PCR is a technique used to amplify a specific DNA sequence. It involves repeated cycles of heating and cooling of the DNA sample to denature and separate the DNA strands, followed by primer annealing and polymerase extension. This results in exponential amplification of the target DNA sequence. PCR requires a DNA template, DNA polymerase, primers, nucleotides, and repeated cycling between high and low temperatures. It has applications in research, forensics, medicine and molecular biology.

1. PCR
Md Ishtiyak Jafar

2. Cloning
It refers to the process of producing large no.
of identical copies from one single original
DNA molecule or fragment.
Such a population is called clone.

3. Cloning- 2 methods
A. Cell based cloning using living organism.
B. Cell free cloning using PCR.

4. • PCR method developed by Kary Mullis and Michael Smith in
1983.
• PCR is an in vitro DNA amplification procedure in which
millions of copies of a particular sequence of DNA can be
produced within a few hours.

5. PRINCIPLE OF PCR
 PCR is based on ability of DNA polymerase to synthesize complementary
strand to the template strand.
 As DNA polymerase can add a nucleotide only onto a 3'-OH group, it
needs an artificial DNA strand (called DNA primer) of about 18 to 25
nucleotides complementary to 3’ end of the DNA template.
 primer can bind only when DNA strands are separated. This is generally
done by heating.
 The primers anneal to the single-stranded DNA template at specific
temperature (depends on primer sequence) and then DNA-Polymerase
binds to this double stranded DNA produced.

6.  The again reaction mixture is heated to 72°C (extension); a
temperature optimum for DNA- polymerase functions. This
starts synthesis of the new DNA strand. Then reaction mixture is
cooled to lower temperature for short term storage, if required.
This completes one cycle.
 After first cycle, one DNA molecule has become two. After
multiple cycle of the PCR reaction, the specific sequence will be
accumulated in billions of copies.

7. REQUIREMENTS FOR PCR
1.DNA template:
• DNA template is DNA target sequence.
• High temperature is applied to separate both the DNA
strands from each other.

8. 2. DNA polymerase:
• DNA polymerase sequentially adds nucleotides
complimentary to template strand at 3’-OH of the bound
primers and synthesizes new strands of DNA
complementary to the target sequence.
• The most commonly used DNA polymerase is Taq DNA
polymerase (from Thermus aquaticus, a thermophillic
bacterium) because of high temperature stability.
• Mg2+ ions in the buffer act as co-factor for DNA
polymerase enzyme.

9. 3. Primers:
• Primers are synthetic DNA strands of about 18
to 25 nucleotides complementary to 3’ end of
the template strand.

10. • Two primers must be designed for PCR; the forward primer and the
reverse primer.
The forward primer is complimentary to the 3’ end of antisense strand (3’-5’)
and the reverse primer is complimentary to the 3’ end of sense strand (5’-3’).

11. 4. Nucleotides (dNTPs or deoxynucleotide
triphosphates):
All types of nucleotides are "building blocks" for new DNA strands and
essential for reaction.
It includes Adenine(A), Guanine(G), Cytosine(C), Thymine(T) or Uracil(U).

12. PROCEDURE OF PCR
• This is done on an automated cycler, which can heat and
cool the tubes with the reaction mixture in a very short
time.
• There are three major steps in a PCR, which are repeated
for 30 or 40 cycles.
1. Denaturation
2. Annealing
3. Extension
4. Final hold

13. 1. Denaturation at 94°C :
• During the heating step (denaturation), the reaction
mixture is heated to 90°C for 15 sec, which causes
separation of DNA double stranded.
• 2. Annealing at 54°C :
• This step consist of cooling of reaction mixture after
denaturation step to 54°C, which causes hybridization
(annealing) of primers to separated strand of DNA
(template).

15. 3. Extension at 72°C :
• The reaction mixture is heated to 72°C which is the ideal working
temperature for the Taq polymerase.
• The polymerase adds nucleotide (dNTP's) complimentary to
template on 3’ –OH of primers thereby extending the new strand.
4. Final hold:
• First three steps are repeated 35-40 times to produce millions of
exact copies of the target DNA.
• Once several cycles are completed, during the hold step, 4–15 °C
temperature is maintained for short-term storage of the amplified
DNA sample.

17. PCR-an exponential cycle:
• As both strands are copied during PCR, there is an
exponential increase of the number of copies of the gene.

18. Variants of PCR
1. Reverse Transcription PCR:
• RNA is used as a template to produce cDNA which is
complementary to the RNA.
• catalyzed by reverse transcriptase enzyme.
• The RNA template is annealed to synthetic oligonucleotide
(oligo dT) primer which extends to produce cDNA strand
which is amplified by PCR.

20. 2. Real Time PCR:
• RT-PCR also known as kinetic PCR, Quantitative
PCR (QPCR) or qPCR or qrtPCR
• Is used to amplify and simultaneously quantify a target
DNA.
• Fluorescent labels are used to quantitate DNA at the
end of each cycle

21. APPLICATIONS OF PCR
 Used in molecular biology and genetic disease research to identify new
genes.
 Viral targets, such as HIV-1 and HCV (Hepatitis C virus) can also be
identified and quantified by PCR
 In fields such as anthropology and evolution, sequences of degraded
ancient DNAs can be tracked after PCR amplification. The source DNA
from blood, chorionic villus, amniotic fluid, semen, hair root, saliva can be
PCR amplified to produce in huge amounts, which can further be studied
through Gel analysis, Restriction digestion, Sequencing etc.

22. PCR permits early diagnosis of malignant
diseases such as leukemia and lymphomas.
This technique is used for introduction of
mutations at the desired place in a DNA
sequence by altering the sequences of
primers.

23. • Used in molecular biology and genetic disease
• Viral targets, such as HIV-1 and HCV (Hepatitis C virus)
can also be identified and quantified.
• In fields such as anthropology and evolution
• early diagnosis of malignant diseases such as leukemia
and lymphomas
• for introduction of mutations at the desired place in a
DNA sequence by altering the sequences of primers.

24. THANK YOU

25. Nucleotide probes

26. NUCLEOTIDE PROBES
• A probe is defined as a single stranded piece of DNA, labelled
(either with radioisotope or with non-radioactive label), the
nucleotide sequence of which is complementary to the target
DNA.
• It is a single stranded piece of DNA (sometimes RNA), which
can range in size from as little as 15 bp to several hundread
kilobases.
• It can identify, through base pairing, a specific DNA fragment of
the library, which contains complementary sequence.

28. • A probe DNA will form complementary base
pairing with another DNA strand.
• mRNA can be used as a probe: it will bind to the
DNA fragment that contains exon sequences of
it’s gene.
• RNA probe, termed riboprobe, can be produced
by in vitro transcription of cloned DNA inserted
into a plasmid vector.
• Synthetic oligonucleotide probes; constructed
by chemical methods, are most commonly used

29. PROBES MUST HAVE A LABEL TO BE
IDENTIFIED
• Probes are labelled with the radioisotopes, such as 32P.
• These probes can be detected by autoradiography, which
involves placing the sample in direct contact with the
photographic material, usually X-ray film.
• Non-radioactive molecule such as biotin or fluorescent dye.
• Alternatively, end-labelling probes with fluorescent tags can
be used. The latter are visible under the UV-Lamp

30. Biotinylated Probes

31. USES OF NUCLEOTIDE PROBES:
I. To search specific DNA sequences of DNA library,
II. In southern & Northern blot techniques, probes
are used to identify DNA or RNA fragments
respectively.
III. Monoclonal Abs are used as probe to search
protein fragments on Western Blot.
IV. In diagnosis of genetic disorders, such as Sickle cell
anaemia, Thalassaemia, Cystic fibrosis etc.

32. • Probes are used to identify which band on a
gel or which clone in a library contains the
target DNA, a process called screening.

34. DNA fragment
coding for HbS