RELEVANT LEARNING OUTCOME:
(a) Describe the principles and procedures of these molecular techniques:
a. polymerase chain reaction (including its advantages and limitations);
🕐Estimated time for this section: 30 minutes
In 1985, Kary Mullis invented the process known as polymerase chain reaction (PCR), in which a small amount of DNA can be copied in large quantities over a short period of time. Mullis won the 1993 Nobel Prize in chemistry for inventing polymerase chain reaction, or PCR.
SYBR is a dye that emits prominent fluorescent signal when it binds at the minor groove of DNA, nonspecifically.
8. Real-time PCR (qPCR) - Lecture Notes
To determine the amount of PCR product made using primers tagged with fluorescent dye (SYBR green).
Commonly used to measure gene expression.
As it does not involve the running of gels, it is a powerful and rapid technique for measuring and quantifying the changes in gene expression particularly when multiple samples and different genes are being analysed.
FYI:
qPCR is a technique used to monitor the progress of a PCR reaction in real-time.
At the same time, a relatively small amount of PCR product can be quantified.
qPCR is based on the detection of the fluorescence produced by a reporter molecule which increases, as the reaction proceeds.
How is PCR different from Real-time PCR?
PCR shows presence or absence of DNA, while qPCR shows presence and amount of DNA.
Find out more about the differences between PCR & qPCR: https://www.torontech.com/articles/difference-between-pcr-and-real-time-pcr/
Refer to your lecture notes to learn about:
the ingredients in the PCR reaction mixture and what each one does;
the three stages of PCR, the temperatures used, and what happens during each stage.
You are commonly given a temperature graph like the one on the left. You can explain the graph in this way.
Temperature is increased to about 95 °C from 1-2s to melt the double stranded DNA
The temperature is lowered from 1.5-2s to allow annealing of the primers (approximately 55 °C)
The temperature is set to 70–72 °C from 50°C for the polymerase to extend the primers (2.5-3s)
Amplification steps are usually repeated 30–40 times.
Credit: Micro-polymerase chain reaction for point-of-care detection and beyond: a review microfluidics and nanofluidics (Article)
👁️🗨️Watch the animation to learn more about the steps involved in the polymerase chain reaction (PCR).
Questions:
What are the three main temperature steps in PCR, and what happens to the DNA at each step?
Why do scientists use a special enzyme (like Taq polymerase) that can survive high temperatures in PCR?
How does PCR make millions or even billions of copies of a DNA sequence from just one starting DNA molecule?
Useful interactive activities to learn more about natural process of PCR and uses of PCR.
Find the answers to the following questions on the website:
How much DNA do you need to start PCR?
Can PCR work with RNA?
Wouldnt increase temeprature to 95 degree kill cells (during DNA replication)?
Q1. For each of the statement, write down the correct concept
Misconception:
Elongation of the DNA primer during PCR occurs from 3' to 5' direction
Correction: DNA elongation occurs in 5’ to 3’ direction.
Misconception:
2. Primers used for PCR are RNA in nature
Correction: The primer used in PCR is DNA in nature.
Misconception:
3. Fresh batch of Taq polymerase has to be added in every cycle of PCR.
Correction: All the reagents required for the many cycles are added into the tubes at the start of the experiment.
Misconception:
4. Primers bind to 5’ end of the template DNA for PCR
Correction: The primer does not bind to the extreme end of DNA, but to the 3’ ends of both template strands flanking the target DNA sequence.
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Q3. Multiple copies of a wanted DNA fragment can be made by the polymerase chain reaction (PCR).
Which description of this procedure is wrong?
A) After ‘n’ turns of the PCR cycle, up to 2n copies of the wanted DNA are produced.
B) Using a heat-stable enzyme, such as Taq polymerase, means that the enzyme does not lose activity over time.
C) Using an enzyme with a high optimum temperature allows DNA polymerisation above the annealing temperature.
D) Using specific primers means that only the wanted DNA is replicated.
B
Attempt Qn 1-6 of the Molecular techniques Learning Goals
Check in with your teacher for the following simulation.
Labster: Polymerase Chain Reaction
In the Polymerase Chain Reaction (PCR) simulation, you will be thrown right into a crime scene where a murder has taken place. After investigating the crime scene, your first task is to collect blood samples in the hope that the murderer has left traces of their DNA.
Analyze DNA, See the structure of DNA and its replication up close, Identify the murderer
In the PCR simulation, you will look at collected and other prepared samples from the suspects on a gel and then compare the patterns that emerge.
Will you be able to identify the murderer?
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