1. Variants of PCR Lecture 4

2. Colony PCR
Multiplex PCR
Nested PCR
Reverse transcriptase PCR
Quantative PCR
Hot Start PCR
Touch down PCR

3. Colony PCR
PCR screening of bacterial (E Coli) and yeast transformants containing cloned inserts
to determine insert size and/or orientation in the vector.

4. The presence of an insert and its size can be determined by growing each colony in liquid
Plasmid purified by a boiling or alkaline preparation protocol,
Digestion of the plasmid with restriction enzyme(s) that excises the insert
separation by agarose gel electrophoresis

6. Multiplex PCR
several pairs of primers annealing to different target sequences.
This permits the simultaneous analysis of multiple targets in a single sample.
testing for genetic mutations, six or more amplifications might be combined
analysis of microsatellites and SNPs.

7. Nested PCR
Two pairs of primers instead of one pair are used to amplify a fragment.
In the first PCR, one pair of primers is used to generate DNA products, which may contain products amplified from non-target areas.
Template (product of first PCR) in a second PCR, using one ('hemi-nesting') or two different primers whose binding sites are located (nested) within the first set, thus increasing specificity.

10. Reverse transcriptase
detect RNA expression levels. qualitative study of gene expression.
detect gene expression through creation of complementary DNA (cDNA) transcripts from RNA.
quantification of RNA, by incorporating qPCR into the technique
qRT-PCR, RT-qPCR

12. most powerful, sensitive, and quantitative assay for the detection of RNA levels as compared to northern blot.
expression analysis of single or multiple genes
expression patterns for identifying infections and diseases.
May be either one step or two step RT-PCR

14. Real time or Quantative PCR
amplify and quantify targeted DNA molecule.
amplified DNA is detected as the reaction progresses in real time.
1) non-specific fluorescent dyes that interclate with any double-stranded DNA
2) sequence-specific DNA probes oligonucleotides labeled with a fluorescent reporter which permits detection only after hybridization of the probe with its complementary DNA target

16. Applications
 rapidly detect nucleic acids that are diagnostic of, infectious diseases,cancer and genetic abnormalities.
detect newly emerging diseases, such as new strains of flu
in the fields of food safety, food spoilage and fermentation and for the microbial risk assessment of water quality.
It is also used for the determination of zygosity of transgenic animals used in research

17. Hot start PCR
Hot Start PCR avoids non-specific amplification of DNA by inactivating the taq polymerase at lower temperature.
dsDNA is denatured by heating the sample at its denaturing temperature and then the temperature is suddenly reduced to 55 degree C at which primer and Taq-polymerase is added

18. specific antibodies are used to block this Taq-polymerase at annealing temperature.
When the temperature raises for amplification to 72 degrees, the specific antibody detaches from Taq-polymerase and the amplification with greater specificity starts.

19. Touchdown PCR Primers will avoid amplifying nonspecific sequences.
The annealing temperature during a polymerase chain reaction determines the specificity of primer annealing.
The melting point of the primer sets the upper limit on annealing temperature. At temperatures just below this point, only very specific base pairing between the primer and the template will occur.

20. Touchdown PCR uses a cycling program annealing temperature is gradually reduced (e.g. 1-2°C /every second cycle).
The initial annealing temperature should be several degrees above the estimated Tm of the primers.
The annealing temperature is then gradually decreased until it reaches the calculated annealing temperature of the primers or some degrees below. Amplification is then continued.