5. Running the denaturating agarose gel: Place the lid onto the buffer chamber and perform electrophoresis at 5v/cm until the dye front reaches the 2/3 length of the gel ( Figure 18.4).

Figure 18.4 : Running of the denatured agarose gel

6. Staining of agarose gel:

1. In a RNase-free container, agarose gel is dipped into the 0.5M ammonium acetate for 40mins at RT.

2. Drain off the solution and dip the block in the 0.5M ammonium acetate containing 0.5µg/ml ethidium bromide.

3. Incubate on RT for 30-40mins.

4. If required and the stain is too intense, it can be destain by 0.5M ammonium acetate for another 60mins.

5. Transfer the gel to a UV chamber and capture the image with the gel documentation unit.