August 31, 2022

Agarose Substitution for Electrophoresis - Week 3

First and foremost, I apologize for the delay. I never like to deviate from the schedule, but the maintenance was so time-consuming that I didn't have time to decently write a post. However, the post today will be worth the wait! About one-third of my project was completed as of last Friday with the completion of my controls! So for this post, I'll briefly describe my control group and the results that were yielded from it.

Controls

As those who may have read the article attached to the Week 0 post know, this research is based on the premise that a starch, such as corn starch, has the capabilities of replacing agarose in gel electrophoresis. However, the paper reported on issues surrounding the visualization of the DNA post-electrophoresis. I wanted to test how valid their work was and pick up on the nuances of their work that were not described. To be able to do this, a corn starch gel and agarose gel were made.

The corn starch gel was made up of modified corn starch. The reason for the modification of corn starch was to reduce the temperature required to gelatinize and improve the gelling property of corn starch. Once the corn starch was modified, it followed a similar protocol to most gels. Differing from the paper, however, the corn starch and agarose gels were cut in half and placed in the same gel bed. The reason for this was to reduce the potential error that could occur from running the gels in two separate electrophoresis boxes. That's why the "Frankenstein" or "chimera" gel came to be!

A photo of the "chimera gel" (corn starch on the left, agarose on the right); notice the difference in clarity between the two gels

Results

The results were almost as expected: bands appeared on the agarose gel, but not on the corn starch gel. However, The corn starch gel appeared to still have the dye migrate through, as shown in the image below. While the bands still are not present, migration of the DNA and dyes did occur.

A photo of the "chimera gel" (corn starch on the bottom, agarose on the top) under intense UV light; take notice of the slight green blur in the corn starch; this is the dye!

Discussion

So the results are in for the control! The biggest takeaway here is that the corn starch gel worked better than expected. While it definitely is not in a usable form yet, there's greater potential for the tapioca starch, assuming it creates a clearer gel, to allow for accurate visualization of DNA bands. I can make this conclusion based on the migrated dye; since the dye migrated, the gel was able to create a matrix of some sort that allows for the gradual movement of molecules.

Closing Remarks

With every coming day, my belief in the research I'm doing grows stronger. With this stage of the research being done, I can officially move into modifying the tapioca starch and creating the tapioca gel. I do expect there to be plenty of differences, especially surrounding the different properties of tapioca starch, but a gel should be producible nevertheless. I'm excited to write my post as I slowly shift into exploring the unknown.