Running a Gel

Load your DNA samples in corresponding wells in the gel. Remember that DNA is negatively charged and runs towards the positive electrode. The gel wells should be nearer towards black electrode and farther from red electrode (DNA should run to the red end). Turn on the power to run the gel with the voltage set at 60-80 volts for 40 minutes for small gels and 90-100 volts for 1-2 hours for larger gels. Agarose gels run at high voltage may result in melting the gel and distortion of bands. One can confirm that the gel is running by checking for bubbles from the electrodes. Switch off the power at the end of the run. The next step is visualization of gel for bands (Fig. 2).

Figure 2: A. Agarose gel running unit. B. Loading of agarose gel.

Visualization

Ethidium bromide (EtBr) is traditionally used as a dye that binds to DNA and fluoresces under ultraviolet light. EtBr causes mutation and must be handled as hazardous waste. Due to the hazardous nature of the EtBr, recently non-toxic dyes have been introduced in which the gels have to be stained first and then destained to visualize the bands. But, if you are using EtBr as a dye to visualize DNA bands you need to be more careful in handling as to prevent the hazardous effect of EtBr. The EtBr gels have to be disposed separately in hazard wastes disposal bags.