Polymerase Chain Reaction

Problem Suppose you have a patient with an infection or a heritable disease. You want to know which infection or disease it is and….. you want to know it fast and ..... from as little material as possible Is that feasable?

Which DNA technologies are available? Southern blot In situ hybridization Sequencing PCR

What is relevant in medical diagnostics? SSS Speed the faster the better Sensitivity sample size Specificity reliability of diagnosis

Which type of DNA can be used for what. genes Which type of DNA can be used for what? genes - repeat DNA: centromere DNA telomere DNA CA repeats - junk DNA

Which type of DNA can be used for what? Junk ??? Repeat identification Gene diagnosis of disease ‘foreign’ DNA detection of infection CA-repeats turn out to be useful for identification of individuals. What is a CA repeat? Why? Mutations in genes can lead to hereditary diseases. PCR (in combination with sequencing) helps to detect such mutations. PCR can amplify non-self DNA assist in detecting infections of viruses, bacteria or parasites.

CA-repeats turn out to be useful for identification of individuals. What is a CA-repeats CA-repeats turn out to be useful for identification of individuals. 5’ 3’ ---------- CACACACACACACA------------ Primer primer Fixed location in the genome but the length Differs among individuals

Principal of a PCR assay on CA repeats CA repeats vary in length from 4 to 40 bp and can be found on10.000 positions in the genome. Of each CA-repeat an individual gets one copy of the father and one copy of the mother. The number of primer sets in the PCR determines the specificity of the identification.

PCR PCR, polymerase chain reaction, is an in-vitro technique for amplification of a region of DNA whose sequence is known or which lies between two regions of known sequence Before PCR, DNA of interest could only be amplified by over-expression in cells and this with limited yield

1966, Thomas Brock discovers Thermus Aquaticus, a thermostable bacteria in the hot springs of Yellowstone National Park 1983, Kary Mullis postulated the concept of PCR ( Nobel Prize in 1993) 1985, Saiki publishes the first application of PCR ( beta-Globin ) 1985, Cetus Corp. Scientists isolate Thermostable Taq Polymerase (from T.Aquaticus), which revolutionized PCR

Reaction Components DNA template Primers Enzyme dNTPs Mg2+ Buffers

1- DNA template DNA containing region to be sequenced Size of target DNA to be amplified : up to 3 Kb

2- Primers 2 sets of primers Generally 20-30 nucleotides long Synthetically produced complimentary to the 3’ ends of target DNA not complimentary to each other

Primers Not containing inverted repeat sequences to avoid formation of internal structures 40-60% GC content preferred for better annealing Tm of primers can be calculated to determine annealing T0

3-Enzyme Usually Taq Polymerase or anyone of the natural or Recombinant thermostable polymerases Stable at T0 up to 950 C High processivity Taq Pol has 5’-3’ exo only, no proofreading

The PCR Cycle Comprised of 3 steps: 1. Denaturation of DNA at 950C - 2. Primer hybridization ( annealing) at 40-500C 3. DNA synthesis ( Primer extension) at 720C

Standard thermocycle

RT-PCR Reverse Transcriptase PCR Uses RNA as the initial template RNA-directed DNA polymerase (rTh) Yields ds cDNA

rTth DNA polymerase is a thermostable DNA polymerase derived from the thermophilic bacteria Thermus thermophilus (Tth) HB8.  The enzyme has a reverse transcriptase activity in addition to a 5’→3’ polymerase activity and a double strand specific 5’→ 3’ exonuclease activity in the presence of Mn2+ ions.

Detection of amplification products Gel electrophoresis Sequencing of amplified fragment Southern blot etc...

Applications Genome mapping and gene function determination Biodiversity studies ( e.g. evolution studies) Diagnostics ( prenatal testing of genetic diseases, early detection of cancer, viral infections...) Detection of drug resistance genes Forensic (DNA fingerprinting)

Advantages Automated, fast, reliable (reproducible) results Contained :(less chances of contamination) High output Sensitive Broad uses Defined, easy to follow protocols

In Conclusion PCR is sensitive and versatile diagnostic tool: 1) to detect hereditary diseases 2) to detect infections 3) to monitor development of a disease 4) to identify fathers or other criminals PCR is extremely useful if one . 1) knows the sequence of a gene. 2) carefully selects primers 3) avoids contamination

Instrumentation

Real Time PCR

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