at the ends of linear chromosomes
At the ends of eukaryotic chromosomes are repetitive DNA regions called telomeres. Conventional DNA replication machinery cannot completely copy the very end of the lagging-strand template after the final RNA primer is removed.
Without a specialized solution, chromosome ends would progressively shorten during repeated rounds of replication.
An enzyme called telomerase helps address this problem in cells where it is active. Telomerase extends the chromosome’s telomeric DNA, providing additional template sequence that allows the chromosome end to be replicated.
Telomerase activity is tightly regulated and differs among cell types. It is particularly important in cells that need extensive or repeated proliferation.
The complete sequence at a glance
The major events can be followed in this order:
- An origin of replication is activated.
- Helicase unwinds the DNA double helix.
- Single-strand-binding proteins stabilize the separated strands.
- Topoisomerases relieve twisting and tension ahead of the replication fork.
- Primase makes short RNA primers.
- DNA polymerase extends the primers with DNA nucleotides.
- The leading strand is synthesized continuously.
- The lagging strand is synthesized as Okazaki fragments.
- RNA primers are removed and replaced with DNA.
- DNA ligase seals the remaining breaks.
- DNA polymerases and repair systems correct copying errors.
- Replication is completed, with telomere-maintenance mechanisms addressing the ends of linear chromosomes.
The central principle throughout the process is simple: each original DNA strand acts as a template for a new complementary strand. The enzymes and specialized steps exist largely to solve the physical and chemical problems created by that principle—opening a stable double helix, starting synthesis, maintaining the required direction of DNA synthesis, joining separately made pieces, correcting mistakes, and completing chromosome ends.
