5 ways to destroy your agarose gel

Pouring and running an agarose gel is a simple and routine procedure that you probably learned soon after joining your first lab. A procedure that couldn’t possibly go wrong. Or so you’d think. In fact, there are a surprising number of ways to destroy your agarose gel. Here are some of my favorites:

1. Use water instead of buffer for the gel or running buffer

Agarose gels are cast and run using TAE or TBE buffer. Since both of these buffers are clear, it’s easy to mistake them for water. If you do use water though, your gel will melt shortly after applying charge to the gel box – say goodbye to your samples!

2. Forget to add ethidium bromide

In a rush, it’s easy to forget adding ethidium bromide to your agarose before casting the gel. Without it, of course, it will be impossible to visualize your DNA. You can rescue an unstained gel by shaking it in an ethidium bromide solution after it’s done running; but then you have a large volume of waste to dispose of.

3. Use the wrong percentage (or type) of agarose

The standard percentage of agarose used to run a DNA gel is usually around 1.0%. Using a higher agarose percentage enhances resolution of smaller bands; conversely, using a lower agarose percentage allows the smaller bands to run through the gel quickly, giving you better resolution and separation of higher molecular weight bands. If you use the wrong percentage, it can be difficult to visualize your bands reliably. Be careful when you start decreasing the percentage of agarose in your gel, as they become weak and much more prone to breakage.

Low melting point agarose is used for specialized applications, such as in-gel ligation. These gels are very “soupy” and fragile, even at comparable percentages, so make sure you grab the right reagent before mixing up a batch of agarose.

4. Switch the leads from the power source

One of the most frustrating mistakes you can make is to accidentally switch the leads on your power source, so that the gel runs backwards. Since the wells are so close to the end of the gel, you will most likely lose all of your samples before you catch the mistake. If you see your bands heading in the wrong direction, though, just switch the leads and run it back in the other direction.

5. Drop your gel on the way to the imager

Seriously – don’t let this happen to you.

What’s your favorite way to destroy an agarose gel?

4 Comments

  1. Pat Arbour-Reily on February 17, 2017 at 5:23 pm

    I was called back to the gel area by a panicked student worker …I viewed his gel, melted from the middle, outward, steam rising ( all borders of the gel still gelled…but not for long). A new experience for me in spite of having run gels for almost 4 decades.) I checked electrical parameters of the run , on the power supply. Yup, a problem. Apparently , the gel was made correctly but the running buffer used was the 5X stock . Student had neglected to dilute, as per written instructions ( AND, of course, hands on demos , when he was trained)…..He hadn’t bothered to check the voltage nor amperage ,either , when starting the run, also in the instructions…I guess he felt that was a waste of a precious 3 seconds of time ?
    I thought, SURELY, that I had made every mistake humanly possible, in my decades in the lab….I was wrong. LOL! A learning experience for myself and the student involved.

  2. Katherine on January 5, 2017 at 8:47 pm

    If you realize partway through running that you forgot the ethidum bromide, you can also just add it to the bottom of the gel. Thanks to its charge it will run the opposite direction of your samples. It won’t look pretty, but you’ll be able to see your samples.

  3. Tzar-ina on May 16, 2013 at 10:39 am

    I did just that, made my gel in water and forgot to add TAE buffer. Because I read this article immediately after I realized what I had done, I stopped the electrophoresis and yes my gel did melt a little, but thankfully my sample is still in there. Can I even rescue it, using a gel purification kit?

    • Nick Oswald on May 16, 2013 at 3:20 pm

      You should be ok with the gel purification kit…… good luck ! 🙂

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