When loading samples they do not stay in the gel pockets, instead they travel downwards between the gel and the gel plate.
• It is important to use gel plates that originated from the same gel cassette. This is due to the nature of the plastic pins connecting the two plates in the original cassette. When separating the plates these pins break apart differently in each cassette.
The cassette is leaking when casting the acrylamide gel.
• Make sure the agarose has fully sealed the gap between the plates (on the outside of the cassette) (Fig. 2C). If necessary fill up gap with agarose (Fig. 3A).
• Make sure that the tall and short plates are secured with foldback clips before the agarose solidifies. Do not move the cassette when the agarose has not solidified yet.
• Make sure the tape is covering the slot well. Press the tape on well, and make sure the tape adheres well to the plastic all around the slot
• Leakage is usually not a problem. However, if necessary, to check whether the assembly does not leak, fill the cassette with water and check for leakage. Then pour out the water, and insert parts of a paper towel or Whatman Blotting paper, to remove any remaining water.
During electrophoresis the samples move towards the left and right side of the gel rather than move straight down.
• This is likely due to the current not only going from top to bottom of the gel but also through the sides of the gel
• Make sure you use 1% agarose made in deionised or distilled water, but not in buffer
• Fill just enough running buffer into the bottom chamber. If the bottom chamber must be filled up all the way, then apply plastic scotch tape along the left and right side of the cassette to prevent current to enter through the sides of the cassette.
The slots contain pieces of agar, preventing proper loading of samples
• The comb thickness may not match the void between the plates (i.e. the thickness of the comb is less that the gap between the plates). In this case a thin layer of acrylamide polymerises in the space between the comb and the plate. Once the comb is removed, this layer of acrylamide usually tears and settles in the wells, cannot be removed, and affects sample loading.
• If the comb has the proper thickness, and problems still occur, secure the comb with a foldback clip immediately after pouring the gel.