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
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.
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.
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.
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.
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.
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.
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.
Difference between AGE and PAGE
Difference between stacking gel and resolving gel
Use of TEMED and APS
Orientation of gel (vertical versus horizontal)
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
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 con