Electrophoresis FAQ

What should I do with my DNA samples when I receive them?
The DNA samples usually contain DNA that is already cut with restriction enzymes and then placed in a stabilized salt solution. If you will be using them within the next few weeks, they may be stored at room temperature. If you will not be using them in the next several weeks, store them frozen until needed.

I went to use my buffer left over from last year but it had a white precipitate in it, can I still use it?
Sometimes concentrated buffer (and diluted buffer containing impurities) may develop a white precipitate or some crystals on the bottom. If only a small amount of precipitate is present, you may filter the buffer through filter paper abd then dilute it according to the instructions. If the amount of precipitate is severe, it may be better to dispose of the buffer and use fresh material.

What is the loading dye for?
The loading dye, also referred to as the tracking dye, serves two functions. The first function is weight. The loading dye is made with a high concentration of sugar, which is heavier than the buffer solution in the tank. This causes the dye (and DNA contained within the dye) to sink to the bottom of the wells in the gel during the gel loading procedure. The second function is that it gives an indication of when to turn off the power to the electrophoresis chamber, since the DNA cannot be seen when the gel is running in the chamber. The dye moves faster than most of the DNA fragments. When the dye has reached the end of the gel, it is time to turn off the power.

My students do not have time to finish the electrophoresis and the gels are still running. What should I do?
Electrophoresis is a time consuming process and quite often students do not have the luxury of loading, running, and staining their gels in one class period. If the students must leave, continue to monitor the gel in their absence. When the loading dye reaches the end of the gel, turn off the power.

Do I have to stain the gel immediately after finishing the electrophoresis run?
After you have run an electrophoresis gel, the DNA is embedded in the matrix of the agarose. If the students will be in lab the next day, simply leave the gel in the chamber and allow the students to remove it and perform the staining procedure the next day. If they will not be back in lab for several days, remove the gel from the chamber, place it in a Ziploc-style bag, and add a couple of milliliters of buffer from the chamber. Place the sealed gel in the refrigerator until the next lab period.

Can I reuse the buffer in the chamber after I have run a gel in it?
The buffer in the chamber may be used a couple of times. However, after each run the capacity of the buffer to carry electrical current is diminished. It is not recommended that you use the buffer for more than two or three electrophoresis runs.

I have a battery powered electrophoresis chamber. Can I hook it up to another power supply instead of using batteries?
No. The battery powered chamber is designed to only be used with five 9-volt batteries (45 volts) or less. Even a low voltage power supply may still carry a higher amperage than five batteries. High enough amperage may be dangerous and the battery powered chamber lacks some of the safety features found in chambers that attach to more sophisticated power supplies.