Biotech Basics: Avoiding Agarose Microwave Explosions

Oh the dreaded agarose microwave explosion! One second your solution is not boiling at all and the next it’s erupted like a volcano. The result: agarose splattering the top and sides of your microwave, a rapidly solidifying pool of the slimy stuff gathering on the bottom, and the frustration and rush of having to find a way to quickly make new agarose gels. Many labs assume this mishap is almost inevitable if you make gels regularly and respond by having agarose only microwaves. But it doesn’t have to be this way! Here are some of our tried and true tips for successfully heating agarose.

1. Swirl and swirl again. 

Most explosions are caused by superheating which is when a solution is heated to (or past) its boiling temperature but has so much surface tension that the telltale air bubbles of boiling can’t form. The problem with this is that once bubbles do form they abruptly reduce the solution’s surface pressure which creates an enormous amount of energy. This energy gets channeled into a rapidly boiling solution (good), a solution that pushes out of the container (not good), and – in some cases – a shattered container (really not good.) 

The fix? After one minute of heating your agarose solution, stop the microwave, remove the beaker, and give the solution a preemptive mix by swirling it several times. Repeat this mixing as soon as you see the solution start to boil. But be careful! Mixing can cause rapid boiling even outside of the microwave.  

An added benefit of mixing is that it helps to evenly distribute heat. Microwaves are notorious for uneven heating (just think about the last microwave lunch you had) but swirling the solution counteracts this.  

2. Use small heating bursts. 

I once heard preparing agarose gel solution compared to blowing up a balloon. The first few breaths require a bit of force to expand the balloon. However, once this happens, it’s better to blow the balloon up gently to avoid an overfilled or popped balloon. It’s the same with gels. After the initial one minute heat up continue to heat the solution using 10-15 second microwave bursts.

This is especially important because it’s very hard to pinpoint exactly how long to heat a particular agarose gel solution. Factors that influence how long an agarose solution needs to be heated include the type of agarose used, the percentage of the gel, the volume being prepared, the particular settings of the microwave, the size of your container, how scratched or smooth the container is, your altitude…..you get the picture. Given this range, it’s best to err on safe size and avoid overheating or superheating by using several short bursts in the microwave. 

If hovering over the microwave and resetting it every 10-15 seconds drives you crazy consider switching the power setting of your microwave to defrost and using bursts of 1-3 minutes. At this lower power setting, the solution takes longer to dissolve but is less prone to explosions. For some of us, minute intervals also make multitasking easier. See the next tip for a similar strategy.  

3. Have a “dummy load”.

Some scientists swear by the practice of placing an additional beaker filled with water in the microwave and heating both the water and agarose solution simultaneously. They may be right! The “dummy load” absorbs a portion of the microwave’s energy. This accomplishes the same thing as lowering the power setting on your microwave – it slows down the heating process. Such gentle heating reduces the risk that you’ll overshoot your goal and overheat or superheat your solution.

4. Leave room for boiling and expansion. 

If you’ve ever ordered any of our Melt and Pour UltraSpec-Agarose™ products you may have initially thought “they didn’t fill it all the way!”. You’re right and that’s been done very intentionally. Using bigger containers and filling these containers only partway doesn’t necessarily protect against over boiling and foaming. However, it does prevent the rapidly boiling/foaming solution from bubbling out of the container and making a big mess. This applies to agarose solutions that are made in beakers too. In fact, many labs recommend beakers that are 2 to 4 times the volume of the solution when preparing agarose gels as a way to contain any spillovers. 

5. Pause after mixing the agarose powder and buffer solution. 

Give your solution a minute or two to fully hydrate after you’ve combined the powder and buffer. This reduces the risk of foaming which creates a mess similar to the one observed after a superheating explosion. It also makes dissolving easier thus shortening the heating process.

6. Skip the microwave!

That’s right you can avoid microwave heating altogether and circumvent many of these problems by using a rice cooker to prepare your solution! Interested in this fast, simple, and inexpensive solution? Then check out our video EdvoTech Tips: Quick and Easy Agarose Gel Preparation.

7. Bonus tip: Pause after heating the solution. 

Allowing your final solution to cool to 60oC before pouring it into the gel cassettes can reduce the number of in-gel bubbles. This tip has two important caveats. First, don’t let the solution go too far below this 60oC temperature as it will begin to solidify and clump within the container. And second, allow the gel to cool gradually. Speeding up the cooling process by putting the container in a refrigerator etc. can lead to irregularities in the gel matrix and distorted bands. 

If you’re reheating a pre-made agarose solution that has been bottled the same rules apply. In particular, it’s very important to repeatedly mix the container during the initial heating steps by squeezing and shaking. This is because pockets of liquid within the still semisolid matrix are especially prone to superheating. Similarly, these tips can also be used when preparing agar plates.

Image Credits

Top Volcano Image from Darkimages08, CC BY-SA 4.0 https://creativecommons.org/licenses/by-sa/4.0, via Wikimedia Commons