I ran a 15% SDS-PAGE gel. After the end of the run the lower bands of the marker/ladder were visible clearly. But when the gel was stained with commassie stain, the lower half of the bands in the gel disappeared.
Later the same reagents and conditions were used to run a gel of 12.5%, that ran and stained properly.
What could be reason for such observation?
You must have been using a pre-stained ladder whose lower bands were visible to you? Did you leave the gel in the destaining solution for too long?
I think the con. of gel of 12.5% was more more accurate than 15% SDS-PAGE gel for the marker/ladder.
I'm not sure you've provided enough detail; however, based on what you have provided, you might have destained the gel for too long, especially if the protein concentration was very low. Were you using a prestained size ladder?
I was using a pre-stained ladder. Destaining was not done for too long. Even the pre-stained ladder bands became invisible after destaining.
That's really odd and I am myself quite surprised. I am using Tris-glycine buffer.
I haven't had that happen to me with Tris-Glycine buffer except when I have destained for exceptionally long periods of time and had very low concentrations of protein. I'll ponder this some more, but at the moment, I don't have any answers for you.
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