5 Ways to Make SDS-PAGE A More Approachable Topic

Introduction: SDS-PAGE

Gel electrophoresis techniques are one of the most common lab practices. They are widely used in both academia and industrial research.  The most widely known ones are AGE (agarose gel electrophoresis and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). While AGE is primarily used for relatively bigger macromolecules like DNA (50–20,000 bp), SDS-PAGE is used primarily for smaller ones like proteins (5-250,000 Dalton) or DNA (5-500 bp).

Any biological research dealing with these macromolecules as separate entities require their isolation from the bio-sample. Since none of the molecules (macro and micro) exist as a single entity, their isolation can be challenging and cumbersome. But with the invention of SDS-PAGE, scientists made the isolation of proteins a very easy task!

Until this point, everything looks fancy and clear. The real challenge begins when students face issues while learning about this topic. Though they and their educators both acknowledge the power of SDS-PAGE, several issues have surfaced that give this topic a bad reputation and tag of being “too complex”.

We, at Labster, understand this issue and have gathered some resources to make this learning journey easier for students. We also understand how difficult it can be for educators and teachers to explain a technique as complex as this with no visual aids or availability of a real experimental setup. We’ll list the most common issues faced by students and simultaneously provide practical solutions for educators to resolve them. By the end, we’ll share why a virtual lab simulation will prove useful not only for your students but also for you as an educator to deliver concepts more effectively.

3 reasons why SDS-PAGE can be tricky to teach or learn

There are three reasons why students feel challenged by the topic of SDS-PAGE. Acknowledging these issues is the first step toward making the topic more approachable. 

1. The technique is very extensive

SDS-PAGE is even more complex than AGE. There’s a long list of variables involved in this technique ranging from SDS, APS, TEMED, acrylamide, methylenebisacrylamide, buffers (2 types; stacking and separating) and water. Although students are fascinated by the vertical nature of this gel (in contrast to the horizontal gel of AGE), learning about SDS-PAGE turns out unnerving for young learners. The list of variables doesn’t end here as there are additions in the sample preparation, gel running buffer, and gel staining steps. The extensive nature and steps of SDS-PAGE are bound to overwhelm the students.

2. Visualization is a task

Students fail to follow the protocol as textual details of each step blow their minds. There is a dearth of visually engaging flowcharts and animated videos that could ease capturing the essence of the technique. On top of this, the lab setup for SDS-PAGE has several things to be taken care of. With no video guidance, students get frustrated when the experiments fail due to one or the other issue in the lab setup.

3. Too many peculiar details and warnings

There are too many details that need to be taken care of. The concentration of stacking gel and resolving gel is different. The ratio of acrylamide and methylenebisacrylamide is definite. Gel pore size is dependent on the protein in question. Gel can’t be over-run, tank buffer can’t be overheated, and well can’t be overloaded.  Students get overwhelmed with so much information. Not knowing the reasons behind each one of these warnings can make it a lot for them to remember and comprehend. 

5 ways to make SDS-PAGE a more approachable topic to understand

To address the problems encountered while teaching SDS-PAGE, educators can engage the under-listed solutions in their classes. These can clarify many instrumental aspects of the major techniques involved. 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. Conduct active discussions to build the core concepts

Before letting your students dive into intricacies of the practical handling, it would be advisable to first clarify their basic idea of the biological cells, structures, macromolecules, charges, etc. You can opt for interactive discussions where core concepts are built. Such a practice will ensure that running an SDS-PAGE gel isn’t just a mechanical job but a well-thought and scientifically-planned experiment. You can use the hints enlisted below.

1. Difference between AGE and PAGE
2. Difference between stacking gel and resolving gel
3. Use of TEMED and APS
4. Orientation of gel (vertical versus horizontal)
5. Gel concentration, Pore size and Protein separation

If your students are educated about these preliminary topics, learning the technique of SDS-PAGE won’t be as challenging as it is otherwise. 

Figure: An indicative value of gel concentration corresponding to the protein size in question. Image Source

2. Introduce the inventors 

The technique can be introduced to students as a manifestation of human curiosity. No scientist is working on a specific science problem alone in the world at any point in time. Many others are working simultaneously on it. Similar is the story of the invention of SDS-PAGE. L. Ornstein and B. J. Davis (1960) deserve credit for the novel concept of stacking gel in SDS-PAGE. The breakthrough of switching to polyacrylamide gels which had higher stability and almost zero risk of microbial decomposition was made by David F. Summers in 1965 while dealing with poliovirus proteins. He also recommended the usage of SDS in the polyacrylamide gel (due to its denaturing effect).  Ulrich K. Laemmli, who worked on the bacteriophage T4 as a postdoctoral fellow, detailed the SDS-PAGE technique that he employed to characterize the proteins in the bacteriophage's head in 1970. There’s another lesser-known name in the invention of SDS-PAGE, Jake Maizel. It’s reported that Jake and Laemmli, combinedly invented the technique.  

Although history is interlinked, the motto of telling this history should be clear. Students should feel motivated to start innovating as they learn the SDS-PAGE technique.

Figure: a snippet showing the separation of different protein molecules based on size. It is a part of the SDS-PAGE simulation by Labster. It is available for University and College courses.

3. Give room for trials and errors

Since there are too many peculiarities in the SDS-PAGE technique, allowing your students to experiment is a good way to let them learn and develop an interest in practical lab handling. Allowing your students to do a few of the under-listed things can help them gain better perspectives of the details.

1. Elimination of stacking gel (letting only resolving gel in the apparatus)
2. Skipping size markers (size references to check the size of our protein)
3. Using random electrical settings  (voltage and current)
4. Skipping the use of removable protein stain
5. Connecting the wrong electrodes in an electrophoresis chamber
6. Using different concentrations of gels

As your students perform these alternative ideas, they might or might not get optimal results. But that will efficiently teach them the idea behind perfect optimizations of the SDS-PAGE techniques. 

4. Tell the utilities and applications

Educators can make their students intrigued about this topic by salting out the practical applications of the technique. We have listed some of them for you to begin with.

1. Biochemistry (For proteins isolation and analysis)
2. In combination with western blotting (For separating a specific protein from a protein mixture)
3.  In mass spectrometry (for sample preparation)
4. In medical diagnostics (Example: As a part of HIV test)

Figure: A snippet from the SDS-PAGE simulation by Labster. It is available for University and College courses.

5. Use virtual lab simulations

Since SDS-PAGE is a complex topic to teach in conventional classroom setups, utilization of interactive and fun-based methods is highly recommended. In the dearth of such options, students tend to cram the technique protocols without understanding the fundamental idea that underlies its functioning. To avoid such a scenario, we at Labster have developed an engaging and interactive tool.

We bring virtual laboratory simulations that can ease your process of lecture delivery and lab handling sessions. You can make more insightful points as students are rendered with better visual options. The 3D simulations help them understand the intricacies of PAGE apparatus and the chemicals involved. 

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 SDS-PAGE simulation from Labster here or get in touch to find out how you can start using virtual labs with your students.