Polymerase chain reaction description and its uses in Agriculture

1. Topic of Presentation:
Polymerase Chain Reaction
Presented To:
Sir Abdul Rahman
Presented By:
Attiq Ur Rehman Gohar
Ammad Ahmad
Saad Ur Rehman
Ismail Channar

2. Contents
• DNA
• What is PCR?
• History of PCR
• Components of PCR
• Principles of PCR
• Basic Requirements
• Instrumentation
• PCR Programme
• Advantages of PCR
• Applications of PCR

3. DNA
DNA has four nitrogen bases.
• Two are purines ( 2 ringed base )
– Adenine ( A ), Guanine ( G )
• Two are pyrimidines ( 1 ringed base )
– Cytosine ( C ), Thymine ( T )

4. • DNA Sugar
– Deoxyribonucleic acid
• RNA Sugar
– Ribonucleic acid

5. DNA has four nitrogen bases.
• Two are purines ( 2 ringed base )
– Adenine ( A ), Guanine ( G )
• Two are pyrimidines ( 1 ringed base )
– Cytosine ( C ), Thymine ( T )

6. • These four bases are linked in a repeated
pattern by hydrogen bonding between the
nitrogen bases.
• The linking of the two complementary strands
is called hybridization.

7. Example of bonding pattern.
Primary strand
CCGAATGGGATGC
GGCTTACCCTACG
Complementary strand

8. DNA Molecule
AdenineAdenine
ThymineThymine
GuanineGuanine
CytosineCytosine

9. A purine always links with a pyrimidine base to
maintain the structure of DNA.
Adenine ( A ) binds to Thymine ( T ), with two
hydrogen bonds between them.
Guanine ( G ) binds to Cytosine ( C ), with three
hydrogen bonds between them.

10. What is PCR?
• PCR is a technique that takes specific
sequence of DNA of small amount and
amplifies it to be used for further testing.
• In vitro technique
In vivo
(Cloning)
In vitro
(PCR)
DNA amplification

11. Short History of PCR
• 1983: Dr. Kary Mullis developed PCR
• 1985: First publication of PCR by Cetus Corporation
appears in Science.
• 1986: Purified Taq polymerase is first used in PCR
• 1988: PerkinElmer introduces the automated
thermal cycler.
• 1989: Science declares Taq polymerase "molecule of
the year.

12. Short History of PCR
• 1990: amplification and detection of specific DNA
sequences using a fluorescent DNA-binding dye,
laying the foundation for future "real-time" or
"kinetic" PCR.
• 1991: RT-PCR is developed using a single
thermostable polymerase, rTth, facilitating
diagnostic tests for RNA viruses.
• 1993:Dr. Kary Mullis shares Nobel Prize in
Chemistry for conceiving PCR technology.

13. Short History of PCR
• 1999: Dynal launches DRB-36 HLA-typing kit for
tissue typing.
• 2003: HIV-1 MONITOR Test, version 1.5 Product
Family
• AMPLICOR® CT/NG Test for Chlamydia trachomatis,
• AMPLICOR® CT/NG Test for Neisseria gonorrhoeae

14. Priciple of PCR
•Purpose:
•Stages:
•Components:

15. Purpose
• To amplify a lot of double-stranded DNA molecules
(fragments) with same (identical) size and sequence
by enzymatic method and cycling condition.

16. Stages
• 1. Denaturation of ds DNA template
• 2. Annealing of primers
• 3. Extension of ds DNA molecules

17. Denaturation
• Temperature: 92-94C
• Double stranded DNA melts single stranded
DNA
92C
3’5’
3’ 5’
+
5’3’
5’ 3’

18. Annealing
• Temperature: ~50-70C (dependant on the melting
temperature of the expected duplex)
• Primers bind to their complementary sequences
5’3’
5’ 3’
Forward primer Reverse primer

19. Extension
• Temperature: ~72C
• Time: 0.5-3min
• DNA polymerase binds to the annealed primers and
extends DNA at the 3’ end of the chain
Taq
5’
3’
Taq5’

20. Cycling

21. Products of Extension
3’5’
3’ 5’
3’5’
3’ 5’
Taq
Taq

22. Overall Principle of PCR
• DNA – 1 copy
• Known sequence Sequence of interest Known sequence
• PCR

23. Chemical Components
• Magnesium chloride: .5-2.5mM
• Buffer: pH 8.3-8.8
• dNTPs (deoxynucleotide triphosphates): 20-
200µM
• Primers: 0.1-0.5µM
• DNA Polymerase: 1-2.5 units
• Target DNA: ≤ 1 µg

24. Basic requirements for PCR
reaction
• 1) DNA sequence of target region must be
known.
2) Primers - typically 20-30 bases in size.
These can be readily produced by commercial
companies. Can also be prepared using a DNA
synthesizer

25. Basic requirements for PCR
reaction
• 3) Thermo-stable DNA polymerase - eg Taq
polymerase which is not inactivated by
heating to 95C
4) DNA thermal cycler - machine which can be
programmed to carry out heating and cooling
of samples over a number of cycles.

26. Instrumentation

32. Three Aspects of PCR
• Specificity
• Efficiency
• Fidelity

33. Things to try if PCR does not work
• A) If no product ( of correct size ) produced:
– 1 Check DNA quality
– 2 Reduce annealing temperature
– 3 Increase magnesium concentration
– 4 Add dimethylsulphoxide ( DMSO ) to assay ( at around
10% )
– 5 Use different thermostable enzyme
– 6 Throw out primers - make new stocks

34. Things to try if PCR does not work
• B) If extra spurious product bands present
– 1 Increase annealing temperature
– 2 Reduce magnesium concentration
– 3 Reduce number of cycles
– 4 Try different enzyme

35. Example of PCR programme
• Initial denaturation 95C for 5 mins
• Thermo-cycle file - 30 cycles of
• Denaturation : 95C for 30 secs
• Annealing : 55C for 30 secs
• Extension : 72C for 45 secs
• Final extension 72C for 5 mins
• Holding ( soak ) file usually 4C

36. Advantages of PCR
• Small amount of DNA is required per test
• Result obtained more quickly - usually within 1
day for PCR
• Usually not necessary to use radioactive
material (32P) for PCR.
• PCR is much more precise in determining the
sizes of alleles - essential for some disorders.
• PCR can be used to detect point mutations.

37. Applications of PCR
Generation of probes
Generation of cDNA libraries
Production of DNA for sequencing
Analysis of mutations
Diagnosis of monogenic diseases (single gene disorders)
PCR use in Pre-implantation Genetic Diagnosis (PGD).
PCR in forensic science
Comparison of gene expression
Cloning novel members of protein families using homology
PCR
Detection of bacteria and viruses(HIV-1, Chlamydia
trachomatis, Neisseria gonorrhea )
Forensic testing and many others

38. Applications of PCR
Molecular Identification Sequencing Genetic Engineering
Molecular Archaeology Bioinformatics Site-directed mutagenesis
Molecular Epidemiology Genomic Cloning Gene Expression Studies
Molecular Ecology Human Genome Project
DNA fingerprinting
Classification of organisms
Genotyping
Pre-natal diagnosis
Mutation screening
Drug discovery
Genetic matching
Detection of pathogens

39. Conclusion
PCR is not only vital in the clinical laboratory by
amplifying small amounts of DNA for STD
detection, but it is also important for genetic
predisposing for defects such as Factor V
Leiden.
The PCR technology can also be employed in law
enforcement, genetic testing of animal stocks
and vegetable hybrids, and drug screening
along with many more areas.