Agarose gel electrophoresis is one of the most common biotechnology experiments in high school and undergraduate teaching laboratories. Unfortunately, it also tends to require at least 45 minutes to perform… assuming that everything works exactly as it should, nobody makes a mistake, and your students know what to do. Suddenly that 45 minute experiment is stretching towards an hour, the bell has rung, and you are frantically trying to take photos of the gels while your next students are filing into the room. Fortunately, there are a few easy tips and tricks that you can incorporate into your agarose gel electrophoresis experiments to ensure you get beautiful results as quickly as possible.
1) Prepare your gels in advance – One of the easiest ways to save time is to prepare your gels ahead of time. Melting, pouring, and waiting for gels to solidify can take around 30 minutes. Fortunately, you can store agarose gels in the refrigerator until needed. Simply place the gel into a ziplock bag with a small amount of buffer (1-2 mL is enough) and refrigerate until needed. This even works for gels with SYBR Safe or other fluorescent stains!
2) Select the correct voltage – Choosing the correct voltage is key to getting the fastest results possible. Very simply, the higher the voltage the faster the gel runs. Unfortunately, this also comes with additional heat. Balancing the two is key to getting fast AND beautiful results. For most experiments, 150V is a great option!
3) Think thin – Thicker gels, those made with a higher volume of agarose, have multiple advantages. They are easier to handle and less likely to break when being moved from the tray to another location. Additionally, thicker gels will have deeper sample wells, making them easier to load and increasing the sample volume that can be added to each lane. Unfortunately, thicker gels also run more slowly. To speed up your experiment, consider having students pour a thinner gel – for the Edvotek 7x7cm and 14x7cm trays we recommend 25 mL and 50 mL gels, respectively. For the EDGE Integrated electrophoresis system try a 40 mL gel. In all cases, the gels will still easily hold up to 30 uL of sample, but will run up to 20% faster.
4) Concentrate on the concentration – Agarose gels act as a molecular sieve to separate DNA strands based on their length, with shorter fragments having an easier time migrating than longer fragments. Higher concentrations of agarose will effectively slow down the migration of DNA fragments, while lower concentrations allow DNA to migrate faster. However, it’s important to remember that every experiment is different and the concentration of agarose should ideally be optimized based on the sizes of DNA fragments that are being separated. For very large DNA fragments, anything over 4000 bp in length, a 0.8% gel will allow for quicker migration. However, if you are trying to identify small DNA bands you might need a 1.5% or 2% gel for best results.
5) Choose the right buffer – The two most common buffers for DNA electrophoresis experiments are TAE and TBE. Both buffers provide electrolytes, to allow the electrical current to flow through the gel, while keeping the experiment at the proper pH. TBE buffer is often preferred for smaller DNA fragments while TAE can resolve larger fragments into slightly sharper bands. However, in practice the two buffers are generally interchangeable. Interestingly, lowering the concentration of your buffer can actually speed up the experiment. Diluting the buffers to 0.5X with distilled or deionized water (a 1:1 mix) can increase the speed of your electrophoresis experiments by up to 25%. Be warned: doing this can also cause your buffer to heat up more quickly, so check in often while your experiment is running!
Hopefully these tips will help you fit DNA electrophoresis experiments into your classrooms! For more agarose gel tips check out the resources available at: https://www.edvotek.com/learning-center-electrophoresis