5 Ways to Make ‘RNA Extraction’ A More Approachable Topic

Akanksha Saxena

Introduction: RNA Extraction: Sample and purify mRNA from pigs Virtual Lab

Every phenotypic characteristic of a living entity, whether it is eye color, height, or susceptibility to obesity, is wholly or partially governed by the genetic code. As science develops, humanity is becoming able to decode the vast majority of the genetic code that nature has meticulously encoded for us in the form of DNA.

Genes are specific stretches of DNA that code for a trait, but they are unable to express the final trait on their own. The basics of life have an intermediary component called RNA. DNA is first transcribed to RNA and RNA is translated to proteins that finally bring about the trait expression.

The significance of this RNA molecule becomes apparent when we learn that every cell in our body, including skin, fat, and follicle (hair) cells, contains the same amount of DNA. Because RNA expression varies depending on the cell's location and function, different sets of proteins are produced that can serve various roles as per the cell’s requirement. 

This makes RNA a very important molecule for advanced studies. RNA is the major molecule of concern in various research fields, including studies about the ‘likelihood to develop diabetes and obesity, ‘the pathway used in the synthesis of essential oils in lavender’, and ‘the measurement of olive oil output’.

Now when these studies begin, the first and foremost step is ‘RNA extraction’. Due to several petty and complex reasons, students are quite intimidated by this technique. For educators dealing with this technique, we have strived to gather some resources in this article. As you read, you’ll be portrayed with the basic issues that students face and some practical solutions that you can apply to overcome the same. We, at Labster, understand that teachers and educators, though passionate about their respective subjects, fall short due to a lack of resources and guidance. 

Continue reading to gain valuable perspectives. By the end, we’ll convince you why a virtual lab simulation will prove helpful not only for your students but also for you as an educator to deliver concepts more efficiently

3 reasons why ‘RNA Extraction’ can be tricky to teach or learn

There are 3 major reasons why students are overwhelmed by the topic of RNA Extraction. Acknowledging these issues is the first step toward making the topic more approachable. 

1. Fundamental concepts are weak

This is the primary cause of students confusing one step of the RNA extraction process with another. Lack of clarity about the roles of different chemicals like lysis buffer and its components (detergent, chaotropic agent  & reductant), chloroform, isopropanol, isoamyl alcohol, ethanol, guanidium thiocyanate, etc makes the subject appear hefty and challenging to understand. Many students also don’t understand the basic difference between DNA and RNA structure and nature. Students frequently end up damaging their RNA in the middle of the extraction process because they are unaware that RNA is extremely unstable and needs careful handling.

2. Inability to visualize what’s happening at the microscopic level

Students become demotivated since they can't visualize any of the actual processes that take place when they add each chemical listed in the RNA extraction protocol provided to them in the class. Cells of our body are microscopic entities (in the range of micrometers), while DNA and RNA inside the cell are even smaller (in the range of nanometers). Although light microscopes and electron microscopes (See Microscopy simulation from Labster) can be used to visualize cells and DNA/RNA respectively, visualization of a process like RNA extraction (alternatively called RNA isolation) in real-time isn’t possible using microscopes. Additionally, educators are left without any options for making the subject engaging and simple to understand due to the dearth of animated simulations and graphical materials in the public domain.

3. Unaware about the real-world use of RNA extraction

Students frequently perceive science lab experiments as having a narrow scope, especially in real life, and the majority of educators in the field also fail to persuade the students otherwise. This makes the classes and lab sessions monotonous and attending them becomes merely a compulsion to score good marks. Unawareness of practical applicability and goal-driven teaching makes lessons like DNA and RNA extraction too mechanical and less intellectual. 

5 ways to make ‘RNA Extraction’ a more approachable topic to understand

To address the issues encountered while teaching RNA Extraction, educators can engage the under-listed solutions in their next classes. These can shed light on how to handle each issue that students encounter. They will not only make lessons clearer and simpler for your students to understand, but they will also make teaching easier for educators like you.

1. Strengthen the fundamental concepts

This is the first piece of advice we have for all educators who will be teaching theoretical and practical classes on RNA extraction. We highlight some of the concepts that need to be delivered with clarity and objectivity.

  1. DNA-vs-RNA: A student with no idea about how DNA and RNA differ from each other in structure and function, can rarely isolate the concerning molecule without degrading it. Since RNA is relatively less stable than DNA, its extraction demands utmost care and precision.
  2. Lysis buffer-vs-Elution buffer: Explaining the roles and chemical contents of these buffers is of prime importance. A key problem for students is frequently their inability to construct their protocols with specific chemical contents when they don't have access to extraction or isolation kits. Therefore, teaching them the basics of these kits is very important.
  3. Functions of various lab instruments and techniques: Teaching the fundamental concepts underlying the operation of the various lab instruments used in RNA extraction steps, such as the weighing machine, centrifuge, biosafety cabinet (laminar flow), incubator, vortex, spin win microcentrifuge, spectrophotometer, gel apparatus, gel documentation systems, etc. also becomes crucial. Due to the high cost of these devices, any improper handling in a scientific setting could turn out quite costly apart from ruining the experiment.

Likewise, you can take one fundamental topic at a time (like the role of “Magnetic Beads Purification [purification of mRNA from total RNA]”, “RNA quality checks using a spectrophotometer and gel electrophoresis”, etcand explain it before you start the real lab experiment of RNA extraction. 

For gel electrophoresis, you can use the Gel Electrophoresis simulation from Labster.

For spectrophotometers, you can use the Spectrophotometers: Building and exploring the instrument simulation and Spectrophotometry: Learn the Beer-Lambert law with absorbance experiments simulation from Labster.

workbench 2 rna extraction

Figure: Asnippet showing workbench setup for RNA extraction. It is available in the RNA Extraction: Sample and purifies mRNA from pigs simulation from Labster. The simulation is available for High School and University/College courses.

2. Teach using more illustrations, flowcharts, animations, mind maps and engaging videos

Using flowcharts and simple mind maps will assist your students to retain all information in their notebooks and minds because the various procedures of RNA extraction are challenging to memorize when learned separately. The assimilation of information could be made simpler and more practical for students if the infographics depicted the objectives of the experiments, the chemicals used, their concentrations and mechanisms of action (MOA), specific warnings at each step, specificity of pH and temperatures to maintain, distinctions of aqueous and organic phases, and distinctions of pellet and supernatant at different steps.

Alternatively, you can use the RNA Extraction simulation from Labster in your next class which simplifies your work and makes all the above-listed points easily deliverable. 

workbench rna extraction

Figure: Infographics like this can help your students better understand the different steps of RNA extraction. It is available in the RNA Extraction: Sample and purifies mRNA from pigs simulation from Labster. The simulation is available for High School and University/College courses.

3.  Emphasize how crucial it will be for future research

Before beginning the practical lab session, students should be educated to understand the significance of RNA in multiple disciplines of biological research whether it be biotechnology, medical diagnostics, metabolic engineering, therapeutic industries and many more. Their appreciation of the RNA extraction method will grow as a result, and they will be inspired to learn it. You can quote examples like:

  • Use of RNA in studying different developmental stages of plants and their responses to different environmental stresses. 
  • Use of RNA to make cDNA for next-generation RNA-Seq (See Bioinformatics simulation for RNA-Seq).
  • Use of RNA in novel gene discovery. 
  • Use of RNA for genetic screening in medical diagnostics (searching for abnormal gene expressions linked to diseases and cancers). 
  • Use of RNA in Northern blotting (for studying ‘specific gene expression patterns’, ‘for comparing gene expression between different organisms’ like in RNA Extraction: Sample and purify mRNA from pigs simulation from Labster where the expression of a speculated obesity-linked gene from fat tissues is compared between 2 pigs- one lean and one obese pig).

You can quote several other examples to make your students motivated to learn the basic methodology of RNA extraction. Learning the basics with complete dedication can make troubleshooting in their future research works easier.

Farmer Greg

Figure: A snippet showing the sample collection step from 2 pigs for RNA expression studies. It is available in the RNA Extraction: Sample and purifies mRNA from pigs simulation from Labster. The simulation is available for High School and University/College courses.

4. Give them calculation drills to make reagent preparation simple

When given the task of performing real-time calculations, many biology students tremble and falter. Educators need to pay due attention to these recurrent problems in biology batches. Since RNA extraction is a chemical extraction, many different reagents have to be prepared. Also, their concentrations are very specific for each step. The entire experiment can be ruined by any peaks and valleys in the concentrations. Therefore, teaching them the basic units of measurement, Molar concept and interconversions can help them a lot. 

5. Use virtual lab simulations

RNA extraction can be a very challenging concept to teach in conventional classroom setups. There are several reasons for it, the prime one being the dearth of interactive and engaging classroom tools like videos, animations and simulations. To make your students see what happens at each step of RNA extraction at a microscopic and nano-scale,  we, at Labster, have an opportunity for you. You can utilize Labster's RNA Extraction simulation in your next class and see the difference for yourself. 

Your lecture delivery and lab management sessions will be made easier by Labster's virtual laboratory simulations. Because students have access to superior picture alternatives, you may make more insightful points. We save the day with the help of our gamification components. Our virtual learning platform uses this method of interactive, immersive instruction to strengthen the fundamental concepts for future scientists in making.  

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

rna extraction

Figure: A snippet from RNA Extraction: Sample and purify mRNA from pigs simulation by Labster. The simulation is available for High School and University/College courses.

a man sitting in front of a computer monitor
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