PCR and its types

POLYMERASE CHAIN REACTION POLYMERASE CHAIN REACTION “ Hands on training in Biotechnology” (2011) Centre of Excellence in Agri-Biotechnology, SVPUAT,Meerut,UP. R.Sujatha, Scientist B, New Delhi.

CONTENTS: History of PCR Polymerase Chain reaction Steps involved Factors for optimal PCR Variations of PCR Comparison PCR & Cloning Advantages Limitations

History OF PCR As is the photo copier a basic requirement in an office,so is the PCR machine in a molecular biology Laboratory !!!!!!!!! PCR is DNA replication in a test tube……..

Great mind behind this PCR : Kary Banks Mullis Developed PCR in 1985 and was awarded nobel prize in 1993. PCR machine otherwise called Thermocycler. - 1983—Kary Mullis, a scientist working for the Cetus Corporation was driving along US Route 101 in northern California when he came up with the idea for the polymerase chain reaction. -1985—the polymerase chain reaction was introduced to the scientific community at a conference in October .Cetus rewarded Kary Mullis with a $10,000 bonus for his invention -Later, during a corporate reorganization, Cetus sold the patent for the PCR process to a pharmaceutical company Hoffmann-LaRoche for $300 million.

Polymerase Chain Reaction(PCR) PCR targets and amplifies a specific region of a DNA strand. It is an invitro technique to generate large quantities of a specified DNA. Often, only a small amount of DNA is available eg.A drop of blood, Semen strains, Single hair, vaginal swabs etc. Two methods currently exist for amplifying the DNA or making copies Cloning —takes a long time for enough clones to reach maturity PCR —works on even a single molecule quickly

DNA Template Primers Taq polymerase Deoxynucleoside triphosphates(dNTPs) Buffer solution Divalent cations(eg.Mg 2+ ) Requirements of PCR

STEPS INVOLVED: DENATURATION: The reaction mixture is heated to a temperature between 90-98° C so that the ds DNA is denatured into single strands by disrupting the hydrogen bonds between complementary bases. Duration of this step is 1-2 mins.

ANNEALING: Temperature of reaction mixture is cooled to 45-60° C Primers are jiggling around caused by ??????? Primers base pair with the complementary sequence in the DNA. Hydrogen bonds reform. Annealing fancy word for renaturing.

EXTENSION: The temperature is now shifted to 72° C which is ideal for polymerase. Primers are extended by joining the bases complementary to DNA strands. Elongation step continues where the polymerase adds dNTP's from 5' to 3', reading the template from 3' to 5' side, bases are added complementary to the template. Now first cycle is over and next cycle is continued ,as PCR machine is automated thermocycler the same cycle is repeated upto 30-40 times.

Factors for Optimal PCR : PCR Primers -correctly designed pair of primers is required -primer dimer,hairpin formation should be prevented -length of primer DNA Polymerase -Thermus aquaticus-170° F -Taq polymerase is heat resistant -It lacks proof reading exonuclease activity -Other polymerases can be used .eg: Tma DNA Polymerase from Thermotoga maritama, Pfu DNA Polymerase from Pyrococcus furiosus.

Annealing Temperature - Very important since the success and specificity of PCR depend on it because DNA-DNA hybridization is a temperature dependent process. If annealing temperature is too high,pairing between primer and template DNA will not take place then PCR will fail. Ideal Annealing temperature must be low enough to enable hybridization between primer and template but high enough to prevent amplification of nontarget sites. Should be usually 1-2° C or 5° C lower than melting temperature of the template-primer duplex

Melting Temperature Temperature at which 2 strands of the duplex dissociate. It can be determined experimentally or calculated from formula Tm = (4(G+C)) + (2(A+T)) G/C content ideally a primer should have a near random mix of nucleotides, a 50% GC content there should be no PolyG or PolyC stretches that can promote non-specific annealing

Variations of PCR: PCR is highly versatile technique and has been modified in variety of way to suit specific applications. Inverse PCR -In this method amplification of DNA of unknown sequence is carried out from known sequence. - This is especially useful in identifying flanking sequences of various genomic inserts.

Anchored PCR A small sequence of nucleotides can be attached or tagged to target DNA. - The anchor is frequently a poly G to which a poly C primer is used.

Reverse transcriptase PCR - It is employed for amplification of RNA molecules . - RT-PCR is widely used in expression profiling , to determine the expression of a gene or to identify the sequence of an RNA transcript.

RACE PCR -Used to obtain 3' and 5' end sequence of cDNA transcripts.

It is used to amplify and also for quantification and detection of DNA sample. Real time PCR using DNA dyes Fluorescent reporter probe method -Detection and quantitation of fluorescent reporter the signal of which increases in direct proportion to the amount of PCR product in a reaction -Does not measure the amount of end product but its production in real time Quantitative real time PCR (Q-RT PCR)

- TaqMan probes are designed such that they anneal within a DNA region amplified by a specific set of primers. As the Taq polymerase extends the prime rand synthesizes the nascent strand, the 5' to 3‘ exonulease activity of the polymerase degrades the probe that has annealed to the template. Degradation of the probe releases the fluorophore from it and breaks the close proximity to the quencher, thus relieving the quenching effect and allowing fluorescence of the fluorophore. Fluorescence detected in the real-time PCR thermal is directly proportional to the fluorophore released and the amount of DNA template present in the PCR.

Asymmetric PCR - It is used for synthesis of Single stranded DNA molecules useful for DNA sequencing -The two primers are used in the 100:1 ratio so that after 20-25 cycles of amplification one primer is exhausted thus single stranded DNA is produced in the next 5-10 cycles. Allele- Specific PCR - Selective PCR amplification of the alleles to detect single nucleotide polymorphism (SNP) -Selective amplification is usually achieved by designing a primer such that the primer will match or mismatch one of the alleles at the 3’ end of the primer .

Other types of PCR Overlap extension PCR Assemble PCR Helicase dependent amplication Intersequence-specific PCR(ISSR) Ligation-mediated PCR Methylation –specifin PCR Miniprimer PCR Multiplex PCR Nested PCR Solid phase PCR Touch down PCR and so on…………………..

Parameter PCR Gene cloning 1. Final result Selective amplification of specific sequence Selective amplification of specific sequence 2. Manipulation In vitro In vitro and in vivo 3. Selectivity of the specific segment from complex DNA First step Last step 4. Quantity of starting material Nanogram (ng) Microgram (m) 5. Biological reagents required DNA polymerase (Taq polymerase) Restriction enzymes, Ligase, vector. bacteria 6. Automation Yes No 7. Labour intensive No Yes 8. Error probability Less More 9. Applications More Less 10. Cost Less More 11. User’s skill Not required Required 12. Time for a typical experiment Four hours Two to four days

Advantages: PCR in clinical diagnosis PCR in DNA sequencing PCR in Forsenic Medicine PCR in Gene manipulation and expression studies PCR in comparative study of genomics PCR in comparison with gene cloning

Limitations Sequence Information Amplicon size Error rate during amplification Sensitivity to inhibitors Contamination Artefacts

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