DNA replication
in this topic we are going to talking about DNA replication.
What are the steps or mechanisms of replication?
What is the interesting fact in replication?
And the main thing is what I the importance of DNA replication?
But No one is talking about why we have to study this complex mechanism. And where we can further use this to develop molecular techniques or which are the molecular process are based on this principle.
Introduction
Before starting DNA replication, we have to understand what is DNA replication?
What is DNA replication? - it is the biological process in which cell create two identical copies of DNA from the original DNA molecule with high accuracy (fidelity rate).
Before the structure of DNA was known scientist wondered how organism create faithful copies of themselves and, later eukaryotes ability to produce many identical copies of large, complex macromolecules.
The 1940s brought the revelation to the scientist that the DNA was the genetic molecule,
but not until James Watson and Francis Crick conclude its structure did the way in which DNA could act as a templet for the replication and transmission of genetic information become clear.
The basic mechanisms of DNA replication are similar across organisms.
In this article, we will focus on DNA replication as it takes place in bacterial E. coli, But the mechanisms of replication are similar in humans and other eukaryotes.
Let’s take a look at the proteins and enzymes that carry out replication, and how they work together to ensure accurate and complete replication of DNA.
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The basic idea of replication
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DNA replication is semiconservative process, that means each strand of DNA molecule acts as a template for the synthesis of a new, complementary strand.
This process takes one starting DNA molecule to two “daughter” molecules, with each new DNA double helix containing one new and one old strand (parent strand).
As we show above figure its look like very simple process and nothing interesting in it. But what’s most interesting about this process is how it’s carried out in the cell.
Now let’s talk about how DNA replication carried out in cell.
There are main three steps of DNA replication
Initiation
Elongation
Termination
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1)Initiation
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This is the step where DNA replication starts, But the main question is that is there any specific binding site or replication start at random site?
The replication of chromosomal DNA begins at single point known as origin of replication.
Replication fork or evets at the replication fork
Synthesis of DAN replication occurs at the replication fork, the place at which the DAN helix is unwound and individual strands are replicated.
In the E. Coli cell origin of replication is oriC, this site consists of 254 bp long DNA sequence.
The bacterial initiator protein which responsible for triggering DNA replication is DnaA.
DnaA protein bind regions in oriC throughout the cell cycle, but to initiate replication, DnaA protein must bind with few particular oriC sequence which possess five repeats of 9 bp sequence (R site).
When DnaA binds with oriC site after that it recruits a helicase enzyme also known as DnaB helicase.
Helicases are responsible for separating (unwinding) the DNA strands just ahead of the replication fork, using energy from ATP hydrolysis.
Loading of the DnaB helicase is the key stapes in the replication initiation.
As helicase migrates toward 5’ to 3’ direction unwinding of DAN strands travels with it.
but DNA is highly unstable in single strand so what cells can do to separate this single stranded DNA.
At this case cells have specific protein which is single stranded DNA binding proteins (SSBs).
What this protein does?
They bind with DNA after Helicase unwind the strand and keep them separated.
But There is other problem arise for cell when helicase rapidly unwind the double helix it increases tension for remaining DNA molecule.
For reviling this tension topoisomerases takes place in the DNA replication (the replication fork may rotate as 75 to 100 revolutions per second).
This is important because rapid unwinding can lead to the formation of positive supercoils in the helix ahead of the replication fork.
Topoisomerase change the structure of DAN by transiently breaking one or two strands without altering the nucleotide sequence of the DNA.
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Elongation
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In this particular phase of replication includes two different but related operations (Or you can say that related processes also).
That is the leading strand synthesis and lagging strand synthesis.
As we show above at the replication fork several enzymes are important to the synthesis of this both strands.
Let’s take a short summary of that enzymes.
First of all, parent DNA is first unwound by DNA helicase enzyme, and the resulting topological stress is relieved by topoisomerases.
Now each separate DNA strand is than stabilized by SSB proteins.
Up to this point, the mechanism of DNA synthesis is similar for both strands, but from this point, synthesis of leading and lagging strands is sharply different.
Before we jump on to the synthesis of leading and lagging strands let’s discus about why this strand are called leading and lagging strands.
Their name shows their role in replication,
leading strand that means this strand lead the DNA synthesis how this happened that we discus next.
Lagging strand is synthesize slow in compare to leading strand that’s why it called legging strand.
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Leading strand synthesis.
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Synthesis of each strand begins with the synthesis of DNA dependent RNA primer (10 to 60 nucleotide sequence).
Which is synthesized by DNA primase (DnaG protein).
Now primase interact with DnaB helicase to carry out the first RNA primer synthesis.
This primer synthesized in the opposite direction to the DNA helicase is moving.
In effect the 3’ to 5’ strand of DNA become prime leading strand for DNA replication.
Detailed mechanism is illustrated in below figure.
Now, Deoxyribonucleotides are added into the prime leading strand by a DNA polymerase III complex, which linked to the DnaB helicase tethered(bound) to the opposite DNA strand to restrict the movement of the DNA polymerase III.
Leading strand synthesis then proceeds continuously. Keeping pace (motion) with the unwinding of DNA at the replication fork.
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Lagging strand synthesis:
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DNA polymerase always proceeds in 5’ to 3’ direction. So how can both strands be synthesized simultaneously?
If both strands were synthesized continuously while the replication fork moved, so one strand would have to undergo ‘3 to 5’ synthesis.
This problem was resolved by Reiji Okazaki and colleagues in the 1960s.
Okazaki found that one of the new DNA strands is synthesized in short pieces, now these fragments are called Okazaki fragments.
This work ultimately led to the conclusion that one strand is synthesized continuously and other discontinuously.
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Mechanism of Okazaki fragment formation
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As we show RNA primer is synthesized by primase, and then DNA polymerase III binds to the RNA primase and adds deoxyribonucleotides.
In this level the synthesis of each Okazaki fragment seems straightforward. but the reality is quite complex.
Because DNA polymerase move along with the 5’ to 3’ direction, so the one problem faced by all DNA replication machines is how to simultaneously and coordinately replicate two antiparallel DNA strands.
To deal with this problem DNA polymerase III uses the one set of its core subunits (the core polymerase) to synthesize the leading strand continuously, while the other two sets of core subunit from one Okazaki fragment to the next on the looed leading strand.
In vitro, basically there is only two sets of core subunits with DNA polymerase III holoenzyme can synthesis both leading strand and lagging strand.
However, a third set of core subunit increases the efficiency of lagging strand synthesis as well as the processivity of the overall replisome.
Now let’s look no how this set of core subunit work. 
When DnaB helicase, bound in front of DNA polymerase III, unwinds the DNA at the replication fork as it travels along the lagging strand template in the 5’ to 3’ direction.
Primase occasionally associate with DnaB helicase and synthesizes a short RNA primer.
Now a new β sliding clamp is then positioned at the primer by the clamp-loading complex of DNA polymerase III.
When synthesis of Okazaki fragment has been completed.
Replication halts, and the core subunits of DNA polymerase III dissociate from their β sliding clamps (and form the complete Okazaki fragment) and associate with the new clamp.
This initiate the synthesis of a new Okazaki fragment.
Two sets of core subunits may be engaged in the synthesis of two different Okazaki fragment at the same time.
Once an Okazaki fragment has been completed, its RNA primers is removed by DNA polymerase I or RNase H1, and this empty space is replaced with DNA by the polymerase.
Now, the remaining nick was sealed by the DNA ligase.
How DNA ligase join DNA?
DNA ligase catalyzes the formation of phosphodiester bond between a 3’ hydroxyl at the end of one DNA strand and a 5’ phosphate at the end of another strand.
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Proofreading
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As you read above that the DNA replication is occurred with the very high-fidelity rat.
It incorporates the one wrong nucleotide once per 104- 105 nucleotide polymerized.
The accuracy of replication relies on the ability of replicative DNA polymerases to select correct nucleotide for the polymerization reaction and remove mistakenly incorporated nucleotide using their exonuclease activity.
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Termination
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As we discussed above that E. Coli genome replication carried out by pairs of replication fork that assemble at the origins of replication and then move opposite.
DNA replication finish when the two-replication fork of the circular E. Coli chromosome meet at a termination site (ter).
This Ter sequence are arranged on the chromosome to create a trap that a replication fork can enter but can not leave.
On the other hand, the Ter sequence function as binding sites for the protein called “Tus”.
which is act as a terminus utilization substance.
Now the Tus-Ter complex can arrest a replication fork form only one direction.
Because only one Tus- Ter complex function per replication cycle- the complex first encountered by any one of replication fork.
At that point opposite replication fork generally halt when they collide (clash or meet).
So, when first (arrested) fork meets the Tus-Ter complex other fork halts.
After that final few hundred base pair of DNA between these large protein complexes are then replicated (this mechanism is un known yet).
But the question is that how fork movement is stopped?
There are two problem that must be solved by replisome.
Formation of interlinked chromosome called catenanes.
Dimerized chromosome.
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Catenanes formation
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Catenanes are produced when topoisomerase break and rejoin DNA strand to ease supercoiling ahead of the replication fork.
Now the separation of catenated circles in E. Coli requires topoisomerase IV (a type II Topoisomerase).
Topoisomerase Iv breaks the both strand of one molecule, pass the other molecule through the break, and t hen rejoin the strands.
Then the separated chromosomes then segregate into daughter cells at cell division.
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Dimerized chromosome
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It is formed when two chromosomes joined together and form a single chromosome twice as long.
Dimerized chromosomes are results from DNA recombination that some time occurs between two daughter molecules during DNA replication.
The terminal phase of replication of other circular chromosome, including many of the DNA viruses that infect eukaryotic cells, is similar.
Now let’s move on our most awaited question
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What is the importance of replication and why we have to study DNA replication?
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Let’s first discus importance of replication.
As we know the DNA is the genetic material of the cell. It passes the information to the next generation.
This information is essential for life. It helps to cell to function normally.
There are millions of cells died every day in our body or in ecosystem. If this essential information not pass to the next generation so the function of ecosystem disturbs.
To deal with this problem parental cell generate the copies of their DNA and pass this to new daughter cell.
Now let’s talk about why we have to study DNA Replication
Most important thing which come into our mind is, **
why we have to know is why we have to study this?
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As we know DNA replication is the most essential process in cell, without this life doesn’t exist.
With the study of DNA replication, we know how cell pass their information to the next generation.
And the most important thing we develop several molecular techniques which are based on replication.
For example: - polymerize chain reaction (PCR)
As you know the PCR technique is used for the multiplication of the DNA. This complete process is based on the principle of DNA replication
On the basis of replication process scientist developed the artificial plasmid that have replication site in their sequences so that they use proteins and enzymes of cell and replicate itself with cell.
Now a days our lots of therapeutic activity are based on the DNA replication.
In this activity we target the enzymes and protein which are actively participate in the DNA replication.
For targeting specific protein or enzyme we have to study the mechanism of DNA replication in different organisms, because every organism has their own replication mechanism.
For example: in E. Coli there are five DNA polymerase enzymes and eukaryotic cell possess only three DNA polymerase.
Scientist developed several drugs that target the enzymes and protein that are actively participate in DNA replication.
You get the list of this therapeutic drug and their action site from this link
referances
DNA replication| why we have to study DNA replication?
