The comb in gel electrophoresis creates small pockets, called wells, where you load your DNA, protein, or other samples before running them through the gel. Without these wells, there would be no defined starting point for your samples, and the entire technique wouldn’t work. The comb is placed into the liquid gel before it solidifies, and once the gel hardens around the teeth, removing the comb leaves behind a neat row of uniform wells ready for loading.
How the Comb Creates Wells
A gel electrophoresis comb looks exactly like a hair comb: a flat strip with evenly spaced teeth hanging down from it. The process is straightforward. You slot the comb into grooves on the casting tray before pouring the hot, melted gel (usually agarose or polyacrylamide). The liquid gel flows around each tooth and fills the tray. Once it cools and solidifies at room temperature, you pull the comb straight up and out. Each tooth leaves behind a small rectangular pocket in the gel surface.
These wells are the only way to get your samples into the gel in an organized, separated fashion. Each well holds one sample, so when an electric current pulls the molecules through the gel, every sample travels in its own lane. That lane separation is what lets you compare different samples side by side on the same gel.
Comb Size Controls Sample Volume
Combs come in different configurations, and the number and width of the teeth directly determine how many samples you can run and how much liquid each well holds. A 6-tooth comb with wide teeth (about 9 mm each) creates wells that hold up to 102 microliters in a 1 cm thick gel. A 12-tooth comb with narrower teeth (about 3.7 mm) produces smaller wells maxing out around 42 microliters, but gives you twice as many lanes.
Choosing the right comb depends on the experiment. If you need to load a large volume of a dilute sample, wider teeth give you bigger wells. If you’re screening many samples at once and only need a small amount in each lane, a comb with more teeth is the better choice. Some combs are even designed with 4.5 mm spacing between wells to align perfectly with multichannel pipettes, letting researchers load dozens of samples quickly in high-throughput workflows.
Gel thickness also matters. A thicker gel paired with the same comb produces deeper wells that hold more volume. For instance, the same 8-tooth comb creates wells holding 72 microliters in a 1.5 mm thick gel but only 48 microliters in a 1.0 mm thick gel.
Proper Comb Placement
Where and how you position the comb affects the quality of your results. The comb should sit vertically, perpendicular to the gel surface, and parallel to the top edge of the tray. The casting tray itself needs to be on a level surface so the gel sets evenly around the teeth. If the tray is tilted, the wells will have uneven depths, which leads to inconsistent sample loading.
One critical rule: don’t push the comb all the way to the bottom of the gel. A thin layer of gel must remain beneath the teeth. If the teeth touch the tray floor, samples will leak straight through the bottom of the well and smear across the gel instead of migrating cleanly through their lane. The wells also need to be positioned near the negative electrode (cathode) end of the gel, because DNA and most nucleic acids carry a negative charge and migrate toward the positive electrode. Placing wells at the wrong end means your samples would run off the edge.
Removing the Comb Without Damaging Wells
Pulling the comb out incorrectly is one of the most common ways to ruin a gel before you even start the experiment. The gel needs to be fully solidified before you attempt removal. Rushing this step leaves soft, deformed wells that won’t hold samples properly.
When the gel is ready, pull the comb out slowly, steadily, and straight up. Jerky or angled movements can tear the thin walls between adjacent wells, causing neighboring samples to mix during loading. Using a clean comb also matters: residue from previous experiments can stick to the teeth and create rough, uneven well surfaces. Overfilling the casting tray is another pitfall. Too much gel means the liquid rises above the teeth, and when you remove the comb, the wells may be connected at the top or poorly defined.
If wells are damaged, there’s no fix. You have to pour a new gel. Taking an extra minute to check comb positioning and waiting for full solidification saves significant time in the long run.
Handcast vs. Precast Gel Combs
In a handcast gel, you install the comb yourself before pouring and are responsible for every aspect of placement, timing, and removal. This gives you full control over well size and number, since you can swap between different combs depending on the experiment.
Precast gels come from manufacturers with wells already formed. The comb was inserted during manufacturing and removed under controlled conditions, so the wells are uniform and consistent every time. You simply peel off a protective strip and start loading. Precast gels save time and reduce variability, but they cost more and limit your options for well configuration. For labs running the same standard protocols repeatedly, precast gels are convenient. For experiments requiring custom well sizes or unusual lane numbers, handcasting with a chosen comb is the way to go.