Gel electrophoresis: Unique separation uses, beyond biomolecules

Margarita Milton

Gel electrophoresis is a technique used to separate biomolecules by size and charge. Being such a common workhorse in the biology lab, it is hard to find a modern paper with more than two lines dedicated to this method. However, gel electrophoresis is not typically used by organic and inorganic chemists, so I found it interesting to find papers where people used it for the separation of materials other than biomolecules.

Gold and silver nanoparticles were separated by gel electrophoresis in a paper by Hanauer and coworkers. Gold nanoparticles have multitudes of applications, ranging from optical and electronic devices to drug delivery platforms. The size and shape of gold and silver nanoparticles determines their color. The nanoparticles are usually not monodisperse when they are formed, so much research has been done to purify them. The scientists in this paper picked gel electrophoresis because multiple lanes can be run for comparison, and charged groups can be attached to nanoparticles to make them move in an electric field.

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Sulfur binds strongly to gold, which is why DNA, RNA, proteins, drugs, etc., can be functionalized with thiols and then attached to gold nanoparticles. In this paper, the scientists attached polyethylene glycol chains with thiols and carboxylic acids groups (SH-PEG-COOH) to gold and silver nanoparticles because in the pH 9 Tris-borate EDTA buffer, the acids would be negatively charged and moved toward the positive terminal. Nanoparticles come in different shapes, such as spheres, rods, and triangles. The separation of gold nanorods from the other shapes was good: 25% in the original sample and up to 69% in the gel electrophoresis band. The silver nanoparticles were more of a mixture, but rods were purified up to 60% in the slowest moving fraction. The way they determined this composition in the bands was quite innovative, using two techniques that agreed well with each other. They measured the light transmitted through the nanoparticles (extinction spectroscopy) and also used Transmission Electron Microscopy (TEM). They let the agarose gel run until the bands were separated. Then they stopped it and inserted TEM grids right in front of each band. They ran the gel again and the nanoparticles smashed into the grid like bumper cars!

Another group of unusual materials for gel electrophoresis is carbon nanotubes. Pristine carbon nanotubes can be described as basically soot and have no charge. They do not move through the gel. Though not the first to try gel electrophoresis, Mesgari and coworkers obtained high yield of semiconducting carbon nanotubes by dispersing them in a charged polymer. Similar to gold nanoparticles, carbon nanotubes made in the bulk are not all identical. There is a mixture of metallic and semiconducting types, and only semiconducting tubes function in field-effect transistors. Metallic types, however, selectively bind to certain amine or amide-containing substances, such as chondroitin sulfate, which is actually a biomacromolecule. The backbone of chondroitin sulfate is hydrophobic so that it wraps around the hydrophobic nanotube, with the charged groups sticking out. It does not bind to semiconducting nanotubes.

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The mixture of semiconducting tubes and metallic tubes wrapped with chondroitin sulfate was loaded onto a large, preparative scale gel electrophoresis device. This setup resembled an electrified column chromatography machine more than a typical gel container. The metallic tubes were pulled down the gel because of the charged groups. The semiconducting tubes stayed at the top and the scientists collected them and made field-effect transistors with good characteristics. The yield of semiconducting tubes was 25%, which seems low, but there were several sonication and centrifugation steps where they had to remove aggregates.

These experiments are certainly more complex than the one experience I had with gel electrophoresis back in high school. I don’t remember what we were separating, but I did a very good job of using the micropipette on my first attempt and loaded the wells perfectly. My teammates trusted me and did not even ask for a try. The teacher was so impressed that he took my gel to show some other teams that had messed up their wells. On the way over he dropped the gel on the floor. I had to load it again while he cleaned the floor—and I don’t think I did it again quite so nicely.

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Margarita Milton grew up in New York City. She received her BS in Chemistry from Stony Brook University after working on the synthesis of aromatic belts in the lab of Nancy Goroff. She is currently a graduate student in the Nuckolls Lab at Columbia University, where she creates novel architectures involving perylene diimides. In her spare time, Margarita likes to read and write.

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