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DNA Replication

Author: Sophia

what's covered
In this lesson, you will learn how DNA copies itself. This is a critical function of DNA because it allows DNA to carry information from parent to daughter cells and in other ways. Additionally, it must be highly accurate and yet able to vary so that genetic variability provides a substrate for evolution. To understand these in later topics and technologies that use parts of DNA replication, it is essential to understand the details of the process. Specifically, this lesson will cover the following:

Table of Contents

1. An Introduction to DNA Replication

The structure of DNA provided an intriguing hint about its mechanism of replication, as noted by James Watson and Francis Crick in their famous publication introducing their model (Watson and Crick, 1956). As you learned in the tutorial on DNA structure, nitrogenous bases bond according to complementary base pairing rules. This means that it is possible to determine the sequence of bases on one strand simply by knowing the sequence of bases on the other strand and provides a possible mechanism for replication of one DNA molecule to make two new molecules.

However, this simple overview betrays the complexity of the overall process. For example, the composition of daughter molecules was originally unclear. The image below shows three possible outcomes of replication. If replication were conservative, a parental double-stranded DNA (dsDNA) molecule would undergo replication to produce one daughter molecule identical to itself and one entirely new molecule. If replication were dispersive, then each daughter molecule would have two strands each composed of a mixture of parental and new nucleotides. If replication were semiconservative, then each parental molecule would produce two daughter molecules that each had one half of the parental molecule and one new half.

Diagram showing 3 models of DNA replication. In the conservative model the original double helix produces two double helices; one of which has two of the parent strands and one of which has two of the new strands. Another round produces 4 helices; one of which has two of the parent strands and three of which have all new strands. In semiconservative replication the first round leads to two double helices each with one old strand and one new strand. The next round leads to four double helices; two of these have an old and a new strand and two have all new strands. In dispersive replication each new round of replication results in strands with random bits from the parent strand and random bits of new strands.

In 1958, Matthew Meselson (1930–Present) and Franklin Stahl (1929–Present) performed an experiment that determined that DNA replication was semiconservative. The experiment was designed so that there were three clearly distinct predictions based on whether DNA replication was conservative, semiconservative, or dispersive. The steps of the experiment were as follows.

step by step
Step 1: They grew Escherichia coli bacteria for several generations in a medium containing “heavy” nitrogen atoms (straight N presuperscript 15) instead of the more common straight N presuperscript 14 atoms.
Step 2: Over time, this heavy nitrogen was incorporated into the nitrogenous bases of the bacterial DNA. The parental DNA could now be distinguished from other DNA.
Step 3: They moved the bacteria into medium containing straight N presuperscript 14 for a single generation, allowing the cells to produce daughter DNA molecules.
Step 4: They harvested the bacterial cells and isolated the DNA.
Step 5: They used ultracentrifugation to separate DNA by mass. For comparison, they also used ultracentrifugation on DNA from cells grown in straight N presuperscript 14 medium only and cells grown in straight N presuperscript 15 medium only.
Step 6: The daughter DNA had an intermediate mass that was between DNA containing only straight N presuperscript 15 and DNA containing only straight N presuperscript 14, indicating that it had one parental strand with straight N presuperscript 15 strand and one new strand containing straight N presuperscript 14 (i.e., it was semiconservative).

The image below shows the outcomes of centrifugation of the three types of samples as well as the predictions for each hypothesis: conservative, semiconservative, and dispersive. Only semiconservative replication produced results matching those obtained from the experiment after two replications of the DNA, producing an intermediate band (with one heavy band from the parent and one newly formed light band) in the first replication and then a mix of intermediate bands and light bands (from new DNA formed from the light strands of parents and new light strands) in the second replication. Conservative replication would have kept the original molecule with production of a new light molecule and dispersive replication would have mixed the strands so they would contain a mix of heavy and light nucleotides forming intermediate bands in the first and second replications.

A diagram explaining the Meselson Stahl experiment. In the first part of the experiment DNA is replicated in the presence of heavy 15N medium. This produces all heavy DNA strands. Next they moved the cells to light 14N medium. If DNA was replicated conservatively, one would expect to see one heavy band and one light band. However, they saw only a medium size band. This is consistent with semiconservative and dispersive replication. Finally, they allowed the bacteria to undergo another round of replication in the light medium. If DNA was replicated dispersively, one would expect only a medium size band. However, they saw a medium band and a light band. The only mechanism that explains these results is semi-conservative replication.

term to know
Semiconservative Replication
DNA replication in which each parental molecule produces two daughter molecules that each has one half of the parental molecule and one new half.


2. DNA Replication in Bacteria

Because bacteria have relatively small genomes, they replicate quickly and produce many mutants that can be utilized for research. This is why there has been considerable study of bacterial DNA replication. It only takes 42 minutes for an E. coli bacterium to replicate its entire single circular chromosome, which contains 4.6 million base pairs (Mbp).

Many enzymes and proteins are used in DNA replication, and these are summarized in a table at the end of the tutorial. These molecules prepare DNA for replication, help to hold components in place, and add components as needed.

One of the most important enzymes in this process is DNA polymerase. As its name suggests, DNA polymerase is an enzyme that produces polymers of DNA nucleotides. DNA-dependent DNA polymerases use DNA as a template, meaning that they add complementary nucleotides based on the DNA sequence (the unusual enzyme reverse transcriptase, which HIV uses to copy its RNA genome into cDNA, is an RNA-dependent DNA polymerase). There are several types of DNA polymerases. In prokaryotes, there are three types named using Roman numerals.

DNA polymerase III (also known as DNA pol III) is the enzyme that is responsible for the actual copying of one strand, whereas DNA pol I and DNA pol II are primarily required for repair. During replication, DNA pol III adds complementary base pairs to grow a new strand complementary to the template strand.

Each new nucleotide is added through the formation of a bond between phosphate and a free 3′-OH group. A triphosphate nucleotide, such as the guanosine triphosphate molecule shown below, undergoes bond cleavage to remove two phosphate groups. This exposes the phosphate that will form a new bond called the phosphodiester bond. Additionally, cleavage of the phosphate groups releases the energy needed for bond formation.

Diagram of dGTP. In the center is deoxyribose which is a pentagon shaped sugar. The top point has an oxygen. Then, moving around the shape are carbons 1, 2, 3, and 4; carbon 5 is attached to carbon 4 but not in the ring. Attached to carbon 1 is a structure made of 2 carbon and nitrogen rings bound along their ends; this is guanine. Carbon 2 has only Hs attached to it. Carbon 3 has an H and an OH. Carbon 4 has an N and Carbon 5. Carbon 5 is attached to 3 phosphate groups in a row (labeled triphosphate). Each phosphate group is made of phosphorus attached to 4 oxygen atoms.

terms to know
DNA Polymerase
An enzyme that produces polymers of DNA nucleotides.
Template
A strand of nucleic acid being used to form a complementary strand.

2a. Initiation

The process of replication is divided into three major steps: initiation, elongation, and termination. Initiation of replication occurs at a specific nucleotide sequence called the origin of replication, where various proteins bind to begin the replication process. Like most prokaryotes, E. coli has a single origin of replication.

For replication to occur, regions of DNA have to be made accessible. In chromosomes, DNA is packed around proteins to fit tightly within a cell. The process by which DNA is packed and unpacked through twisting is called supercoiling. It is important to prevent DNA from being too tightly or too loosely wound as other parts of the DNA are unwound for replication. Enzymes called topoisomerases act to make small nicks or cuts in DNA to resolve supercoiling, allowing replication to proceed. In many bacteria and some archaea, a specific topoisomerase called DNA gyrase is used.

Proteins are used to aid the organization of DNA. Specific proteins help bind DNA and aid in packaging. Other proteins bind to the origin of replication. In eukaryotes, DNA-binding proteins called histones are especially important in arranging DNA into compact chromatin. Prokaryotes do not have histones but do have similar proteins that are used to compact DNA in the nucleoid structure.

For bacterial DNA replication to begin, the supercoiled chromosome is relaxed by DNA gyrase. Another enzyme called helicase separates the DNA strands by breaking the hydrogen bonds between the nitrogenous base pairs. As the DNA opens up, it forms an open region called a replication bubble with Y-shaped replication forks at each end. The DNA near each replication fork is coated with single-stranded binding proteins to prevent the single-stranded DNA (ssDNA) from joining back together.

Once ssDNA is accessible at the origin of replication, nucleotides can be added to begin to form new strands. However, DNA pol III cannot start a new strand and can only add nucleotides in the 5′ to 3′ direction. Therefore, an enzyme called RNA primase adds a small sequence of RNA to start the new strand. RNA primase is an RNA polymerase, meaning that it builds polymers of RNA nucleotides.

Once the primer is in place, DNA pol III can begin to add DNA nucleotides and elongation can begin.

terms to know
Initiation of Replication
The specific nucleotide sequence at which replication begins.
Supercoiling
The tight twisting structure of chromosomes.
Topoisomerase
An enzyme that nicks DNA so that supercoiling does not become excessive.
DNA Gyrase
A topoisomerase found in bacteria and many archaea.
Histone
An important type of DNA-binding protein common in eukaryotes.
Helicase
The enzyme that separates DNA strands by breaking hydrogen bonds.
Replication Bubble
The open region where DNA replication is taking place.
Replication Fork
A Y-shaped end of a replication bubble.
Single-Strand Binding Protein
A protein that binds to DNA near a replication fork to help hold the complementary strands apart so that new nucleotides can be added.
Primase
The enzyme that adds a small sequence of RNA to start a new strand during DNA replication.
RNA Polymerase
An enzyme that adds RNA nucleotides to build a strand of RNA.

2b. Elongation

During elongation in DNA replication, the addition of nucleotides occurs at its maximal rate of about 1,000 nucleotides per second. The appearance of half of the replication fork during elongation is shown in the image below.

Diagram of DNA replication. A small inset at the top shows a double strand of DNA separated in the center forming a bubble; the DNA is double stranded on either side of the bubble. The origin of replication is in the midway point of the bubble. On the top strand a solid arrow points to the left from the origin; this is the leading strand. On the right of the origin of replication are short arrows pointing to the left; this is the lagging strand. On the bottom strand a solid arrow pointing to the right from the origin is labeled leading strand and short arrows pointing to the right on the other side of the origin are labeled lagging strands. A larger image shows just the left half of the bubble. The double stranded DNA is no the far left and is labeled 5′ for the top strand and 3′ for the bottom strand. An enzyme to the very far left I is labeled topoisomerase/gyrase. At the point where the double stranded regions splits is a triangle shape labeled helicase. Next to that are smaller shapes labeled single-stranded binding proteins. The top strand shows continuous synthesis of the leading strand; this is shown as a solid arrow under the top strand. The arrow has a 5′ at the right end and a 3′ at the left end. The template strand at the top has a 3′ at the right and a 5′ at the left. At the end of the arrow (near where the DNA is newly being separated by the helicase) is DNA polymerase 3 and a sliding clamp that span both strands. The bottom strand of DNA has more components. Just after the single stranded binding proteins is RNA primase which attaches RNA primer (shown as a green arrow). Further down the lagging strand template is an existing RNA primer with DNA polymerase III and a sliding clamp spanning primer and the template strand. The polymerase is building a new strand of DNA from the left side (5′) to the right side (3′). Further to the right is a long piece made of RNA primer, then new DNA, then RNA primer, then new DNA all connected. Each of the DNA/RNA combinations are okazaki fragments made in the discontinuous synthesis of the lagging strand. DNA polymerase I is attached to the RNA primer in the center and is replacing it with DNA nucleotides. DNA ligase then binds the individual strands of new DNA together. This is shown in a close-up as two double helices that have all the correct letters in place, but one is missing a connection between two of the nucleotides (this is called a single-stranded gap). DNA ligase forms this last bond and the gap is sealed.

As you learned in the tutorial on DNA structure, a DNA double helix consists of antiparallel strands. Because DNA pol III can only add in the 5′ to 3′ direction, it means that it can only add continuously in one direction. The strands formed in this manner are called leading strands. To make new strands complementary to 5′ to 3′ parental DNA, new nucleotides are added moving away from (rather than toward) the replication fork. Making the other strands called lagging strands requires using small fragments of DNA called Okazaki fragments. Each Okazaki fragment requires its own primer. DNA pol III then adds nucleotides until it bumps into the existing strand and moves back again to begin a new fragment. Because of this process, lagging strands are said to be synthesized discontinuously.

Several things take place simultaneously. A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. Topoisomerase helps to prevent overwinding of the DNA double helix ahead of each replication fork by nicking the DNA backbone and resealing it. The RNA primers are removed by exonuclease activity of DNA pol I and then the gaps are filled in with DNA nucleotides. The gaps between the fragments are sealed by the enzyme DNA ligase, which catalyzes the formation of covalent phosphodiester linkages between the sides of each break.

terms to know
Elongation in DNA Replication
The period of DNA replication during which strand growth is most rapid.
Leading Strand
A strand of DNA synthesized continuously in a 5′ to 3′ direction.
Lagging Strand
A strand of DNA synthesized discontinuously as a series of small 5′ to 3′ Okazaki fragments.
Okazaki Fragment
A fragment of DNA synthesized as part of a lagging strand during DNA synthesis.
Ligase
An enzyme that joins fragments together after primers have been removed and replaced with DNA to stabilize the DNA strand.

2c. Termination

Once the complete chromosome has been replicated, termination of DNA replication occurs. Less is known about this process than about initiation and elongation. Following replication, the resulting complete circular genomes of prokaryotes are concatenated, meaning that the circular DNA chromosomes are interlocked and must be separated from each other using cuts by bacterial topoisomerase IV. After the molecules have separated, topoisomerase reseals the cuts. This process is not necessary in eukaryotes, which have linear DNA molecules.

did you know
Because eukaryotes do not need bacterial topoisomerase IV, medications called quinolones target these enzymes to treat bacterial infections.

The table below summarizes the enzymes and proteins that work together during bacterial DNA replication.

The Molecular Machinery Involved in Bacterial DNA Replication
Enzyme or Factor Function
DNA pol I Exonuclease activity removes RNA primer and replaces it with newly synthesized DNA
DNA pol II Primarily involved in repair; has 3′ to 5′ nuclease activity and may aid in repairing lesions
DNA pol III Main enzyme that adds nucleotides in the 5′ to 3′ direction
Helicase Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases
Ligase Seals the gaps between the Okazaki fragments on the lagging strand to create one continuous DNA strand
Primase Synthesizes RNA primers needed to start replication
Single-stranded binding proteins Bind to ssDNA to prevent hydrogen bonding between DNA strands, reforming ds DNA
Sliding clamp Helps hold DNA pol III in place when nucleotides are being added
Topoisomerase II (DNA gyrase) Relaxes supercoiled chromosome to make DNA more accessible for the initiation of replication; helps relieve the stress on DNA when unwinding by causing breaks and then resealing the DNA
Topoisomerase IV Introduces single-stranded break into concatenated chromosomes to release them from each other and then reseals the DNA

watch
DNA Replication: Copying the Molecule of Life

term to know
Termination of DNA Replication
The series of steps that complete DNA replication to produce two distinct DNA molecules.


3. DNA Replication in Eukaryotes

DNA replication in eukaryotes has some important distinctions from DNA replication in prokaryotes. In part, this results from the fact that eukaryotes have much larger, more complex genomes arranged as multiple linear chromosomes. As shown in the image below, eukaryotes have multiple origins of replication on each chromosome that extend until they meet. Although this helps to reduce the time needed to replicate the entire genome, the rate of replication is approximately ten times slower than prokaryotic replication.

A diagram showing two strands of parental DNA. Then an arrow showing multiple replication bubbles with an origin of replication in each. Arrows point to the left and right from each origin of replication. New strands of DNA are shown being formed. One of the bubbles has the left half of the bubble in a box labeled replication fork. The next image shows the replication bubbles getting longer. The final image shows two new DNA strands, each with one old strand and one new strand.

Despite these important differences, the most essential steps of replication are the same in prokaryotes and eukaryotes. Although there are more types of polymerases, the basic process of elongation using leading and lagging strands is the same.

A prereplication complex composed of several proteins, including helicase, forms at the origin of replication and recruits other components involved in the initiation of replication. These components include eukaryotic topoisomerase, single-stranded binding protein, RNA primase, and DNA polymerase.

Eukaryotic DNA polymerases are named using Greek letters. During elongation, DNA pol delta (δ) continuously synthesizes the leading strand and pol epsilon (ε) synthesizes the lagging strand. A sliding clamp protein holds DNA polymerase in place against the DNA. Instead of a DNA polymerase (used by bacteria), the enzyme ribonuclease H (RNase H) removes the RNA primer. After the primer is replaced with DNA nucleotides, DNA ligase seals the strands to stabilize them.

One important difference between prokaryotic and eukaryotic DNA replication results from the linear chromosomes of eukaryotes. As the image below shows, there is no way to make primers at the very end of linear chromosomes (noncoding repetitive sequences called telomeres). Over time, this means that the DNA becomes progressively shorter unless an enzyme called telomerase acts to fill the gaps as shown in the image.

Diagram of telomerase. The top image shows a long strand of DNA with 5′ on the left and 3′ on the right. The complementary strand is much shorter and shows 3′ on the left and 5′ on the right. A circle labeled telomerase contains a complementary strand that matches the 3′ end of the upper strand and also extends past the 3′ end of the top strand. Caption: Telomerase has an associated RNA that complements the 3′ overhang at the end of the chromosome. Next, the top strand of DNA replicates using the overhang of the strand within the telomerase. Caption: The RNA template is used to synthesize the complementary strand. Next, the telomerase moves to the new 3′ end of the top strand. Caption: Telomerase shifts and the process repeats. Finally, The top DNA strand has multiple extensions. RNA primer binds near the 3′ end and builds a new strand of DNA towards the left until it meets up with the existing strand.

did you know
With certain important exceptions, most cells have a normal lifespan and then undergo senescence (aging). The shortening of chromosomes is an indicator of cell age associated with this process. One way that cancer cells differ from healthy cells is that they sometimes have mutations that increase their telomerase activity and keep their chromosomes longer than they would otherwise be. There is interest in using these mutations and changes in telomerase activity as targets for cancer treatments (McKelvey et al., 2020; Graham and Meeker, 2017).

The table below summarizes some of the distinctions between bacterial and eukaryotic replication. Note that Archaea are not included in this table. Archaea have unique characteristics distinct from the other two domains but that is beyond the scope of this lesson (e.g., Sarmiento et al., 2014; Pérez-Arnaiz et al., 2020).

Comparison of Bacterial and Eukaryotic Replication
Property Bacteria Eukaryotes
Genome structure Single circular chromosome Multiple linear chromosomes
Number of origins per chromosome Single Multiple
Rate of replication 1,000 nucleotides per second 100 nucleotides per second
Telomerase Not present Present
RNA primer removal DNA pol I RNase H
Strand elongation DNA pol III pol δ, pol ε

terms to know
Telomere
A noncoding repetitive sequence at the end of a eukaryotic chromosome.
Telomerase
An enzyme that prevents shortening of telomeres during replication.


4. DNA Replication of Extrachromosomal Elements

A unique type of replication called rolling circle replication is used by some bacterial plasmids, some bacteriophages, and some eukaryotic viruses. This type of replication is only possible for DNA that is circular (as in plasmids) or capable of circularization (as in some viruses). The process in bacteria is summarized in the steps and image below.

step by step
Step 1: An enzyme nicks one of the two strands of the dsDNA molecule at the double-stranded origin (dso) site.
Step 2: DNA pol III binds to the 3′-OH group of the nicked strand and begins to unidirectionally replicate the DNA using the un-nicked strand as a template, simultaneously displacing the nicked strand.
Step 3: Completion of DNA replication at the site of the original nick results in full displacement of the nicked strand, which may recircularize into a ssDNA molecule.
Step 4: RNA primase synthesizes a primer to initiate DNA replication at the single-stranded origin (sso) site of the ssDNA molecule, resulting in a dsDNA molecule identical to the other circular DNA molecule.
Diagram of DNA replication. A circle of double-stranded DNA has a region labeled SSO near a region labeled DSO. A nick forms in DSO and DNA polymerase III begins copying and displacing the nicked strand. This forms a new ring made of an old and a new strand of DNA; the second old strand of DNA is outside of this ring but eventually rejoins the nicked strand. DNA ligase then separates the dsDNA (synthesis of first strand) and the lone ssDNA. The ssDNA then has the second strand synthesized and become a ds DNA as well.

term to know
Rolling Circle Replication
A type of DNA replication used by DNA that is circular or capable of circularization. In bacteria, one strand is displaced and can recircularize while a new complementary strand is added to the other parent strand.

summary
In this lesson, you learned about the mechanism of DNA replication and important terminology. Then you learned the steps of DNA replication in bacteria: initiation, elongation, and termination. These steps are similar to the steps of DNA replication in eukaryotes, but there are also important differences. Some of these differences have been useful in developing medications to target bacteria. Additionally, the linear nature of eukaryotic chromosomes means that they shorten during replication in the absence of the enzyme telomerase. Because this enzyme is important in many cancer cells, it is another clinically relevant aspect of replication. Finally, you learned about DNA replication of extrachromosomal elements focusing on how circular bacterial plasmids sometimes replicate using the rolling circle mechanism.

Source: THIS TUTORIAL HAS BEEN ADAPTED FROM OPENSTAX “MICROBIOLOGY.” ACCESS FOR FREE AT openstax.org/details/books/microbiology. LICENSE: CC ATTRIBUTION 4.0 INTERNATIONAL

REFERENCES
Crick, F. H. & Watson, J. D. (1953). Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171, 737–738. www.nature.com/articles/171737a0

Graham, M. K., & Meeker, A. (2017). Telomeres and telomerase in prostate cancer development and therapy. Nature reviews. Urology, 14(10), 607–619. doi.org/10.1038/nrurol.2017.104

Kuznetsova, A. A., Fedorova, O. S., & Kuznetsov, N. A. (2022). Structural and Molecular Kinetic Features of Activities of DNA Polymerases. International journal of molecular sciences, 23(12), 6373. doi.org/10.3390/ijms23126373

McKelvey, B. A., Umbricht, C. B., & Zeiger, M. A. (2020). Telomerase Reverse Transcriptase (TERT) Regulation in Thyroid Cancer: A Review. Frontiers in endocrinology, 11, 485. doi.org/10.3389/fendo.2020.00485

Pérez-Arnaiz, P., Dattani, A., Smith, V., & Allers, T. (2020). Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open biology, 10(12), 200293. doi.org/10.1098/rsob.200293

Sarmiento, F., Long, F., Cann, I., & Whitman, W. B. (2014). Diversity of the DNA replication system in the Archaea domain. Archaea (Vancouver, B.C.), 2014, 675946. doi.org/10.1155/2014/675946

Terms to Know
DNA Gyrase

A topoisomerase found in bacteria and many archaea.

DNA Polymerase

An enzyme that produces polymers of DNA nucleotides.

Elongation in DNA Replication

The period of DNA replication during which strand growth is most rapid.

Helicase

The enzyme that separates DNA strands by breaking hydrogen bonds.

Histone

An important type of DNA-binding protein common in eukaryotes.

Initiation of Replication

The specific nucleotide sequence at which replication begins.

Lagging Strand

A strand of DNA synthesized discontinuously as a series of small 5′ to 3′ Okazaki fragments.

Leading Strand

A strand of DNA synthesized continuously in a 5′ to 3′ direction.

Ligase

An enzyme that joins fragments together after primers have been removed and replaced with DNA to stabilize the DNA strand.

Okazaki Fragment

A fragment of DNA synthesized as part of a lagging strand during DNA synthesis.

Primase

The enzyme that adds a small sequence of RNA to start a new strand during DNA replication.

RNA Polymerase

An enzyme that adds RNA nucleotides to build a strand of RNA.

Replication Bubble

The open region where DNA replication is taking place.

Replication Fork

A “Y”-shaped end of a replication bubble.

Rolling Circle Replication

A type of DNA replication used by DNA that is circular or capable of circularization. In bacteria, one strand is displaced and can recircularize while a new complementary strand is added to the other parent strand.

Semiconservative Replication

DNA replication in which each parental molecule produces two daughter molecules that each has one half of the parental molecule and one new half.

Single-Strand Binding Protein

A protein that binds to DNA near a replication fork to help hold the complementary strands apart so that new nucleotides can be added.

Supercoiling

The tight twisting structure of chromosomes.

Telomerase

An enzyme that prevents shortening of telomeres during replication.

Telomere

A noncoding repetitive sequence at the end of a eukaryotic chromosome.

Template

A strand of nucleic acid being used to form a complementary strand.

Termination of DNA Replication

The series of steps that complete DNA replication to produce two distinct DNA molecules.

Topoisomerase

An enzyme that nicks DNA so that supercoiling does not become excessive.