Various model of DNA replication

1. Various model of replication
1. Rolling circle replication
2. Theta mode of replication
3. Replication of linear ds-DNA
4. Replication of the 5’ end of linear chromosome (Telomere Replication)
1. Rolling circle replication
Rolling circle replication (RCA) is a process of unidirectional nucleic acid
replication that can rapidly synthesize multiple copies of circular molecules
of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular
RNA genome of viroids. Some eukaryotic viruses also replicate
their DNA or RNA via the rolling circle mechanism.
As a simplified version of natural rolling circle replication, an isothermal DNA
amplification technique, rolling circle amplification was developed. The RCA
mechanism is widely used in molecular biology & biomedical nanotechnology,
especially in the field of biosensing.
Circular DNA Replication
• Rolling circle DNA replication is initiated by an initiator protein encoded by
the plasmid or bacteriophage DNA, which nicks one strand of the double-
stranded, circular DNA molecule at a site called the double-strand origin, or
DSO.

2. • The initiator protein remains bound to the 5' phosphate end of the nicked
strand, and the free 3' hydroxyl end is released to serve as a primer for DNA
synthesis by DNA polymerase III.
• Using the unnicked strand as a template, replication proceeds around the
circular DNA molecule, displacing the nicked strand as single-stranded DNA.
• Displacement of the nicked strand is carried out by a host-encoded helicase
called PcrA (the abbreviation standing for plasmid copy reduced) in the
presence of the plasmid replication initiation protein.
• Continued DNA synthesis can produce multiple single-stranded linear
copies of the original DNA in a continuous head-to-tail series called
a concatemer.
• These linear copies can be converted to double-stranded circular molecules
through the following process:
➢ First, the initiator protein makes another nick in the DNA to
terminate synthesis of the first (leading) strand.
➢ RNA polymerase and DNA polymerase III then replicate the
single-stranded origin (SSO) DNA to make another double-
stranded circle.
➢ DNA polymerase I removes the primer, replacing it with DNA,
and DNA ligase joins the ends to make another molecule of
double-stranded circular DNA.

3. As a summary, a typical DNA rolling circle replication has five steps:
Circular dsDNA will be "nicked".
The 3' end is elongated using "unnicked" DNA as leading strand
(template); 5' end is displaced.
Displaced DNA is a lagging strand and is made double stranded via a series
of Okazaki fragments.
Replication of both "unnicked" and displaced ssDNA.
Displaced DNA circularizes.
2. θ (Theta) mode of replication
The theta mode of replication is adapted by the prokaryotes to replicate their
genetic material. The circular DNA has only a single origin of replication, unlike
the eukaryotic DNA with multiple origins of replication for faster process. The two

4. complementary strands of the parental DNA separate at the origin of replication
by the action of helicase enzyme which literally unzips the strands by breaking the
bonds. DNA polymerase enzyme then comes into action and starts the process of
replication in the 5′ to 3′ direction. Once the replication is done, ligase enzyme
glues the loose ends together and two daughter strands are formed. During the
breaking of the strands by helicase enzyme, the circular DNA forms the Greek
symbol ‘θ’ like structure, and so the name.
Process of DNA replication (Theta model) –
Initiation of replication occurs at a specific region called origin of
replication.
ds-DNA denatures to form ss-DNA, denatured segment of DNA is called
the replication bubble.
DNA unwinds and y-shaped structure is formed known as the replication
fork.
In such cases, bidirectional replication occurs.
The fork is generated by a complex of 7 proteins called primasome that
includes – Dna G primase, Dna B helicase, Dna C helicase assistant, Dna T,
Primase A, B and C.

5. The replicating bacterial chromosome was first determined by JOHN
CAIRNS in 1963 By means of autoradiography.
✓The autoradiographs showed that the chromosomes of E.coli are circular
structures that exist as theta shaped intermediates during replication is
called theta model of replication.
✓ The autoradiographs further indicated that the unwinding of two
complementary parent strands and their semiconservative replication occur
simultaneously or are closely coupled.
✓ Bacterial genomes are replicated bidirectionally from a single point, which
means that two replication forks should meet at a position diametrically opposite
the origin of replication on the genome map.
✓since the parental double helix must rotate 360° to unwind each helix is
achieved by the action of enzyme TOPOISOMERASE.

6. 3. Replication of linear ds-DNA (bidirectional replication)
This is related to most nuclear dsDNA viruses, and many phages. Located in host
cell nucleus (eukaryots) or cytoplasm (prokaryots). This kind of replication is used
by all cellular organisms and some DNA viruses. It is the most classical way of
replicating genomic nucleic acid.

7. DNA replication begins at specific locations in the genome, called “origins”.
A topoisomerase unwinds the DNA double-strand at the origin of
replication.
ssDNA-binding proteins cover the single strand DNA created in the
replication bundle.
A primase synthesizes short RNA primers that are then used by the DNA
polymerase to prime DNA synthesis.
The DNA polymerase and associated factors begins to elongate the leading
strand at the fork. For the lagging strand Okazaki fragments are elongated
after sequential RNA primer synthesis by the primase.
The lagging strand RNA primers are removed and Okazaki fragments
ligated.
The replication forks go on until they reach the end of linear genome or
until they meet at the opposite side of a circular genome.
After synthesis, topoisomerase allows separation of the two strands
resulting from the replication.
4. Replication of the 5’ end of linear chromosome (Telomere
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 of each daughter DNA strand, such
that the two daughter DNAs have their 3′ overhangs at opposite ends.

8. 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.
It can be removed but cannot be replaced. RNase H and FEN1 are the enzymes
remove RNA primers, but addition of new DNA will take place by the DNA
Polymerase only if the DNA Polymerase possess strand 5′ to it (“behind” it) to
extend. Though, there is no more DNA in the 5′ direction DNA polymerase cannot
replace the RNA with DNA. Hence, both daughter DNA strands have an
incomplete 5′ strand with 3′ overhang. 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.