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![Page 1: Polymerase Chain Reaction (PCR) and Its Applications by Ayaz Najafov Boğaziçi University Department of Molecular Biology and Genetics.](https://reader030.fdocuments.us/reader030/viewer/2022032703/56649d205503460f949f47a4/html5/thumbnails/1.jpg)
Polymerase Chain Reaction Polymerase Chain Reaction (PCR) and Its Applications(PCR) and Its Applications
by
Ayaz Najafov
Boğaziçi UniversityDepartment of Molecular Biology and Genetics
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What is PCR?What is PCR?
It was invented in 1983 by Dr. Kary Mullis, for which he received the Nobel Prize in Chemistry in 1993.
PCR is an exponentially progressing synthesis of the defined target DNA sequences in vitro.
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What is PCR? : What is PCR? : Why “Polymerase”?Why “Polymerase”?
It is called “polymerase” because the only enzyme used in this reaction is DNA polymerase.
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What is PCR? : What is PCR? : Why “Chain”?Why “Chain”?
It is called “chain” because the products of the first reaction become substrates of the following one, and so on.
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What is PCR? : What is PCR? : The “Reaction” ComponentsThe “Reaction” Components
1) Target DNA - contains the sequence to be amplified.
2) Pair of Primers - oligonucleotides that define the sequence to be amplified.
3) dNTPs - deoxynucleotidetriphosphates: DNA building blocks.
4) Thermostable DNA Polymerase - enzyme that catalyzes the reaction
5) Mg++ ions - cofactor of the enzyme
6) Buffer solution – maintains pH and ionic strength of the reaction solution suitable for the activity of the enzyme
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The ReactionThe Reaction
THERMOCYCLERPCR tube
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Denature (heat to 95oC)
Lower temperature to 56oC Anneal with primers
Increase temperature to 72oC DNA polymerase + dNTPs
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DNA copies vs Cycle number
0
500000
1000000
1500000
2000000
2500000
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Cycle number
DN
A c
op
ies
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Applications of PCRApplications of PCR
• Classification of organisms
• Genotyping• Molecular archaeology
• Mutagenesis• Mutation detection• Sequencing• Cancer research
• Detection of pathogens
• DNA fingerprinting
• Drug discovery• Genetic matching• Genetic engineering
• Pre-natal diagnosis
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Applications of PCR
Basic Research Applied Research• Genetic matching
• Detection of pathogens
• Pre-natal diagnosis
• DNA fingerprinting
• Gene therapy
• Mutation screening
• Drug discovery
• Classification of organisms
• Genotyping
• Molecular Archaeology
• Molecular Epidemiology
• Molecular Ecology
• Bioinformatics
• Genomic cloning
• Site-directed mutagenesis
• Gene expression studies
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Applications of PCR
Molecular Identification Sequencing Genetic Engineering
• Molecular Archaeology
• Molecular Epidemiology
• Molecular Ecology
• DNA fingerprinting
• Classification of organisms
• Genotyping
• Pre-natal diagnosis
• Mutation screening
• Drug discovery
• Genetic matching
• Detection of pathogens
• Bioinformatics
• Genomic cloning
• Human Genome Project
• Site-directed mutagenesis
• Gene expression studies
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MMOLECULAROLECULAR IIDENTIFICATION:DENTIFICATION:
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Detection of Unknown MutationsDetection of Unknown MutationsMolecular Identification:
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SSCP gels: “shifts” representing a mutation in the amplified DNA fragment
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Classification of OrganismsClassification of Organisms
1) Relating to each other
2) Similarities
3) Differences
* Fossils
* Trace amounts
* Small organisms
! DNA !
Molecular Identification:
Insufficient data
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Rademaker et al. 2001
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Detection Of PathogensDetection Of Pathogens
Molecular Identification:
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Detection Of PathogensDetection Of Pathogens
Sensitivity of detection of PCR-amplified M. tuberculosis DNA. (Kaul et al.1994)
Molecular Identification:
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Sensitivity of detection of PCR-amplified M. tuberculosis DNA. (Kaul et al.1994)
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GenotypingGenotyping by STR markers by STR markers
Molecular Identification:
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Prenatal DiagnosisPrenatal Diagnosis
644 bp
440 bp
204 bp
Molecular analysis of a family with an autosomal recessive disease.
Molecular Identification:
• Chorionic Villus
• Amniotic Fluid
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SSEQUENCINGEQUENCING
Nucleotides (dNTP) are modified (dideoxynucleotides = ddNTP)
NO polymerisation after a dideoxynucleotide!
Fragments of DNA differing only by one nucleotide are generated
Nucleotides are either or
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Classical Sequencing GelClassical Sequencing Gel
Sequencing:
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Reading Classical Sequencing GelsReading Classical Sequencing Gels
Sequencing:
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Sequencing:
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SummarySummary
blood, chorionic villus, amniotic fluid, semen, hair root, saliva
68,719,476,736 copies Gel Analysis, Restriction Digestion, Sequencing
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ConclusionConclusion
The speedspeed and easeease of use, sensitivitysensitivity, specificityspecificity and
robustnessrobustness of PCR has revolutionised molecular biology
and made PCR the most widely used and powerful
technique with great spectrum of research and
diagnostic applications.