5 Ways to Make PCR (Polymerase Chain Reaction) a More Approachable Topic

Introduction: PCR

PCR has become a household term after the COVID-19 pandemic. Everyone has at least undergone one RT-PCR test for coronavirus diagnosis in the past 2 to 3 years. Now when we utter the word PCR, we expect it to be a magical technique for the detection of viruses. But that isn’t all that PCR is used for. The myriad of applications that PCR finds make it more than magical; some might say mystical!

Being one of the most groundbreaking discoveries of the 20th century, PCR has helped in propelling genomic research which finds usage in a multitude of fields like medicine, STEM research, forensics, etc. PCR is an acronym for Polymerase Chain Reaction, a molecular technique for generating millions of copies of DNA using some reagents put together in a PCR tube.

A deeper understanding of what goes on at the molecular level when DNA replicates can ease the process of explaining the PCR technique to students who often stumble when encountering it for the first time.

For teachers explaining PCR in their classes, this article can provide help as it highlights the blocks encountered by students and lists practical solutions to solve them. By the end, we’ll convince you why a virtual lab simulation will prove useful not only for your students but also for you as an educator to deliver concepts more efficiently.

3 reasons why PCR can be tricky to teach or learn

There are 3 reasons why students dread the topic of the PCR technique. Acknowledging these blocks is the first step toward making the topic more approachable. 

1. Difficulty conceptualizing

Since DNA replication lies at the heart of PCR, confusion perpetuating from the very foundation can make PCR look complex. Mere textual sources further meddle with the students’ brains and leave them clueless. Imagining how the DNA polymerase makes its way into the double-stranded DNA and channels the addition of dNTPs one after another can be difficult for students. No matter how many 2-D diagrams are employed, the struggle of the imagination game is daunting for students.

2. Headache called “memorization of terminologies, steps, and reagents” 

There is an array of reagents used in the PCR technique ranging from primers, PCR buffers, dNTPs, DNA polymerase, purified DNA, additional cations, PCR additives, etc. Blindly cramming these terminologies might make students go awry. Plus such cramming isn’t also far-sighted. Not knowing the roles and purposes of reagents in the PCR mix can turn out disastrous for students when practically setting PCR reactions in the lab. This not only robs them of the charm to do research in the future but also makes classroom teaching less conducive.

3. Lack of confidence in calculations

For experienced scholars, setting PCR reactions is a mere play of optimizing the working concentrations of different reagents as per sample DNA. But it is demoralizing for the young students who face trouble in concentration calculations. The concepts of mili, micro, nano, pico, femto and the inter-conversions create worrisome situations for many. Teachers and educators also find it difficult to explain and simplify these calculations.

5 ways to make PCR a more approachable topic to understand

In order to address the blockades encountered while teaching the PCR technique, educators can engage the under-listed solutions in their classes. These can clarify many instrumental aspects of PCR. Not only can they make teaching easier for educators like you but will also make lessons clearer and easier to assimilate for your students.

1. Relating to the inventors

It is always inspiring and more engaging when students can relate to technology as a part of human efforts. Educators can make a point that no technique or technology has landed from space on Earth, rather it is the fruit of concerted scientific efforts and remarkable human intellect that shaped scientific discoveries and inventions. Bringing forth the journey of Kary Mullis, the inventor of the PCR method can help your students immerse into an “emotion of belonging” to the Science field. If you put forward a brief history of Kary Mullis, a larger-than-life genius who not only elucidated the science behind PCR but also went on to win the Nobel Prize for his invention in 1993, students can feel connected to your lectures and the science of PCR as a whole!

Kary Mullis, who was a technician at Cetus Corporation and used to prepare oligonucleotides for other scientists, proposed the idea of PCR. His well-known “eureka! moment” while driving down the hill after a camping trip with his girlfriend is phenomenal. He cracked the code of hijacking the DNA replication process that nature carries out inside the cells. His continuous grind to understand how repeated cycles of oligo-additions under a specified cycle of temperature alterations can yield millions of copies of DNA finally turned out successful.

Such story-telling and connecting the dots between scientific grinds and success can inspire students while maximizing interactive teaching sessions. You can provide recent research papers, op-ed articles, small abstracts, etc, and share them with students to further explore!

 Figure: Kary Mullis. Image Source

2. Telling applications in practical life

Just like an infant’s mind is curious when you make them see the direct utilization of their new-found abilities, similarly, a student learns a technique with utmost interest only when its applications are chalked out in front of them. 

Although PCR arrived into the general public consciousness only after the Covid situation, PCR has displayed its immense practical potential across varied fields for almost 40 years now. As children these days relate quite quickly to modern web series and novels, as educators you can exemplify the extensive use of PCR in crime dramas. DNA from the blood, fluid, and hair samples collected from the crime scenes need to be amplified via PCR before testing them to find the identity of the offender. Without PCR amplification, the amount of DNA would be too little to be detected by the test. Look at the detective in the image below collecting samples. Such examples can make the topic promising and more engaging. 

A snippet from the PCR simulation from Labster’s virtual laboratory is available for Professional and University / College classes. 

Further ending the lecture with some examples of genomic techniques like prenatalsex testing, human genome sequencing, and paternal testing, all of which require PCR employment as their foremost step can instill an approach of reading beyond the lines in your students.

3. Easing out the name-game

When students are told the names of the PCR reagents or steps, some obvious freak-out reactions are very common. As we are very well aware of the concept of ‘associative learning’ and its benefits in the development of robust long-term memory, using techniques like drawing analogies, relating instances to real-life situations, making 3-D models, etc can aid the process of concept establishment.

• Drawing analogies- When you talk about primers, you can explain it in relation to the ‘wall primer’ that is applied before the actual painting. Just like white-washing without a wall primer doesn’t give neat wall paint, a PCR process without PCR primers won’t give DNA copies. 

• Understanding orientations using 3D models- Students tend to get confused between sense-antisense strands, coding-noncoding (template) strands, +/- strands. Since the double-stranded DNA structure and the passage of DNA polymerase aren’t easily visualized using 2D representations in textbooks, you can make 3D models explaining the orientation. Or alternatively, you can just simply use Labster’s PCR simulation to explain how the technique works.

This snippet from the PCR simulation by Labster’s virtual laboratory shows all the PCR prerequisites. It is available for Professional and University / College classes. 

• Understanding PCR steps- Essentially, the 4 different steps of PCR aren’t difficult to understand if the students have clarity of DNA replication. Otherwise linking the steps to a real-life situation can make them better comprehend the PCR cycle. If you compare PCR to a ‘yogurt preparation recipe’, it might make it interesting for your students.

• Denaturation: This 1st step of PCR resembles the ‘milk boiling step’.  

• Annealing: This 2nd step of PCR resembles ‘inoculum/starter addition’.

• Extension: This 3rd step of PCR resembles the ‘resting phase of the milk’ where the added starter with all the microbes converts the milk to curd.

• Final extension: This 4th stage of PCR resembles the ‘cooling phase’ where you transfer the curd to the refrigerator for the final setting.

4. A practical session and calculations

Since everything in a PCR reaction is microscopic, from primers to template DNA, from DNA polymerase to dNTPs, students aren’t able to visualize what’s really happening. After running a PCR reaction, introducing them to the science of visualization using ‘agarose gel electrophoresis’ can help in understanding the intricacy of the process. 

If feasible, teachers can also get some of their targeted ‘PCR-amplified regions sequenced’ and amaze the students with the marvel of DNA nucleotide data.  

Also, introducing the concept of dilutions, molar concepts, and practicing calculations or inter-conversions between different units can help them easily calculate the reagent concentrations for PCR reactions. An easy method to learn the most commonly used prefixes is to use this mnemonic: Mad Mary Never Plays Football (mili, micro, nano, pico, femto). Each of them varies by a factor of 10-3 (10-3, 10-6, 10-9, 10-12, 10-15)and is extensively used in molecular biology.

5. Use virtual lab simulations

Since DNA essentially is a microscopic entity, visualization is a constraint in the learning process of the students. With virtual laboratory simulations from Labster 2.0, teachers can make more insightful points as students are rendered with better picture options. The 3D simulations help them better understand the double-stranded structure of DNA, the binding sites of PCR primers, and also how millions of copies are generated from even a single copy of sample DNA.

Your students don’t have to struggle to imagine different steps of PCR themselves as our interactive PCR simulation along with gamification elements come to the rescue. By using this way of active and immersive teaching, our virtual learning platform takes an advent in the field of Science to make the upcoming scientists thorough with the “basics of their respective subjects”. 

You can learn more about the PCR simulation here or get in touch to find out how you can start using virtual labs with your students.

This snippet from Labster’s PCR simulation shows the lab setup for setting a DNA amplification reaction. It is available for Professional and University / College classes.