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SDS-PAGE Tips and Tricks to Save You Time

Posted in: Protein Expression and Analysis
SDS-PAGE Tips and Tricks to Save You Time

Today, SDS-PAGE is one of the basic methods in biology labs. As a beginner in my lab, I had little help, so my first SDS-PAGE gel took two whole days! Since then, I’ve learned a lot about how to make the process faster.

Here are some SDS-PAGE tips and tricks that I learned to help you save time:

Make Stuff Ahead of Time

Here is a list of components that you can store and use later:


You might already know this, but it is not bad to repeat it. You can make all your gel buffers in large amounts at one time and use them as you go along. One more option is to make them 10x concentrated.

Some labs also reuse the gel running buffer a few times.   In that case, put a label on the bottle of your buffer where you can put a stripe each time you use it, so it is easy to follow usage.

Ammonium Persulfate (APS)

Yes, it can be aliquoted and stored at -20°C for long-term storage. At first, I was making fresh APS each time before electrophoresis. But it turns out that is ok to dissolve it, aliquot it, and store it at -20°C. Thaw it just before use.

Alternatively, if you run SDS-PAGE gels frequently, you can keep your APS in the fridge at 4°C for about a month before it goes bad.


Gels can be prepared ahead of time and stored at 4°C (fridge). Of course, this doesn’t mean that you can leave it there forever, but for two weeks, it is ok.

How to store it? Well, first it depends on which equipment you use. For example, I am using Mini-protean II and III. I can store the gels in each case, but it is easier with the Mini-protean III because I can remove the gels from the casting stand and casting frames without the plates separating.

Whichever equipment you use, it is important to keep the gels wet. To do so, remove the comb and wrap each gel separately in paper towels, and wet everything with dH2O. Then put the gel in a plastic bag or box. If it is hard to wrap it in a towel due to the equipment, you can wrap the whole thing in cellophane wrapping or put it in a plastic bag.


Ok, you probably know that you can store your samples at -20°C. But I want to point out that you can go a step further and prepare your samples and store them. You can mix them with master mix, heat them, and after that, store them. Just before you want to load your samples on the gel, thaw them a bit and centrifuge them. My colleagues store their samples this way for one year without compromising results.

Some More Time-Saving, Experiment-Saving SDS-PAGE Tips

Change Your Overlay

I was taught to overlay the separating gel with dH2O after pouring. But it is faster and actually better if you use isopropanol instead of water. Isopropanol protects gels from oxygen better, therefore your gel will polymerize faster when you use it instead of water.

Don’t Lose Your Marbles

A friend of mine gave me a handy tip. If you don’t have an adequate amount of electrophoresis buffer, add some marbles (yes, the ones that we used to play with) to raise the level of buffer (like Archimedes’ Eureka story). But be careful: Make sure you use transparent marbles and not colored ones; according to the story, they can release color.

Transfer the Buffer

Don’t you hate it when your running buffer leaks out of the inner chamber? If the level of the buffer falls enough, your wells will get dry and your gel won’t run correctly. A tip that saved my electrophoresis: if you are losing buffer, just stop the electrophoresis and take buffer from the outer chamber, put it back into the inner chamber, and press start again. You might have to repeat the process until your run is done. I know that it is not the best option, but at least it works!

I must confess, now that I know these SDS-PAGE tips, it’s an easy-to-do experiment. I hope these SDS-PAGE tips will also help you save time and money.

Are you sick of leaky gels and wonky wells? Download our free SDS-PAGE gel recipe and casting protocol cheat sheet. It works—at any percent.

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Image Credit: krytofr


  1. Natalia on June 9, 2019 at 6:30 pm

    Thanks for those, the suggestions with isopropanol and marble might come in handy.
    Also, I have another suggestion for APS that I’ve used: you can make some dry aliquots to match your usual amount needed (write the exact weight on the tube to know how much water to add!) and store it in room temperature. It dissolves well enough – it might actually be quicker than thawing a frozen liquid aliquot.

  2. Minh Tran on April 17, 2019 at 4:14 pm

    To stop buffer leaking out of the inner chamber, I fill up the outer chamber until the level of buffer in the inner and outer chamber are the same level (like the liquid in a U-tube).

  3. mansi gujrati on November 30, 2016 at 4:31 am

    other alternate to marbles are cool packs ! have one cool pack in the outer chamber it raise the level of the buffer and also helps maintain the volume in inner tank 🙂

    • Amit Verma on June 23, 2017 at 7:14 am

      Using cool packs are really handy, as it is readily available in lab.
      To me, it offers one more advantage, that is, it keeps your entire running set up at low temperature. So, if your protein is temperature sensitive and degrades quickly before you visualize it by staining or transferring it to the membrane for westerns; putting cool packs are going to be a life saver.

      Thanks Mansi for nice suggestion.

  4. KPX on October 12, 2016 at 5:41 pm

    Even quicker: Add some glycerol to the separating gel, then you can pour two gels one after another.
    source : , see “Alternative Casting Procedure”

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