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PRESENTED BY NAVEED UL MUSHTAQ

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POLYMERASE CHAIN REACTIONNAVEED UL MUSHTAQ

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CONTENTS:

Basic concept of PCR. Steps in PCR. Quantitative real time polymerase chain

reaction. Fluorescent dyes and probes. Advantages real-time PCR. Real-time PCR primer Primer design software

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INTRODUCTION

• The polymerase chain reaction (PCR) is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

• There are three major steps involved in the PCR technique: denaturation, annealing, and extension.

INTRODUCTION

• Polymerase Chain Reaction was developed in 1984 by the American biochemist, Kary Mullis. Mullis received the Nobel Prize and the Japan Prize for developing PCR in 1993.

• However the basic principle of replicating a piece of DNA using two primers had already been described by Gobind Khorana in 1971.

• The polymerase chain reaction is a powerful technique that has rapidly become one of the most widely used techniques in molecular biology because it is quick, inexpensive and simple.

Basic concept of PCR

• As the name implies, it is a chain reaction• One DNA molecule is used to produce two copies, then

four, then eight and so forth. • This continuous doubling is accomplished by specific

proteins known as polymerases, enzymes that are able to string together individual DNA building blocks to form long molecular strands.

• To do their job polymerases require a supply of DNA building blocks, i.e. the nucleotides consisting of the four bases adenine (A), thymine (T), cytosine (C) and guanine (G).

Thermal pool in Yellowstone National Park (Thermus aquaticus)

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NEW PCR OLD PCR

Real time pcr

Steps in PCR

• There are three major steps involved in the PCR technique:

• Denaturation, • Annealing, and • Extension.

Steps in PCR

• In step one; the DNA is denatured at high temperatures (from 90 - 97 degrees Celsius).

• In step two, primers anneal to the DNA template strands. The annealing phase happens at a lower temperature, 50-60°

• In step three, extension occurs at the end of the annealed primers to create a complementary copy strand of DNA. The extension of the primers by Taq polymerase occurs at approx 72°C for 2-5 minutes.

• DNA polymerase I cannot be used to elongate the primers as one would expect because it is not stable at the high temperatures required for PCR.

Quantitative real time polymerase chain reaction

• Quantitative real time polymerase chain reaction is a technique based on the PCR, which is used to amplify and simultaneously quantify a targeted DNA molecule.

• Traditionally, PCR is performed in a tube and when the reaction is complete the products of the reaction (the amplified DNA fragments) are analyzed and visualized by gel electrophoresis.

• However, Real-Time PCR permits the analysis of the products while the reaction is actually in progress.

Quantitative real time polymerase chain reaction

• This also facilitates the quantitation of the DNA i.e. used to measure the quantity of a PCR product.

• This is achieved by using various fluorescent dyes which react with the amplified product and can be measured by an instrument.

• Fluorescent signal in direct proportion to the number of PCR product molecules (amplicons) generated.

• Data collected in the exponential phase of the reaction yield quantitative information on the starting quantity of the amplification target.

Plateau at cycle 25 due to inhibitory effect of accumulation of pcr product on polymerase

Ct is the number of cycles required for the fluorescent signal to cross the threshold.

Fluorescent dyes and probes

• QRT-PCR methods use fluorescent dyes, such as Sybr Green, EvaGreen or fluorophore-containing DNA probes, such as TaqMan, to measure the amount of amplified product in real time.

Advantages real-time PCR

• Ability to monitor the progress of the PCR reaction as it occurs in real time.

• Ability to precisely measure the amount of amplicon at each cycle, which allows highly accurate quantification of the amount of starting material in samples.

• Amplification and detection occurs in a single tube, eliminating post-PCR manipulations.

• Gene expression analysis.• Cancer research.• Disease diagnosis and management.• Food testing.• Animal and plant breeding.

Real-time PCR primer

• Good primer design is one of the most important parameters in real-time PCR.

• In general, primers should be 18–24 nucleotides in length• Primer pairs should have compatible melting

temperatures (within 5°C) and contain approximately 50% GC content

Primer design software

• Primer design software programs Software can automatically evaluate a target sequence and design primers for it based on the criteria

• OligoPerfect designer• Primer Express software • Vector NTI

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