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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

International Journal of Advanced Research in Biological Sciences

ISSN: 2348-8069
www.ijarbs.com
Review Article

A critical review on PCR, its types and applications

Jagtar Singh1 , Niti Birbian2, Shweta Sinha2and Akshra Goswami2

1
Associate Professor, Department of Biotechnology, Panjab University, Chandigarh, India.
2
Department of Biotechnology, Panjab University, Chandigarh, India.
*Corresponding author: [email protected]

Abstract
The invention of polymerase chain reaction (PCR) has been a milestone in the history of biological and medical sciences. The
applications of PCR have not only completely revolutionised the research in the field of molecular genetics as well as animal and
plant biotechnology, but the technique has also proved its relevance and ingenious utility in other fields of forensic sciences,
molecular systematics, molecular epidemiology, archaeology, anthropology, evolutionary genetics, etc. as well. The conventional
PCR led to the emergence of RT-PCR, qPCR and combined RT-PCR/q-PCR. PCR has also enabled the successful completion of
the ‘human genome project’ by enabling the amplification and sequencing of the human genes, which has further laid the
foundation of genetic engineering and has now even made it possible to make useful changes in the genome of an organism. The
variants of PCR are now being successfully used in most of the recent advances made in the sciences of modern era.

Keywords: Standard PCR- Variants, RT-PCR, qPCR, RT-PCR/qPCR combined.

Introduction

Polymerase Chain Reaction (PCR)

A stepping stone in the field of molecular genetics was Kary Banks Mullis in the year 1983, while he was
laid by James D. Watson and Francis Crick in the year working as a biotechnologist in Cetus Corporation,
1953 by proposing a double helix structural model of Emeryville, California, USA. In 1985, a joint venture
DNA (Watson and Crick, 1953). In the early 1960’s, was established between Cetus Corporation and
significant advances were made in elucidation of the Perkin-Elmer, another US based Biotech Company to
genetic code and synthetic oligonucleotides were used design thermal cycler instruments and reagents for
as primer templates for DNA polymerase by Dr. H. PCR and in 1987, a press release announced the
Gobind Khorana, for which he was also awarded the availability of the "PCR-1000 Thermal Cycler" and
Nobel prize in the year 1968 (Khorana et al., 1976). In "AmpliTaq DNA Polymerase" commercially. The
1971, Kjell Kleppe, a researcher in Khorana’s invention won him laurels of the Nobel Prize in
laboratory, described the replication of a segment of Chemistry as well as the Japan Prize in the year 1993
DNA by a two-primer system (Kleppe et al., 1971). (Shampo and Kyle, 2002).
Polymerase chain reaction is an in vitro technique that
Essential Components of Standard PCR
enables replication and amplification of a DNA
sequence to billions fold amplitude (Mullis and Component of reaction mixture:
Faloona, 1987; Saiki et al., 1988). The technique of
polymerase chain reaction (PCR) was invented by Taq/other thermostable polymerases

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80
Template DNA contaminants from the DNA sample.
Primers (web.stanford.edu).
dNTPs
MgCl2 Primers
Autopipettes/Plasticwares/Gloves
Thermal cycler The most important consideration for amplification of
a target site within a region of the genome is the
Component of reaction mixture primer designing. A successful primer is mostly
designed for achieving two goals i.e. specificity and
Taq/other thermostable polymerases efficiency. Both of these goals can be achieved if the
primers are designed carefully enough so as to avoid
In 1969, Thomas D. Brock isolated Thermus false positive results. Following are the considerations
aquaticus, a new species of thermophilic bacterium that should be kept in mind while designing the
found in the Lower Geyser Basin of Yellowstone primers.
National Park (Brock and Freeze, 1969). In 1976,
thermostable enzyme ‘Taq polymerase’ was isolated Primer Length: The length of a primer is directly
from Thermus aquaticus (Scott, 2008). In 1986, Henry proportional to the specificity of a PCR reaction. The
Erlich announced the use of Taq polymerase in PCR, length also determines the temperature at which the
since it could sustain its activity at a wide range of primers will anneal to the template (Chuang et al.,
high temperatures. Its addition to the PCR mixture 2013). Usually primers are designed between 18 to 24
shortened the entire PCR process by removing the bases long though the minimum length of a primer is
need to manually add fresh DNA polymerase from E determined by the size of the genome (Marshall,
coli, at every cycle of the reaction because of its 2007).
inability to tolerate rapid heating and cooling (Saiki et
al., 1988). The kinetic pathway of Taq polymerase in GC content: GC content is important as it also
the synthesis of template strand by incorporating determines the Tm value of a sequence. 20 base pair
nucleotides was described by Rothwell and Waksman, long oligos having 50% GC content generally have a
2005. Tm value between 56-62०C (Dieffenbach et al., 1993).
Most desirable GC content should be between 40 to
Many other thermostable DNA polymerases are also
discovered that can be used according to their 60०C. More than three G or C nucleotides at the 3' end
applications (Table1). Usually 1-1.5U of Taq DNA of the primer should be avoided as this may lead to
Polymerase is required in 50µl of reaction mix. nonspecific priming.
However, if inhibitors (e.g. low purity of template
DNA) are present in the reaction mix, higher amounts Melting temperature (Tm): Since in a PCR reaction a
of Taq DNA Polymerase (2-3U) may be required to set of primers is used so effort should be made to
obtain a better yield of amplified products. select the pairs that have a Tm in the range of 5०C
within each other, therefore the GC content and length
Template DNA must be chosen accordingly. Usually, the Tm lies in the
Usually 0.01-1ng of template DNA is required for range of 62-70०C (Li, 2007).
plasmid or phage DNA and 0.1-1µg for genomic
DNA, in a total reaction mixture of 50µl. Template Estimation of the melting and annealing
DNA higher than this amount results in nonspecific temperatures of primer: For the primer less than 25
PCR products. Furthermore, DNA should be pure as nucleotides, the approximately Tm is calculated using
even a trace amount of phenol, EDTA, Proteinase K, the following formula:
etc. used during DNA isolation strongly inhibit Taq
DNA Polymerase action. However, ethanol Tm= 4 (G + C) + 2 (A + T)
precipitation of DNA and washing with 70% ethanol
to DNA pellet is usually effective in removing these G, C, A, T - number of respective nucleotides in the
primer.

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80
Table 1: Thermostable polymerases and their applications.

Polymerases Habitat Applications References

(Source)
Tfl nd Tolerate higher concentrations of blood, Kaledin et al., 1980
(Thermus high temperature DNA sequencing
Flavus)
T4 nd 3’ overhang and 5’ fill-in to form blunt Dale et al., 1985;
(Bacteriophage T4 of ends, probe labelling, single strand Kunkel et al., 1987;
E. coli) deletion subcloning, second strand Sambrook et al., 1989
synthesis in site-directed mutagenesis

T7 nd Strand extensions in site-directed Bebenek et al., 1989;

(Bacteriophage T7, mutagenesis, in situ detection of Wood et al., 1993
and trxA gene of E. apoptotic DNA fragments
coli)
Vent/Tli Deep sea 5-15 fold higher activity than Taq DNA Mattila et al., 1991
(Thermococcus hydrothermal vents polymerase, 3'→5' exonuclease activity
litoralis)
rTth Hot spring in Izu, Tolerate high concentration of blood, Myers and Gelfand,
(Thermus Japan reverse transcriptase activity in addition 1991
thermophilus) to a 5’→3’ polymerase activity, 5’→ 3’
exonuclease activity

Ultma Marine geothermal 3′-5′ exonuclease activity Diaz and Sabino, 1998
(Thermotoga area near Vulcano,
maritime) Italy
KOD Solfatara on Kodakara High processivity, fidelity, and Bensona et al., 2003
(Thermococcus Island, Kagoshima, extension rate without the complexity
kodakaraensis) Japan introduced by terminal transferase
activity
Pwo Marine sediments, 3′-to-5′ exonuclease activity, tolerate Cahill, et al., 2003;
(Pyrococcus woesei) beach of Porto high concentration of blood Kanoksilapatham et
Levante, Vulcano al., 2004
Island, Italy
Pfu Marine sediments, 3′-to-5′ exonuclease activity, lowest Cahill, et al., 2003;
(Pyrococcus furiosus) beach of Porto error rate Kanoksilapatham et
Levante, Vulcano al., 2004
Island, Italy
HotTub nd Tolerate high concentration of blood, Kermekchiev et al.,
(Thermus ubiquitous) cDNA synthesis, second strand synthesis 2009
in site- directed mutagenesis, production
of ssDNA probes by primer extension.

nd-
not defined

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80
Restriction site integration: 3-6 nucleotides are added the nucleophilic attack and bond formation and hence
at the 5’ end of the primers so as to successfully polymerization. Also, every enzyme needs cofactor for
provide a site for restriction cutting of the amplified their activation and Mg2+ metal ions act as essential
sequence (Chuang et al., 2008). cofactor for the DNA polymerase in PCR. Mg2+ ion
enter into the protein for joining and creating forces
Primer complementarity: The primer should not be making the polymerase stronger and capable to join
self-complementary or complementary to any other dNTPs but at the expense of specificity. So, increased
primer in the reaction mixture, so as to avoid the intra concentration of Mg2+ in PCR, results in strong band
or inter primer homology as it will lead to primer but chances of non-specific amplification also rises.
dimers (Vallone and Butler, 2004). For this, its concentration must be optimized for every
primer:template system. Also, other components of the
Redundancy: Repeat of a single base or two bases for PCR reaction bind to Mg2+ ion, including primers,
4 or more times should be avoided template, PCR products and dNTPs. Out of these,
(www.lifetechnologies.com). dNTPs have more affinity to bind to the Mg2+ ion and
as free Mg2+ ion are needed to serve as an enzyme
Terminal nucleotide in PCR primer: The terminal cofactor in PCR, the total Mg2+ ion concentration must
position in a primer is essential for eliminating exceed the total dNTP concentration
mispriming. To avoid it, care should be taken to avoid (http://www.promega.com/paguide/chap1.htm). The
primers that are complementary at their 3’ ends as this recommended range of MgCl2 concentration is 1-4
may lead to unnecessary primer dimer formation mM in the standard reaction mixture
(Kwok et al., 1990; Liu et al., 2007). (web.stanford.edu).
Autopipettes/Plasticwares/Gloves
Secondary structures: The secondary structures
should be avoided to the maximum wherever possible. Autopipettes (1-10µl, 10-100µl & 100-1000µl), 0.2ml-
Secondary structures arise as a result of intermolecular 1.5ml microcentrifuge tubes, tips, PCR stands etc. are
or intramolecular interactions. Hairpins, self dimers or required during PCR and for loading the amplified
cross dimers, all arise as a result of secondary product in the agarose gels.
structures (Mergny and Lecroix, 2003). Thermal cycler
dNTPs It is an instrument which changes temperature very
rapidly during each cycles for denaturation, annealing,
The concentration of each dNTP in the final reaction extension and hold process.
mixture is usually 200µM and the concentrations of
each dNTPs (dATP, dCTP, dGTP, dTTP), should be Principle, Procedure and Post amplification
equal. The inaccuracy in the concentration of even a detection of PCR
single dNTP may lead to increase in the
Principle
misincorporation of nucleotides in the new strand.
The principle of PCR is based on the fact that at high
MgCl2 denaturing temperatures nearing 95oC, the two strands
During replication, a lone pair of electron appears in of the target DNA molecule separate due to breaking
the 3'-OH region of the growing chain which is used of A-T and G-C bonds. At the annealing temperatures
for the formation of phosphodiester bond by the Taq in the range of 50-65oC, the complimentary forward
Polymerase. This lone pair of electrons is used to and reverse primers bind at the 3’ end of the flanking
convert dNTP to dNMP by nucleophilic attack on the regions of the separated single stranded target DNA
phosphate atom of α-phosphate, releasing the molecule. The Taq polymerase then extends the new
pyrophosphate (β and γ). But the incoming dNTP has DNA strand by adding dNTPs and the double stranded
four negative charges and due to the presence of these molecule restructures itself at the extension
negative charges, the nucleophilic attack is retarded. temperature of 72oC. This process is repeated several
Therefore, Mg2+ comes to rescue by chelating extra times, generating multiple copies of the target DNA
negative charges of the incoming dNTP, facilitating molecule (Fig. 1). For best results, The European
Molecular Genetics Quality Network (EMQN) good
practice guidelines should be followed (Muller, 2001).
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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Fig. 1: Principle of PCR.

Procedure gel stained in Ethidium bromide (EtBr) solution. EtBr

has been used since many years for the visualization of
Initial denaturation occurs at 90-95oC for 3-5 minutes, nucleic acids in agarose gel. EtBr is also a potent
where the two strands of the double stranded target mutagen, causing mutations in the living cell.
DNA molecule separate. Therefore, gels should be disposed in an appropriately
labelled hazardous waste container with date and
Initial denaturation is followed by 30-35 cycles of handed over to the Environmental Health & Safety
denaturation, annealing and extension. The number of (EHS) department (www.ehs.harvard.edu).
PCR cycles depends on the amount of template DNA
Types of PCR
in the reaction mix and on the expected yield of the
PCR product. Denaturation involves heating the Standard PCR- Variants
double stranded target DNA molecule at 90-95oC for Reverse Transcription-PCR (RT- PCR)
30-55 seconds. Real time-PCR or quantitative PCR (qPCR)
Annealing step allows binding of the complimentary RT-PCR/qPCR combined
forward and reverse primers to the 3’ flanking regions
at 50-65oC for 30-55 seconds. Standard PCR- Variants
Extension step occurs at 72oC for 30-55 seconds by The modifications in the basic technique of PCR led to
adding complimentary dNTPs to the new strands. the development of variants in PCR that are described
After the last cycle, the samples are usually incubated below:
at 72°C for 5-15 minutes to fill-in the protruding ends
of newly synthesized PCR products. Allele specific PCR (Tetra-primer ARMS PCR)
Holding or storage of the PCR products at 4oC for Allele specific PCR allows direct detection of point
infinity. mutation in DNA. This technique requires prior
knowledge of the target DNA sequence such as
Post amplification detection differences between alleles and utilises the primer with
3’ mismatch ends encompassing the single nucleotide
The amplified PCR product is observed as a variations (Newton et al., 1989; Ugozzoli and
fluorescent pink band by agarose gel electrophoresis Wallace, 1991).
following ultraviolet transillumination of the agarose
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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Fig. 2: Allele specific PCR.

Two allele specific primers, one for each allele of the Asymmetric PCR
SNP are required, which contain one of two
polymorphic nucleotides at the 3' end (Fig. 2). A This variation of PCR is used to preferentially amplify
common forward or reverse primer may be used. only one strand of the target DNA molecule by using
Generally, two PCR reactions are needed for detection unequal primer concentrations (Fig. 3), as such
of both alleles of a SNP (You et al., 2008). replication occurs arithmetically by using the excess
primer (Innis et al., 1988).

Fig. 3: Asymmetric PCR.

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Colony PCR of known DNA sequence for PCR (Ochman et al.,

1988).
It is a type of PCR routinely used in bacterial genomic
studies. Insertion of high copy number plasmids such Miniprimer PCR
as pUC 18, pUC 19 or pBluescript in bacteria is
routinely performed for a variety of purposes The standard PCR methods require Taq polymerase
(Kilger et al., 1997) and colony PCR quickly screen whose efficiency of DNA synthesis is less than other
these plasmid inserts. It has several advantages over replicative enzymes due to their longer primers (20-30
the traditional methods of blue/white screening as it nucleotides) requirement (Wang et al., 2004).
can determine both the insert size and orientation in Therefore, new PCR method has been developed
the vector (Plourde-Owobi et al., 2005). In fact, the called miniprimer PCR. In this PCR, engineered Taq
white colonies screened by the traditional blue white polymerase and 10 nucleotides long ‘miniprimers’ are
screening method has to be screened additionally by used. Miniprimer PCR is useful in understanding
the colony PCR method so as to avoid sequencing of microbial biology for identification of conserved DNA
the false positive clones. In addition to this colony sequences such as 16S rRNA (eukaryotic 18S rRNA)
PCR also helps in generating sufficient amount of that is not possible with standard primers (Isenbarger
desired PCR product for sequencing (Carracedo, et al., 2008). Xu et al. evaluated the role of miniprimer
2005). PCR using Titanium Taq polymerase and short
primers, for genotyping the Pantoea stewartii subsp.
Degenerate PCR stewartii, the causal agent of Stewart’s bacterial wilt
on maize (Xu et al., 2010).
It is a variant of PCR which employs degenerate
primers to amplify unknown sequences of DNA, Multiplex PCR
related to a known DNA sequence. Degenerate
primers are designed on the basis of known and Multiplex PCR is a modification of PCR in order to
sequenced gene homologs. This technique allows rapidly detect deletions or duplications in a large gene.
identification of new members of a gene family or In 1988, deletions in the dystrophin gene were first
orthologous genes from different organisms (Lang and detected by multiplex-PCR method (Chamberlain et
Orgogozo, 2011). al., 1988). Multiplex- PCR mix makes use of multiple
primer sets within a single PCR mixture to
Hotstart PCR produce amplicons of varying sizes which are specific
for different sequences of DNA. This variant of PCR,
This technique involves steps of the conventional targets multiple genes at once in a single test run
PCR, except that the Taq polymerase is added after the which would otherwise require several times the
rest of the PCR components are heated to the DNA reagents and more time to perform (Fig. 5). The base
melting temperature, so as to avoid non-specific pair length of the amplicons, should be different
amplification at lower temperatures. Alternatively, enough to segregate well and form distinct bands
covalently bound inhibitors that dissociate from Taq when visualized by gel electrophoresis. Multiplex-
polymerase only after reaching the Tm can also be PCR has been successfully applied in many areas of
added (Chou et al., 1992). DNA testing such as analysis of deletions, mutations
and polymorphisms, microsatellites and SNPs
Inverse PCR (Hayden et al., 2008).

Whereas conventional PCR requires complimentary Nested PCR

primer pair for both the 3’ ends of the target DNA, It is a modification of PCR designed to minimize the
Inverse PCR allows amplification of DNA with only amplification of non-specific and spurious PCR
one known sequence (Fig. 4). This technique requires products, which may result due to primer binding at
a sequence of restriction digestions and ligations unexpected or unwanted sites similar to the target
which result in the formation of a looped DNA DNA. Nested PCR involves 2 sets of primers which
fragment which can further be primed from a section are utilized in two successive runs of the PCR reaction
(Fig. 6). The second set of primers functions to bind to
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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Fig. 4: Inverse PCR.

D
MULTIPLEX PRIMERS:

PCR products
A B C D

Fig. 5: Multiplex PCR.

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Fig. 6: Nested PCR using two set of primers.

a secondary target within the sequence amplified by Virus) (Temin and Mizutani, 1970), which were then
the first set of primers, as it is highly unlikely that the later independently isolated by David Baltimore in
spurious or unwanted sequence will have binding site 1970 from two RNA tumour viruses: R-MLV
for both the sets of primers (Haff, 1994). (Rauscher- Murine Leukemia Virus) and RSV
(Baltimore, 1970). Both shared the 1975 Nobel Prize
Touchdown PCR in Physiology or Medicine for their aforesaid
achievements. Reverse transcriptase enzyme includes
This technique enables ruling out the amplification of an RNA-dependent DNA polymerase, a DNA-
non-specific sequences by using early steps of PCR dependent DNA polymerase and ribonuclease H
cycles at high temperatures and with subsequent activity which work in sync to perform transcription.
cycles, the annealing temperatures are decreased in Apart from functioning in the process of transcription,
increments (Fig. 7). This allows specific primer to retroviral reverse transcriptases have a domain
anneal at the highest temperature that is least belonging to the RNase H family which is vital to their
permissive for non-specific binding and generates only replication. The idea of reverse transcription was very
the sequence of interest (Don et al., 1991). unpopular at first as it contradicted the central dogma
of molecular biology but finally accepted in 1970
Reverse Transcription-PCR (RT- PCR) when the scientists Howard Temin and David
Baltimore both independently discovered the enzyme
This technique enables quantitative detection of levels responsible for reverse transcription, named reverse
of RNA expression by creating complimentary DNA transcriptase.
(cDNA) from RNA with the help of reverse
transcriptase, followed by further amplification of The retroviral reverse transcriptases, including Avian
cDNA using standard PCR. Howard Temin from the Myeloblastosis Virus (AMV) and Moloney murine
University of Wisconsin–Madison made the discovery leukemia virus (MMLV) are the most characterised
of reverse transcriptases in RSV (Rous Sarcoma reverse transcriptases used in the field of molecular
biology.

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Fig. 7: Cycling method of Touchdown PCR.

Fig. 8: One step and two step methods of RT- PCR.

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80
The most preferred reverse transcriptase for long Therefore, by using serial dilutions of a known
mRNA templates is the M-MLV RT because its quantity of standard DNA, the amount of DNA or
RNase H activity is weaker than the commonly used cDNA of unknown sample can be calculated as CT
AMV reverse transcriptase. Progress in the field of value by plotting a standard curve of log concentration
genetic engineering and the development of RT- vs CT.
enhancing buffers have led to the commercial
availability of newer enzymes that offer superior qPCR combines the amplification and detection into a
performance over the naturally occurring reverse single step thereby eliminating the need for any post
transcriptases which have a higher level of amplification processing of the sample (Mackay,
thermostability and a longer shelf life at 50°C. M- 2004). The other advantages of qPCR are sensitivity,
MLV RT used these days is purified from E. coli real time detection of reaction progress, speed of
expressing the pol gene of M-MLV on a plasmid analysis and precise measurement of the examined
(www.lifetechnologies.com) while insect cells material in the sample (Gachon et al., 2004).This is
infected with baculovirus containing the pol gene of due to the presence of either fluorescent dyes or
AMV are used for purification of cloned Avian fluorescently-tagged oligonucleotide probes whose
Myeloblastosis Virus (AMV) reverse transcriptase intensity correlates to the amount of DNA product
(www.lifetechnologies.com). formed (Wong and Medrano, 2005). To facilitate
different types of qPCR reactions, different types of
There are two primary ways to carried out RT-PCR polymerases are used including high fidelity, hot start
i.e. one-step and two-step method (Fig. 8). In one-step, and fast enzymes. Therefore, real-time PCR
all the components including specific primers are put instruments are designed to carry out these reactions
into a single tube as same as the PCR reaction. In a that comprise a thermal cycler for DNA amplification,
two-step method, the first reaction involves the an optical system to excite fluorophores and capture
formation of cDNA with the help of a separate reverse emitted fluorescence from the detection chemistry
transcription reaction and then addition of cDNA to (Fig. 9-A&B), and specialized software to collect and
the PCR reaction. analyze the quantitative data generated
(www.thermoscientificbio.com).

One-step method is a highly advantageous method as

it takes lesser time, is cheaper and requires less RT-PCR/qPCR combined
handling of samples, thereby reducing pipetting errors,
contamination etc. However, the drawback is the later In case of qualitative detection of RNA expression,
analysis of other genes of interest that cannot be reverse transcription (RT-PCR) polymerase chain
amplified as gene-specific primers are used in one reaction technique is used through conversion of RNA
reaction tube for cDNA formation and amplification. template to cDNA where as for quantitative detection
Therefore, aliquot of RNA from the original sample of RNA expression, both RT-PCR and qPCR
must be stored for future testing. But two-step method techniques are merged and this combined technique is
proves to be advantageous as in this method the RNA called qRT-PCR/ quantitative RT-PCR or RT-qPCR
samples are not used in single processing and future (Joyce, 2002; Taylor et al., 2010; Varkonyi-Gasic and
analysis of the gene of interest can be done (Wacker Hellens, 2010).
and Godard, 2005).
Advantages and Disadvantages of PCR
Real time-PCR or quantitative PCR (qPCR) Technique
qPCR introduced in 1992 by Higuchi and co-workers Since amplification is carried out by designing the
(Higuchi et al., 1992) enables detection of fluorescent complementary primers, the technique is highly
reporter dye, such as SYBR Green I to measure the specific. It is relatively fast enough generating a
amplification of DNA at each cycle of PCR. During billion copies of amplification in less than three hours.
the log linear phase of amplification, the fluorescence Based on the type of genetic material (DNA or RNA)
increases to a point which becomes measurable and is suitable modifications can be made easily and the
called as the Threshold cycle (CT) or Crossing point. technique can be easily used for a wide range of

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 Int. J. Adv. Res. Biol.Sci. 1(7): (2014): 65–80

Fig. 9: qPCR: (A) SYBR Green I assay and (B) TaqMan assay.

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applications in almost all sorts of organisms ranging using PCR based tests to study mutations in oncogenes
from microorganisms to plant and animal kingdom. in certain forms of cancer.
Along with huge benefits and applicability, it also has
potential drawbacks. The first and foremost drawback Since antibodies to HIV do not appear until many
is its cost. It is an expensive technique in comparison weeks after infection, PCR based tests have been
to the conventional tests. Performing a PCR require a developed that enable detection of even a single viral
great degree of skill and expertise. Furthermore, to genome among the host cells. Similarly, donated
carry out the PCR one must have a sound blood, newborns and effects of antiviral treatments can
knowledge of the bioinformatics to design primers, to be done immediately (Kwok et al., 1987). Moreover,
incorporate restriction sites etc. The technique is donated blood can also be tested for bacterial
available in only those labs that have specialized contamination using real-time PCR (Dreier et al.,
molecular biology testing and analysis techniques. 2007).
Most of the times nucleic acid from non-viable
organisms is also amplified alongwith the desired In case of Tuberculosis, which otherwise requires
samples. The analysis of samples after PCR exposes a sputum sample collection and culture in laboratory,
researcher to harmful chemicals like EtBr, dyes, PCR based tests have enabled detection of both live
fluorochromes and UV light which are carcinogenic and dead microorganisms. Moreover, detailed gene
(Baechtel, 1989; Butler, 2005). analysis enables detection of antibiotic resistance as
well as effects of therapy (Lindstrom and Korkeala,
Applications of PCR
2006).
Forensic science
PCR based testing has enabled detection of spread of
PCR is an important tool in DNA profiling, infectious microorganisms in domestic or wild
fingerprinting, DNA typing and DNA testing. This animals.
technique enables identification of one person among
millions of others. Samples of DNA extracted from Conclusions
crime scene can be compared with DNA of suspects or
DNA database. Also DNA fingerprinting enables PCR is a highly advanced yet simple technique which
parental testing to identify biological parentage of a has proved its versatility in most fields of biological
child (Saiki et al., 1985; Butler, 2005). and medical sciences due to its ability to yield not only
qualitative but quantitative results also. The invention
Medicine and diagnostics of PCR has been a boon to the modern science with its
applicability in clinical diagnostics, DNA
Prospective parents can be subjected to gene testing fingerprinting, DNA profiling, recombinant DNA
for the presence of genetic diseases and hence the technology apart from its role in other fields of
probability of children being carriers of the same can archaeology, anthropology, forensics as well. The
be ascertained. Prenatal testing can be performed by unravelling of the human genome as well as genomes
amniocentesis, chronic villus sampling or fetal cells of many other organisms including several plant
circulating in mother’s blood to ascertain the species has led to PCR being applied robustly in either
possibility of mutations in the embryo (Saiki et al., one form or another for detailed scientific analysis.
1985). These advancements have resulted in the modification
of basic PCR technique together with RT-PCR, qPCR
Tissue-typing can be done prior to performing organ and combined RT-PCR/qPCR. The future will bring
transplantation by using PCR for checking further novel application of PCR in biological sciences
compatibility between donor and recipient. This which will be accompanied by more sophisticated
method has replaced the traditional antibody based instrument design having high sample throughput and
blood type test for identifying antigens on the surface atomisation. Above all, the prerequisite is the curious
of the body cells and tissues (Quill, 2008). Therapy and ingenious scientists that will upbring these
regimens can be customised for individual patients by inventions.

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Anticancer Res. 28(4A):2001-2007.
AMV reverse transcriptase, cloned, Chuang, L.Y., Y.H., Cheng and Yang, C.H. 2013.
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