DNA Replication

Basics of DNA Replication

DNA replication uses a semi-conservative method that results in a double-stranded DNA with one parental strand and a new daughter strand.

Learning Objectives

Explain how the Meselson and Stahl experiment conclusively established that DNA replication is semi-conservative.

Key Takeaways

Key Points

  • There were three models suggested for DNA replication: conservative, semi-conservative, and dispersive.
  • The conservative method of replication suggests that parental DNA remains together and newly-formed daughter strands are also together.
  • The semi-conservative method of replication suggests that the two parental DNA strands serve as a template for new DNA and after replication, each double-stranded DNA contains one strand from the parental DNA and one new (daughter) strand.
  • The dispersive method of replication suggests that, after replication, the two daughter DNAs have alternating segments of both parental and newly-synthesized DNA interspersed on both strands.
  • Meselson and Stahl, using E. coli DNA made with two nitrogen istopes (14N and 15N) and density gradient centrifugation, determined that DNA replicated via the semi-conservative method of replication.

Key Terms

  • DNA replication: a biological process occuring in all living organisms that is the basis for biological inheritance
  • isotope: any of two or more forms of an element where the atoms have the same number of protons, but a different number of neutrons within their nuclei

Basics of DNA Replication

Watson and Crick’s discovery that DNA was a two-stranded double helix provided a hint as to how DNA is replicated. During cell division, each DNA molecule has to be perfectly copied to ensure identical DNA molecules to move to each of the two daughter cells. The double-stranded structure of DNA suggested that the two strands might separate during replication with each strand serving as a template from which the new complementary strand for each is copied, generating two double-stranded molecules from one.

Models of Replication

There were three models of replication possible from such a scheme: conservative, semi-conservative, and dispersive. In conservative replication, the two original DNA strands,  known as the parental strands, would re-basepair with each other after being used as templates to synthesize new strands; and the two newly-synthesized strands, known as the daughter strands, would also basepair with each other; one of the two DNA molecules after replication would be “all-old” and the other would be “all-new”. In semi-conservative replication, each of the two parental DNA strands would act as a template for new DNA strands to be synthesized, but after replication, each parental DNA strand would basepair with the complementary newly-synthesized strand just synthesized, and both double-stranded DNAs would include one parental or “old” strand and one daughter or “new” strand. In dispersive replication, after replication both copies of the new DNAs would somehow have alternating segments of parental DNA and newly-synthesized DNA on each of their two strands.

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Suggested Models of DNA Replication: The three suggested models of DNA replication. Grey indicates the original parental DNA strands  or segments and blue indicates newly-synthesized daughter DNA strands or segments.

To determine which model of replication was accurate, a seminal experiment was performed in 1958 by two researchers: Matthew Meselson and Franklin Stahl.

Meselson and Stahl

Meselson and Stahl were interested in understanding how DNA replicates. They grew E. coli for several generations in a medium containing a “heavy” isotope of nitrogen (15N) that is incorporated into nitrogenous bases and, eventually, into the DNA. The E. coli culture was then shifted into medium containing the common “light” isotope of nitrogen (14N) and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was centrifuged at high speeds in an ultracentrifuge in a tube in which a cesium chloride density gradient had been established. Some cells were allowed to grow for one more life cycle in 14N and spun again.

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Meselson and Stahl: Meselson and Stahl experimented with E. coli grown first in heavy nitrogen (15N) then in ligher nitrogen (14N.) DNA grown in 15N (red band) is heavier than DNA grown in 14N (orange band) and sediments to a lower level in the cesium chloride density gradient in an ultracentrifuge. When DNA grown in 15N is switched to media containing 14N, after one round of cell division the DNA sediments halfway between the 15N and 14N levels, indicating that it now contains fifty percent 14N and fifty percent 15N.. In subsequent cell divisions, an increasing amount of DNA contains 14N only. These data support the semi-conservative replication model.

During the density gradient ultracentrifugation, the DNA was loaded into a gradient (Meselson and Stahl used a gradient of cesium chloride salt, although other materials such as sucrose can also be used to create a gradient) and spun at high speeds of 50,000 to 60,000 rpm. In the ultracentrifuge tube, the cesium chloride salt created a density gradient, with the cesium chloride solution being more dense the farther down the tube you went. Under these circumstances, during the spin the DNA was pulled down the ultracentrifuge tube by centrifugal force until it arrived at the spot in the salt gradient where the DNA molecules’ density matched that of the surrounding salt solution. At the point, the molecules stopped sedimenting and formed a stable band. By looking at the relative positions of bands of molecules run in the same gradients, you can determine the relative densities of different molecules. The molecules that form the lowest bands have the highest densities.

DNA from cells grown exclusively in 15N produced a lower band than DNA from cells grown exclusively in 14N. So DNA grown in 15N had a higher density, as would be expected of a molecule with a heavier isotope of nitrogen incorporated into its nitrogenous bases. Meselson and Stahl noted that after one generation of growth in 14N (after cells had been shifted from 15N), the DNA molecules produced only single band intermediate in position in between DNA of cells grown exclusively in 15N and DNA of cells grown exclusively in 14N. This suggested either a semi-conservative or dispersive mode of replication. Conservative replication would have resulted in two bands; one representing the parental DNA still with exclusively 15N in its nitrogenous bases and the other representing the daughter DNA with exclusively 14N in its nitrogenous bases. The single band actually seen indicated that all the DNA molecules contained equal amounts of both 15N and 14N.

The DNA harvested from cells grown for two generations in 14N formed two bands: one DNA band was at the intermediate position between 15N and 14N and the other corresponded to the band of exclusively 14N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. Dispersive replication would have resulted in exclusively a single band in each new generation, with the band slowly moving up closer to the height of the 14N DNA band. Therefore, dispersive replication could also be ruled out.

Meselson and Stahl’s results established that during DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are synthesized. The new strand will be complementary to the parental or “old” strand and the new strand will remain basepaired to the old strand. So each “daughter” DNA actually consists of one “old”  DNA strand and one newly-synthesized strand. When two daughter DNA copies are formed, they have the identical sequences to one another and identical sequences to the original parental DNA, and the two daughter DNAs are divided equally into the two daughter cells, producing daughter cells that are genetically identical to one another and genetically identical to the parent cell.

DNA Replication in Prokaryotes

Prokaryotic DNA is replicated by DNA polymerase III in the 5′ to 3′ direction at a rate of 1000 nucleotides per second.

Learning Objectives

Explain the functions of the enzymes involved in prokaryotic DNA replication

Key Takeaways

Key Points

  • Helicase separates the DNA to form a replication fork at the origin of replication where DNA replication begins.
  • Replication forks extend bi-directionally as replication continues.
  • Okazaki fragments are formed on the lagging strand, while the leading strand is replicated continuously.
  • DNA ligase seals the gaps between the Okazaki fragments.
  • Primase synthesizes an RNA primer with a free 3′-OH, which DNA polymerase III uses to synthesize the daughter strands.

Key Terms

  • DNA replication: a biological process occuring in all living organisms that is the basis for biological inheritance
  • helicase: an enzyme that unwinds the DNA helix ahead of the replication machinery
  • origin of replication: a particular sequence in a genome at which replication is initiated

DNA Replication in Prokaryotes

DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. One of the key players is the enzyme DNA polymerase, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.

There are specific nucleotide sequences called origins of replication where replication begins. In E. coli, which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences. The origin of replication is recognized by certain proteins that bind to this site. An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks at the origin of replication are extended bi-directionally as replication proceeds. Single-strand binding proteins coat the strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. DNA polymerase is able to add nucleotides only in the 5′ to 3′ direction (a new DNA strand can be extended only in this direction). It also requires a free 3′-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3′-OH end and the 5′ phosphate of the next nucleotide. This means that it cannot add nucleotides if a free 3′-OH group is not available. Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA, priming DNA synthesis. A primer provides the free 3′-OH end to start replication. DNA polymerase then extends this RNA primer, adding nucleotides one by one that are complementary to the template strand.

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DNA Replication in Prokaryotes: A replication fork is formed when helicase separates the DNA strands at the origin of replication. The DNA tends to become more highly coiled ahead of the replication fork. Topoisomerase breaks and reforms DNA’s phosphate backbone ahead of the replication fork, thereby relieving the pressure that results from this supercoiling. Single-strand binding proteins bind to the single-stranded DNA to prevent the helix from re-forming. Primase synthesizes an RNA primer. DNA polymerase III uses this primer to synthesize the daughter DNA strand. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches called Okazaki fragments. DNA polymerase I replaces the RNA primer with DNA. DNA ligase seals the gaps between the Okazaki fragments, joining the fragments into a single DNA molecule.

The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5′ to 3′ direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5′ to 3′ direction and the other is oriented in the 3′ to 5′ direction. One strand (the leading strand), complementary to the 3′ to 5′ parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. The other strand (the lagging strand), complementary to the 5′ to 3′ parental DNA, is extended away from the replication fork in small fragments known as Okazaki fragments, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them.

The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3′ to 5′, while that of the leading strand will be 5′ to 3′. The sliding clamp (a ring-shaped protein that binds to the DNA) holds the DNA polymerase in place as it continues to add nucleotides. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, while the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly-synthesized DNA (that replaced the RNA primer) and the previously-synthesized DNA are sealed by the enzyme DNA ligase that catalyzes the formation of phosphodiester linkage between the 3′-OH end of one nucleotide and the 5′ phosphate end of the other fragment.

The table summarizes the enzymes involved in prokaryotic DNA replication and the functions of each.

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Prokaryotic DNA Replication: Enzymes and Their Function: The enzymes involved in prokaryotic DNA replication and their functions are summarized on this table.

DNA Replication in Eukaryotes

DNA replication in eukaryotes occurs in three stages: initiation, elongation, and termination, which are aided by several enzymes.

Learning Objectives

Describe how DNA is replicated in eukaryotes

Key Takeaways

Key Points

  • During initiation, proteins bind to the origin of replication while helicase unwinds the DNA helix and two replication forks are formed at the origin of replication.
  • During elongation, a primer sequence is added with complementary RNA nucleotides, which are then replaced by DNA nucleotides.
  • During elongation the leading strand is made continuously, while the lagging strand is made in pieces called Okazaki fragments.
  • During termination, primers are removed and replaced with new DNA nucleotides and the backbone is sealed by DNA ligase.

Key Terms

  • origin of replication: a particular sequence in a genome at which replication is initiated
  • leading strand: the template strand of the DNA double helix that is oriented so that the replication fork moves along it in the 3′ to 5′ direction
  • lagging strand: the strand of the template DNA double helix that is oriented so that the replication fork moves along it in a 5′ to 3′ manner

Because eukaryotic genomes are quite complex, DNA replication is a very complicated process that involves several enzymes and other proteins. It occurs in three main stages: initiation, elongation, and termination.

Initiation

Eukaryotic DNA is bound to proteins known as histones to form structures called nucleosomes. During initiation, the DNA is made accessible to the proteins and enzymes involved in the replication process. There are specific chromosomal locations called origins of replication where replication begins. In some eukaryotes, like yeast, these locations are defined by having a specific sequence of basepairs to which the replication initiation proteins bind. In other eukaryotes, like humans, there does not appear to be a consensus sequence for their origins of replication. Instead, the replication initiation proteins might identify and bind to specific modifications to the nucleosomes in the origin region.

Certain proteins recognize and bind to the origin of replication and then allow the other proteins necessary for DNA replication to bind the same region. The first proteins to bind the DNA are said to “recruit” the other proteins. Two copies of an enzyme called helicase are among the proteins recruited to the origin. Each helicase unwinds and separates the DNA helix into single-stranded DNA. As the DNA opens up, Y-shaped structures called replication forks are formed. Because two helicases bind, two replication forks are formed at the origin of replication; these are extended in both directions as replication proceeds creating a replication bubble. There are multiple origins of replication on the eukaryotic chromosome which allow replication to occur simultaneously in hundreds to thousands of locations along each chromosome.

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Replication Fork Formation: A replication fork is formed by the opening of the origin of replication; helicase separates the DNA strands. An RNA primer is synthesized by primase and is elongated by the DNA polymerase. On the leading strand, only a single RNA primer is needed, and DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches, each of which must start with its own RNA primer. The DNA fragments are joined by DNA ligase (not shown).

Elongation

During elongation, an enzyme called DNA polymerase adds DNA nucleotides to the 3′ end of the newly synthesized polynucleotide strand. The template strand specifies which of the four DNA nucleotides (A, T, C, or G) is added at each position along the new chain. Only the nucleotide complementary to the template nucleotide at that position is added to the new strand.

DNA polymerase contains a groove that allows it to bind to a single-stranded template DNA and travel one nucleotide at at time. For example, when DNA polymerase meets an adenosine nucleotide on the template strand, it adds a thymidine to the 3′ end of the newly synthesized strand, and then moves to the next nucleotide on the template strand. This process will continue until the DNA polymerase reaches the end of the template strand.

DNA polymerase cannot initiate new strand synthesis; it only adds new nucleotides at the 3′ end of an existing strand. All newly synthesized polynucleotide strands must be initiated by a specialized RNA polymerase called primase. Primase initiates polynucleotide synthesis and by creating a short RNA polynucleotide strand complementary to template DNA strand. This short stretch of RNA nucleotides is called the primer. Once RNA primer has been synthesized at the template DNA, primase exits, and DNA polymerase extends the new strand with nucleotides complementary to the template DNA.

Eventually, the RNA nucleotides in the primer are removed and replaced with DNA nucleotides. Once DNA replication is finished, the daughter molecules are made entirely of continuous DNA nucleotides, with no RNA portions.

The Leading and Lagging Strands

DNA polymerase can only synthesize new strands in the 5′ to 3′ direction. Therefore, the two newly-synthesized strands grow in opposite directions because the template strands at each replication fork are antiparallel. The “leading strand” is synthesized continuously toward the replication fork as helicase unwinds the template double-stranded DNA.

The “lagging strand” is synthesized in the direction away from the replication fork and away from the DNA helicase unwinds. This lagging strand is synthesized in pieces because the DNA polymerase can only synthesize in the 5′ to 3′ direction, and so it constantly encounters the previously-synthesized new strand. The pieces are called Okazaki fragments, and each fragment begins with its own RNA primer.

Termination

Eukaryotic chromosomes have multiple origins of replication, which initiate replication almost simultaneously. Each origin of replication forms a bubble of duplicated DNA on either side of the origin of replication. Eventually, the leading strand of one replication bubble reaches the lagging strand of another bubble, and the lagging strand will reach the 5′ end of the previous Okazaki fragment in the same bubble.

DNA polymerase halts when it reaches a section of DNA template that has already been replicated. However, DNA polymerase cannot catalyze the formation of a phosphodiester bond between the two segments of the new DNA strand, and it drops off. These unattached sections of the sugar-phosphate backbone in an otherwise full-replicated DNA strand are called nicks.

Once all the template nucleotides have been replicated, the replication process is not yet over. RNA primers need to be replaced with DNA, and nicks in the sugar-phosphate backbone need to be connected.

The group of cellular enzymes that remove RNA primers include the proteins FEN1 (flap endonulcease 1) and RNase H. The enzymes FEN1 and RNase H remove RNA primers at the start of each leading strand and at the start of each Okazaki fragment, leaving gaps of unreplicated template DNA. Once the primers are removed, a free-floating DNA polymerase lands at the 3′ end of the preceding DNA fragment and extends the DNA over the gap. However, this creates new nicks (unconnected sugar-phosphate backbone).

In the final stage of DNA replication, the enyzme ligase joins the sugar-phosphate backbones at each nick site. After ligase has connected all nicks, the new strand is one long continuous DNA strand, and the daughter DNA molecule is complete.

DNA Replication: This is a clip from a PBS production called “DNA: The Secret of Life.” It details the latest research (as of 2005) concerning the process of DNA replication.

Telomere Replication

As DNA polymerase alone cannot replicate the ends of chromosomes, telomerase aids in their replication and prevents chromosome degradation.

Learning Objectives

Describe the role played by telomerase in replication of telomeres

Key Takeaways

Key Points

  • DNA polymerase cannot replicate and repair DNA molecules at the ends of linear chromosomes.
  • The ends of linear chromosomes, called telomeres, protect genes from getting deleted as cells continue to divide.
  • The telomerase enzyme attaches to the end of the chromosome; complementary bases to the RNA template are added on the 3′ end of the DNA strand.
  • Once the lagging strand is elongated by telomerase, DNA polymerase can add the complementary nucleotides to the ends of the chromosomes and the telomeres can finally be replicated.
  • Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase; telomere shortening is associated with aging.
  • Telomerase reactivation in telomerase-deficient mice causes extension of telomeres; this may have potential for treating age-related diseases in humans.

Key Terms

  • telomere: either of the repetitive nucleotide sequences at each end of a eukaryotic chromosome, which protect the chromosome from degradation
  • telomerase: an enzyme in eukaryotic cells that adds a specific sequence of DNA to the telomeres of chromosomes after they divide, giving the chromosomes stability over time

The End Problem of Linear DNA Replication

Linear chromosomes have an end problem. After DNA replication, each newly synthesized DNA strand is shorter at its 5′ end than at the parental DNA strand’s 5′ end. This produces a 3′ overhang at one end (and one end only) of each daughter DNA strand, such that the two daughter DNAs have their 3′ overhangs at opposite ends

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The telomere end problem: A simplified schematic of DNA replication where the parental DNA (top) is replicated from three origins of replication, yielding three replication bubbles (middle) before giving rise to two daughter DNAs (bottom). Parental DNA strands are black, newly synthesized DNA strands are blue, and RNA primers are red. All RNA primers will be removed by Rnase H and FEN1, leaving gaps in the newly-synthesized DNA strands (not shown.) DNA Polymerase and Ligase will replace all the RNA primers with DNA except the RNA primer at the 5′ ends of each newly-synthesized (blue) strand. This means that each newly-synthesized DNA strand is shorter at its 5′ end than the equivalent strand in the parental DNA.

Every RNA primer synthesized during replication can be removed and replaced with DNA strands except the RNA primer at the 5′ end of the newly synthesized strand. This small section of RNA can only be removed, not replaced with DNA. Enzymes RNase H and FEN1 remove RNA primers, but DNA Polymerase will add new DNA only if the DNA Polymerase has an existing strand 5′ to it (“behind” it) to extend. However, there is no more DNA in the 5′ direction after the final RNA primer, so DNA polymerse cannot replace the RNA with DNA. Therefore, both daughter DNA strands have an incomplete 5′ strand with 3′ overhang.

In the absence of additional cellular processes, nucleases would digest these single-stranded 3′ overhangs. Each daughter DNA would become shorter than the parental DNA, and eventually entire DNA would be lost. To prevent this shortening, the ends of linear eukaryotic chromosomes have special structures called telomeres.

Telomere Replication

The ends of the linear chromosomes are known as telomeres: repetitive sequences that code for no particular gene. These telomeres protect the important genes from being deleted as cells divide and as DNA strands shorten during replication.

In humans, a six base pair sequence, TTAGGG, is repeated 100 to 1000 times. After each round of DNA replication, some telomeric sequences are lost at the 5′ end of the newly synthesized strand on each daughter DNA, but because these are noncoding sequences, their loss does not adversely affect the cell. However, even these sequences are not unlimited. After sufficient rounds of replication, all the telomeric repeats are lost, and the DNA risks losing coding sequences with subsequent rounds.

The discovery of the enzyme telomerase helped in the understanding of how chromosome ends are maintained. The telomerase enzyme attaches to the end of a chromosome and contains a catalytic part and a built-in RNA template. Telomerase adds complementary RNA bases to the 3′ end of the DNA strand. Once the 3′ end of the lagging strand template is sufficiently elongated, DNA polymerase adds the complementary nucleotides to the ends of the chromosomes; thus, the ends of the chromosomes are replicated.

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Telomerase is important for maintaining chromosome integrity: The ends of linear chromosomes are maintained by the action of the telomerase enzyme.

Telomerase and Aging

Telomerase is typically active in germ cells and adult stem cells, but is not active in adult somatic cells. As a result, telomerase does not protect the DNA of adult somatic cells and their telomeres continually shorten as they undergo rounds of cell division.

In 2010, scientists found that telomerase can reverse some age-related conditions in mice. These findings may contribute to the future of regenerative medicine. In the studies, the scientists used telomerase-deficient mice with tissue atrophy, stem cell depletion, organ failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved the function of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans.