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How to Make and Run an Agarose Gel (DNA electrophoresis)

Working with DNA in your lab? Well then here’s a video for you. To check whether your PCR worked, or if you have an insert, you need to run a DNA gel.

Here Dan shows you how to make the agarose gel, and how to load and run your samples as well.

The video shows how to make 25mL of 1% agarose. Make sure to adjust your recipe according to your needs.

  1. Andrew
    When placing your gel into the tank, you should only add enough buffer to barely cover it. Adding too much buffer will cause higher resistance when running which means that the DNA will migrate slower, and could result in smeared bands; not to mention an excess of heat which could disintegrate low percentage gels.
    • labtricks
      Very good point. Thanks Andrew!
    • Mike
      Are you sure? IMHO, adding buffer would be the same thing as increasing the diameter of a wire, so resistance should actually drop, shouldn't it? However, you are right in that the DNA will probably migrate slower, as most of the current will flow through the highly conductive buffer and not through the gel. Or am I totally wrong here? :)
  2. Michael
    The hardest thing for me is to see the well. What can I do to make the wells more visible? And I have no depth perception of the tip if I look at the gel straight up and down if I want to see the well. Similarly, I can't see the well if I look at the gel at an angle to see the depth of the tip. And I noticed you didn't put EB into the gel.
    • labtricks
      Hi Michael, Don't worry, it's hard to find the wells when you are starting out. It will get better with practice :) One common method used for practicing is to take loading dye (without your sample) and load it into extra wells. This will give you an idea of how to find the wells, and how to slowly load without introducing bubbles. Maybe keep a gel on the side and use it to practice loading. And note, you may have to look directly on top or at an angle, or both to find the well. One trick you can try is put a strip of white or coloured tape on the back of the clear tank that is holding the gel, right behind the wells. This can help with locating the wells. About the ethidium bromide, yes we didn't put it in our gel. Not everyone uses EtBr in their gels so we didn't cover that in this video. However, we also use EtBr, but to prevent contamination we don't put it directly in our gel. Instead, after electrophoresis we soak the gel in an EtBr solution under the fumehood. This limits the amount of equipment that comes in contact with EtBr. Good luck with practicing your loading! -Suraaj
  3. Yazil
    I have a question im working on a school project similar to this but it has to do with finding out the color code in candy using agarose gel. On the data table in using it mentioned something about bands but i really have no idea what those have to do wih the experiment. Do you by chance know what their talking about?
    • labtricks
      Hi Yazil, After running and staining the gel, you will see bands on the gel in each lane. The bands correspond to your samples - smaller DNA fragments run further down the gel, while longer DNA molecules will migrate slower and will appear higher on the gel. I suggest you read the info on this website, as it explains this specifically for the candy experiment: http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioChem_p039.shtml?from=TW#background Good luck!