August 7, 2022

Agarose Substitution for Electrophoresis - Week 0

Hey! It's been a while since I've posted on my blog, but school is finally back! As you may expect, I plan on returning to my usual schedule and writing about the various things that I learn in class (well, almost). One of the courses I selected to take was Magnet Research III, which is arguably one of the rarest classes in Wheeler High School history. The class is for those who wish to research a topic independent from a curriculum with the intent of publication or submission into a competition (or for the sake of knowledge!). So for the following semester, I plan to research a topic that truly fascinates me: starch electrophoresis gels! Because of this, expect posts from now till late September to be about updates concerning my research. But let's first take a step back and learn how I got here and where I plan to go.

What in the World is this?

Being a high school student with a healthy addiction to biology, it has become a hobby of mine to look into various academic papers so I can learn about the newest and most innovative discoveries. While perusing Google Scholar and Science Daily, I found a novel paper about substituting agarose for corn starch when making gels for electrophoresis. It struck me as odd at first since there isn't any significant need for new gel electrophoresis protocols when there are many more advanced techniques such as PAGE and capillary electrophoresis. I was severely mistaken. One of the most heartbreaking, yet overlooked things in modern biology education is the price point that many labs are at. This means that lower-income schools are not able to afford many enriching opportunities for their students, creating a gate that only the more wealthy can surpass. Furthermore, developing countries that wish to take part in groundbreaking research are restricted due to the same factors that inhibit lower-income schools from getting access to the same resources.

Because of this disparity, Francis Tanam Djankpa from the University of Cape Coast and his team of researchers sought to find a novel substitute for the least cost-effective item: agarose. Agarose, a polysaccharide purified from seaweed, is the base used in making gels due to its ability to create a matrix for DNA to travel across when gelatinized. However, agarose powder is much harder to find in developing countries and can be priced at (or even more than) $2.70 a gram. Yes, you read that right. $2.70 per gram of purified dried seaweed. How sumptuous! The small joke aside, when you consider that many high school labs have to make multiple gels for a class and that many gels will get unintentionally destroyed by students, the price to make each gel starts to stack up rather quickly.

Starch: Our Savior

So if we want to eliminate agarose as a necessary ingredient to make gels for electrophoresis, the question we must first answer is "what are substitutes that are similar to agarose, but are cheaper to produce and easier to find?" As mentioned above, agarose is a polysaccharide, meaning it is composed of many monosaccharides (most of you could've inferred such, but trust me that it's important). Monosaccharides, aka "simple sugars," are the most basic form of carbohydrates and can serve to create bigger molecules (polysaccharides) to serve various purposes. Of their known purposes, their ability to serve as infrastructure, particularly in plants through the form of starches like cellulose, is of high interest. After all, the matrix which DNA travels through is just a complex structure of polysaccharides. Based on this information, we then just need to find the right starch that can gelatinize under the same conditions and create a similar matrix for DNA to migrate through. That's easier said than done, however.

Agarose is special due to the conditions it is able to handle, making it appropriate to use for electrophoresis purposes. This primarily includes stability under specific temperature conditions when making, storing, and using the gel. To account for this, researchers modified the gels with a buffer wash stage, altering the molecular structure to remain stable under the said conditions. While this definitely expands the horizon of viable starches, there are a couple more problems. The researchers in the paper I mention opted to test the use of corn starch due to its abundance compared to other starches. The drawback, however, is that a higher concentration of starch was required to achieve the same resolution of the DNA at 1 kbps and that the starch itself was translucent to opaque. While the former issue is manageable, the latter creates issues in actually being able to see the location of the DNA once migrated. This makes corn starch under specific modified conditions ineffective at making a valid gel to conduct a lab. This is when I thought of using tapioca starch instead of corn starch. Compared to the milky white color you get from anything involving corn starch as a thickener, tapioca starch gives a more transparent and glossy look. This would make the tapioca starch a much better alternative to being able to see the migrated DNA and enable the alternative gel to be much more useful to schools and even researchers doing post-secondary level research and beyond.

Closing Remarks

Starting tomorrow, I'll be conducting an independent research project inspired by a novel paper aimed at replacing agarose with an alternative starch. This will be the biggest test of all as it draws from all my years of education in biology, chemistry, and even some mathematics. To be quite frank, I don't know if I can pull it off. There is definitely potential in the topic, but I fear that I may not be the trailblazer in this topic of study. However, I believe that whatever results I produce will be of use to further advance the scientific world and reduce the opportunity gap based on financial situation.

Below you can find the original paper that inspired me to delve deeper into this research project. The team that worked on this paper deserves the utmost respect for their dedication to this selfless project. I urge any readers interested in biology or biochemistry to give it a read!