DNA Replication

DNA replication is the natural course of creating two indistinguishable imitations of DNA from one unique DNA molecule. DNA replication happens in all living creatures going about as the most fundamental part of biological inheritance. This is fundamental for cell division during the development and repair of harmed tissues, while it likewise guarantees that every one of the new cells accepts its own duplicate of the DNA. The cell possesses the particular property of division, which makes the replication of DNA fundamental. DNA is comprised of a twofold helix of two complementary strands. The double helix portrays the presence of a Double-stranded DNA which is in this way made out of two linear strands that run inverse to one another and bend together to form. During replication, these strands are separated.  Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near-perfect fidelity for DNA replication. In a cell, DNA replication starts at explicit areas, or beginnings of replication, in the genome which contains the hereditary material of an organism. The unwinding of DNA at the beginning and blending of new strands, obliged by a protein known as helicase, brings about replication forks developing bi-directionally from the beginning. Various proteins are related to the replication fork to help in the initiation and continuation of DNA union. Most noticeably, DNA polymerase blends the new strands by adding nucleotides that supplement every template strand. DNA replication happens during the S-phase of the interphase. DNA replication can also be performed in vitro (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples. In March 2021, researchers reported evidence suggesting that a preliminary form of transfer RNA, a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code, could have been a replicator molecule itself in the very early development of life, or abiogenesis.

Nucleotide 

A nucleotide is a monomer that serves as the building block materials for DNA or RNA. A nucleotide is made up of a Nitrogen base, Sugar and phosphate group.

Nitrogen Base: Adenine, Guanine, cytosine and thiamine are present in DNA and in RNA cytosine is replaced by uracil in RNA. These are the central information-carrying part of nucleotide structure, Nitrogen bases are linked together by hydrogen bonds.

• Adenine: Adenine is purine which are having a double-ringed structure. In DNA Adenine bonds with thymine whereas in RNA it bonds with uracil. ATP utilizes adenine that’s why sugar-phosphate bonds are strong in ATP as well.
• Guanine: Guanine is purine which are having a double-ringed structure. Guanine binds to cytosine through triple bonds. Hence the Guanine and cytosine bonds are stronger.
• Thymine and Cytosine: Thymine and cytosine are pyrimidine nucleotides which are having single ring structures. It bonds with Adenine in DNA.
• Uracil: This is also a pyrimidine structure. it is also in the form of demethylated thymine.

Sugar: In DNA the 5-carbon sugar is deoxyribose and while in RNA it is ribose. The sugar with its exposure to oxygen can bond with the phosphate group of the next molecule and then form a bond which is called a sugar-phosphate backbone. As these bonds are covalent bonds they are far stronger than hydrogen bonds.

Phosphate Group: This is the largest structure of DNA. Phosphate is present in the body in the form of ATP (Adenosine Triphosphate). During DNA replication DNA ligase enzyme finishes the replication by farming the phospho-diester bonds between the sugar molecules of one and the next phosphate group. This creates the backbone of genetic material DNA and RNA.

Nucleoside: Nitrogen base and Sugar excluding the phosphate group is called Nucleoside.

Functions

• Nucleotides act as coenzymes which are required to catalyze many biochemical reactions.
• These are the building blocks of DNA and RNA.
• They act as electron carriers in the redox reactions of electron transport in which NADP and NAD are required.

DNA Replication

The process by which a DNA molecule makes its identical copies is referred to as DNA replication. The replication of DNA occurs during the synthesis phase, or S phase, of the cell cycle, before the cell enters mitosis or meiosis.

The explanation of the construction of the twofold helix gave a clue concerning how DNA is duplicated. Review that adenine nucleotides pair with thymine nucleotides, and cytosine with guanine. This implies that the two strands are reciprocal to one another. For instance, a strand of DNA with a nucleotide succession of AGTCATGA will have a correlative strand with the grouping TCAGTACT.

On account of the complementarity of the two strands, having one strand implies that reproducing the other strand is conceivable. This model for replication recommends that the two strands of the twofold helix separate during replication, and each strand fills in as a layout from which the new reciprocal strand is duplicated.

During DNA replication, every one of the two strands that make up the twofold helix fills in as a layout from which new strands are duplicated. The new strand will be integral to the parental or “old” strand. Each new twofold strand comprises one parental strand and one new daughter strand. This is known as semiconservative replication. At the point when two DNA duplicates are framed, they have an indistinguishable grouping of nucleotide bases and are partitioned similarly into two daughter cells.

DNA Replication

Role of Enzymes in DNA Replication

DNA is made up of a double helix of two complementary stands. During the replication, these stands are separated by many enzymes that participate in DNA replication. the list of enzymes that are involved in DNA replication is as follows.

DNA Helicase prokaryotes/Eukaryotes

DNA helicase was discovered in E.coli in 1976. It is also called helix destabilize enzyme since it separates the two strands of DNA at replication. They are the motor proteins that move directionally along the nucleic acid phospho-diester back bone separating two annealed nucleic acid stands using energy-derived ATP hydrolysis.

DNA Polymerase

DNA polymerases are the enzymes that synthesize the DNA molecules from ribonucleotides, the building blocks of DNA strands. The DNA polymerase reads the existing DNA strand to create the new strands that match the existing one and also performs the proofreading and error correction. The  DNA polymerase catalyzes the  DNA template and directs the extension of the 3′ end of the DNA strand by nucleotide at a time. DNA polymerases can be further divided into two different families which are as follows.

Prokaryotic DNA Polymerase Types and Functions

• DNA Polymerase I is coded by the polA gene. It is a single polypeptide and plays a part in recombination and fixing. It has both 5’→3′ and 3’→5′ exonuclease action. DNA polymerase ⅰ eliminates the RNA primer from the lagging strand by 5’→3′ exonuclease action and furthermore fills the hole.
• DNA Polymerase II is coded by the polB gene. It is comprised of 7 subunits. Its primary job is to repair and furthermore a reinforcement of DNA polymerase III. It has 3’→5′ exonuclease action.
•  DNA Polymerase III is the primary enzyme for replication in E.coli. It is coded by polC gene. The polymerization and processivity rate is the most extreme in DNA polymerase III. It additionally has editing 3’→5′ exonuclease activity
• DNA Polymerase IV is coded by the dinB gene. Its principal job is in DNA fix during SOS reaction when DNA replication is slowed down at the replication fork. DNA polymerase II, IV and V are translation polymerases.
• DNA Polymerase V is likewise engaged with translation synthesis during SOS reaction and DNA repair.

Eukaryotic DNA Polymerase Types and Functions

• DNA polymerase α – It is the principal protein for replication in eukaryotes. It likewise has 3’→5′ exonuclease action for proofreading.
• DNA polymerase γ – The principal capability of DNA polymerase γ is to synthesize primers. The smaller subunit has a primase activity. The biggest subunit has polymerization action. It frames a primer for Okazaki sections, which are then stretched out by DNA polymerase γ.
• DNA polymerase δ – The fundamental capability is DNA repair. It eliminates primers for Okazaki parts from the lagging strand.
• DNA polymerase ε – It is the super replicative enzyme for mitochondrial DNA

DNA clamp in Prokaryotes/Eukaryotes

Sliding clamp proteins are found in all organisms and are called proliferating cell nuclear antigens (PCNA) in eukaryotes and the β clamp in prokaryotes. Both PCNA and β form a ring around DNA, which is made up of two subunits of three domains each in β but three subunits of two domains each in PCNA.

The sliding clamp in eukaryotes is assembled from a specific subunit of DNA polymerase delta called the proliferating cell nuclear antigen (PCNA). The N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.

Single-strand Binding Proteins (SSB) Prokaryotes/Eukaryotes 

These proteins prevent the reannealing and protect the single-stranded DNA from nucleases and prevent the secondary structure formation           

Topoisomerase

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.

DNA topoisomerases prevent and correct types of topological problems. They do this by binding to DNA and cutting the sugar-phosphate backbone of either one (type I topoisomerases) or both (type II topoisomerases) of the DNA strands. This transient break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed. Since the overall chemical composition and connectivity of the DNA do not change, the DNA substrate and product are chemical isomers, differing only in their topology.

DNA Ligase

DNA ligases play an essential role in maintaining genomic integrity by joining breaks in the phosphodiester backbone of DNA that occur during replication and recombination and as a consequence of DNA damage and its repair. Three human genes, LIG1, LIG3 and LIG4 encode ATP-dependent DNA ligases.

Primase

DNA primase is an enzyme whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long.

Classification of DNA Replication

DNA Replication is classified into two types 

DNA replication in Prokaryotes

Review that the prokaryotic chromosome is a round particle with a less broad coil structure than eukaryotic chromosomes. The eukaryotic chromosome is linear and exceptionally wound around proteins. While there are numerous similitudes in the DNA replication process, these primary distinctions require a few distinctions in the DNA replication process in these two living things.

DNA replication has been all around concentrated in prokaryotes, fundamentally in view of the little size of the genome and the huge number of variations accessible. Escherichia coli has 4.6 million base matches in a solitary roundabout chromosome, and every last bit of it gets recreated in roughly 42 minutes, beginning from a solitary beginning of replication and continuing around the chromosome in the two bearings. This implies that around 1000 nucleotides are added each second. The cycle is considerably quicker than in eukaryotes. The table below sums up the distinctions between prokaryotic and eukaryotic replications.

Property	Prokaryotes	Eukaryotes
Origin of Replication	single	Many
Rate of Replication	1000 nucleotide base pairs	50 to 100 nucleotide base pairs
Chromosome Structure	circular	linear
Telomerase	Absent	Present

Enzymes required for DNA replication in prokaryotes

In prokaryotes, three primary kinds of polymerases are known: DNA polymerase I, DNA polymerase II, and DNA polymerase III. It is currently realized that DNA polymerase III is the catalyst expected for DNA synthesis; DNA polymerase I and DNA polymerase II are essential for DNA repair.

Steps involved in Prokaryotic DNA replication

The steps involved in DNA replication are Initiation, Elongation, and Termination.

Initiation

In prokaryotes, DNA replication starts at the region called the region of replication. In E. coli, which has a solitary beginning of replication on its one chromosome (as do most prokaryotes), it is roughly 245 base pairs long and is wealthy in AT sequences. The origin of replication is perceived by specific proteins that tight spot to this site. A chemical called helicase loosens up the DNA by breaking the hydrogen connections between the nitrogenous base matches. ATP hydrolysis is required for this interaction. As the DNA opens up, Y-molded structures called replication forks are shaped. Two replication forks are shaped at the origin of replication and these get expanded bi-directionally as replication continues. Single-strand binding proteins coat the single strands of DNA close to the replication fork to keep the single-abandoned DNA from twisting once more into a twofold helix

Elongation

DNA polymerase can add nucleotides simply in the 5′ to 3′ heading (another DNA strand can be just stretched out toward this path). It likewise requires a free 3′- OH group to which it can add nucleotides by shaping a phosphodiester connection between the 3′- OH end and the 5′ phosphate of the following nucleotide. This basically implies that it can’t add nucleotides if a free 3′- OH bunch isn’t accessible. Then, at that point, how can it add the main nucleotide? The issue is tackled with the assistance of a preliminary that gives the free 3′- OH end. Another catalyst, RNA primase, combines an RNA groundwork that is around five to ten nucleotides in length and complementary to the DNA. Since this succession takes action union, it is suitably called the primer. DNA polymerase can now expand this RNA primer, adding nucleotides individually that are correlative to the template strand. The replication fork moves at the pace of 1000 nucleotides each second. DNA polymerase can reach out in the 5′ to 3′ heading, which represents a slight issue at the replication fork. As we probably are aware, the DNA twofold helix is anti-parallel; that is, one strand is in the 5′ to 3′ heading and the other is situated in the 3′ to 5′ course. One strand, which is reciprocal to the 3′ to 5′ parental DNA strand, is blended ceaselessly towards the replication fork in light of the fact that the polymerase can add nucleotides toward this path. This consistently integrated strand is known as the main strand or leading strand. The other strand, reciprocal to the 5′ to 3′ parental DNA, is expanded away from the replication fork, in little sections known as Okazaki fragments, each requiring a primer to begin the union. Okazaki’s fragments are named after the Japanese researcher who previously found them. The strand with the Okazaki sections is known as the Lagging strand. The main strand can be reached by a single primer, while the slacking strand needs another introduction of a new primer for each of the Okazaki fragments. The general course of the lagging strand will be 3′ to 5′, and that of the main strand 5′ to 3′. A protein called the sliding clamp holds the DNA polymerase set up as it keeps on adding nucleotides. The sliding clip is a ring-moulded protein that ties to the DNA and holds the polymerase set-up. Topoisomerase forestalls the over-twisting of the DNA twofold helix in front of the replication fork as the DNA is opening up; it does as such by causing brief nicks in the DNA helix and afterwards resealing it.

Termination

DNA synthesis continues, and the RNA primers are supplanted by DNA. The preliminaries are taken out by the exonuclease action of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that stay between the recently synthesized DNA (that supplanted the RNA primer) and the recently integrated DNA are sealed by the enzyme DNA ligase that catalyzes the arrangement of a phosphodiester linkage between the 3′- OH end of one nucleotide and the 5′ phosphate end of the other part. When the chromosome has been totally replicated, the two DNA duplicates move into two unique cells during cell division.

DNA Replication in Eukaryotes

DNA replication in Eukaryotes will occur in three stages they are initiation, elongation, and termination which are aided by several Enzymes.

Initiation

Eukaryotic DNA is bound to proteins known as histones to frame structures called nucleosomes. During initiation, the DNA is made open to the proteins and compounds engaged with the replication cycle. There are explicit chromosomal areas called beginnings of replication where replication starts. In certain eukaryotes, similar to yeast, these areas are characterized by having a particular sequence of base pairs to which the replication commencement proteins tie. In different eukaryotes, similar to people, there doesn’t give off an impression of being an agreement grouping for their beginnings of replication. All things being equal, the replication commencement proteins could recognize and identify to explicit alterations to the nucleosomes in the origin locale.

Certain proteins perceive and tie to the origin of replication and afterwards permit different proteins important for DNA replication to identify a similar region. The principal proteins to bind the DNA are said to “recruit” different proteins. Two duplicates of a chemical called helicase are among the proteins enlisted at the beginning. Each helicase loosens up and isolates the DNA helix into single-abandoned DNA. As the DNA opens up, Y-molded structures called replication forks are shaped. Since two helicases bind, two replication forks are framed at the beginning of replication; these are stretched out in the two headings as replication continues making a replication bubble. There are numerous beginnings of replication on the eukaryotic chromosome which permit replication to happen all the while in hundreds to thousands of areas along every chromosome.

Elongation

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

DNA polymerase contains a notch that permits it to tie to a solitary abandoned format DNA and travel one nucleotide at a time. For instance, when DNA polymerase meets an adenosine nucleotide on the layout strand, it adds a thymidine to the 3′ finish of the recently combined strand, and afterwards moves to the following nucleotide on the format strand. This cycle will go on until the DNA polymerase arrives at the finish of the format strand.

DNA polymerase can’t start a new strand blend; it just adds new nucleotides at the 3′ ends of a current strand. All recently integrated polynucleotide strands should be started by a particular RNA polymerase called primase. Primase starts polynucleotide binding by making a short RNA polynucleotide strand complementary to the format DNA strand. This short stretch of RNA nucleotides is known as the primer. When RNA groundwork has been integrated into the format DNA, primase ways out, and DNA polymerase expands the new strand with nucleotides complementary to the template DNA. In the long run, the RNA nucleotides in the primer are eliminated and supplanted with DNA nucleotides. When DNA replication is done, the daughter molecules are made totally of persistent DNA nucleotides, with no RNA segments.

The Leading and Lagging Strands 

DNA polymerase can synthesize new strands in the 5′ to 3′ direction. Accordingly, the two recently blended strands fill in inverse headings in light of the fact that the layout strands at every replication fork are antiparallel. The “main strand” is incorporated consistently toward the replication fork as helicase loosens up the template double-stranded DNA.

The “lagging strand” is synthesized in the path away from the replication fork and away from the DNA helicase loosens up. This lagging strand is orchestrated in pieces on the grounds that the DNA polymerase can blend in the 5′ to 3′ direction, thus it continually experiences the beforehand combined new strand. The pieces are called Okazaki parts, and each section starts with its own RNA primer.

Termination

Eukaryotic chromosomes have numerous starting points of replication, which start replication all the while. Every beginning of replication shapes a bubble of copied DNA on one or the other side of the beginning of replication. At last, the main strand of one replication bubble arrives at the lagging strand of another bubble and the lagging strand will arrive at the 5′ finish of the previous Okazaki piece in a similar bubble

DNA polymerase stops when it arrives at a part of the DNA template that has previously been duplicated. Notwithstanding, DNA polymerase can’t catalyze the development of a phosphodiester connection between the two fragments of the new DNA strand, and it drops off. These unattached segments of the sugar-phosphate spine in a generally full-replicated DNA strand are called nicks.

When all the template nucleotides have been repeated, the replication cycle isn’t yet finished. RNA groundworks should be supplanted with DNA, and nicks in the sugar-phosphate backbone should be associated.

The gathering of cell catalysts that eliminate RNA primers incorporates the proteins FEN1 (flap endonuclease 1) and RNase H. The proteins FEN1 and RNase H eliminate RNA primers toward the beginning of each driving strand and toward the beginning of each Okazaki section, leaving gaps in unreplicated template DNA. When the primer is taken out, a free-drifting DNA polymerase lands at the 3′ finish of the first DNA part and broadens the DNA over the gap. Nonetheless, this makes new nicks (detached sugar-phosphate backbone).

In the last phase of DNA replication, the enzyme ligase joins the sugar-phosphate backbone at each nicks site. After ligase has associated all nicks, the new strand is one long ceaseless DNA strand, and the daughter  DNA molecule is finished.

Inhibitors of DNA Replication

The Agents which inhibit DNA replication are called inhibitors of DNA replication. Some of them are as follows.

 Ethidium Bromide

It is a fluorescent and aromatic compound. it is a tricyclic structure containing the nitrogen atom at the centre of the ring. The structure of ethidium bromide is known as phenanthridine due to its dibenzo pyridine structure. The reason ethyl bromide is more fluorescent after attaching to DNA is due to phenyl moiety.

 Actinomycin D

Actinomycin is produced by streptomycin and it inhibits replication and transcription. Between the two successive GC base pairs, it has a structure called phenoxazone which has an intercalating function in DNA duplex. composition of D-Valine and Sarcosine which stabilizes the intercalating interaction. it is a yellow colour liquid commonly used for the treatment of cancers.

 Daunomycin and Adriamycin

They have a planar aromatic ring which gets intercalated with the Guanine-cytosine pairs of double helical structure and prevents replication.

Aphidicolin

Aphidicolin inhibits the DNA polymerase α, DNA polymerase ε and DNA polymerase δ of the eukaryotes. It inhibits the synthesis of both lagging and leading strands during DNA replication.

 Rifamycin

Rifamycin blocks the RNA polymerase such the leading and lagging strand will not be synthesized thus the DNA replication was inhibited. Rifamycin is an antibiotic synthesized in the bacterium named Amycolatopsis Mediterranei. The rifamycin will bind to the polymerase after the chain elongation started, no consistent process of chain elongation is performed since it blocks the process by binding to the polymerase.

FAQs on DNA Replication

Question 1: What is meant by DNA replication?

Answer:

The process by which DNA molecule makes its identical copies are referred to as DNA replication.

Question 2: What is meant by semi-conservative replication?

Answer:

During DNA replication, every one of the two strands that make up the twofold helix fills in as a layout from which new strands are duplicated. Each new twofold strand comprises of one parental strand and one new daughter strand. This is known as semiconservative replication

Question 3: What are Okazaki fragments?

Answer:

Okazaki fragments are the short lengths of DNA that are produced by the discontinuous replication of the lagging strand.

Question 4: What are the nitrogen base pairs of DNA?

Answer:

Adenine, Guanine, cytosine and thymine

Question 5: Define the initiation process in eukaryotes.

Answer:

During initiation, the DNA is made open to the proteins and compounds engaged with the replication cycle.