Agarose Gel Electrophoresis FAQ Roundup

Our scientists answer many different questions every week from administrators, teachers, and students. These can range from simple clarifications to deeper, thought-provoking investigations, but the most common questions relate to agarose gel electrophoresis. We’ve written a lot about gel electrophoresis over the past few years, including how electrophoresis works, how to prepare your buffers, how to save your gels, using electrophoresis to size your DNA fragments, and how to stain your gels. Today’s blog will attempt to answer the most common electrophoresis questions from the current school year.

Q: My classes are not long enough to complete a full electrophoresis experiment? This current school year has presented countless new challenges to teachers and students, including shortened class periods and hybrid student schedules. Planning ahead and accounting for condensed schedules can help your lab run as smoothly as possible. Fortunately, it is easy to pause your agarose gel electrophoresis experiments and resume at a later time. The experiment can be broken down into discrete segments: 1) Preparing the gels, 2) Running the electrophoresis experiment and staining the gel, 3) Analyzing the results.

  1. Preparing the gels – Agarose gels can be prepared ahead of time and stored until needed. Follow the included instructions to cast your gels (or follow our helpful video tutorials) and allow them to fully solidify. Once prepared, the gels can be stored fully submerged in electrophoresis buffer until needed. If you will be performing the experiment within 24 hours the gels can be stored at room temperature, but for longer storage (up to 2 weeks) they should be refrigerated. If you are using SYBR Safe to visualize your samples, we recommend storing gels in ziplock bags with 2 mL of buffer – fully submerging the gels can lead to the stain diffusing out of the gel.
  2. Running the electrophoresis experiment and staining the gel – The electrophoresis experiment should be run according to the included protocol and then immediately stained. Unfortunately, the agarose gels can not be stored prior to staining as the DNA bands will diffuse into the gel leading to poor results. If you are staining with FlashBlue you can leave the gels to stain overnight in a solution that is 1 mL of FlashBlue stain and 149 mL of water to save time. SYBR Safe stained gels will be ready to visualize immediately after the electrophoresis is complete.
  3. Analyzing the results – Once stained, gels can be stored for up to 1 week for analysis. For more information on storing the gels see a detailed writeup here.
Comparison of DNA samples stored for up to 5 days

Q: My classes are smaller than normal, how long can I store my reagents? Once diluted, electrophoresis buffer can be stored in the refrigerator for six months or longer. Ensure that your buffer has not precipitated and that nothing is growing in the solution before using. Prepared agarose can be stored in the flask that it was heated in for up to 6 months. Tightly cover the flask to prevent evaporation and store in the refrigerator until needed. Unused agarose powder can be stored at room temperature. DNA samples should always be stored in the refrigerator or freezer as indicated on the packaging – in general, tubes of DNA should be stored frozen while QuickStrip DNA samples should be stored in the refrigerator.

For more tips and tricks, check out our quick guides on gel electrophoresis, visualizing DNA, and creating a standard curve. Finally, for the fastest gel electrophoresis experiments possible we recommend the EDGE Integrated Electrophoresis System, which can run a standard gel in under 10 minutes. Stay safe, and let us know if you have any agarose gel questions!

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