Pattern/cloud appearing on agarose gel - (Oct/11/2012 )
The other time I've seen something like this happen is when photographs are taken of the gels when they haven't been drained very well, or the transilluminator not wiped down after the last gel was on it. Although it does't really explain why in most cases you only see it in your loaded lanes.
Just a thought anyway.
When you say you loaded equal amounts of plasmid to the first gel- do you mean volume? Or amount of DNA?
I mean ug. We normally rinse briefly with water right before putting it on transilluminator, but I agree that the second gel photo I sent is not rinsed well. The cloud is inside the gel. I doesn't go away no matter how much I wash it with water.
Those "stars" in the second gel - they look like crud. Maybe dust and bits of old tissue.
What sort of water are you using to make gels up in? Have you tired making gels up in something like milli-q water just to see?
You are cleaning out the flask to make gels beforehand, right? Right?
Try this: make a gel up with a new flask, using new bottled water and fresh agarose. Hell, just new everything but make sure you have new flasks and water.
Vessels and water seem to be something people overlook as a source of contamination.
I'll say this next bit, though from most of the bands I don't think this is an issue, so please don't take it as an insult: when boiling the agarose, make sure that it does boil a little and then swirl to ensure homogeneity of the melt. Then cool so that you can hold it comfortably in your hand (not too hot, not too cool), add your ethidium bromide (unless you stain the whole gel afterwards in a tank of stain) and swirl until it's homogenous.
Pour the gel in a super-clean tank (clean it, then clean it again and then rinse it in the purest water that you have - a new box/bottle if possible).
My hypothesis is that your lab needs a clean and/or the cleaning regime for at least one of your components, be it glassware or tank apperatus has some sort of carry-over on it. You could just have a mucky-pup of a tech in there.
If possible, make a gel in a sister-lab and compare results.
Would you please take a picture with no gel in your gel imager? I think there is fluorescent material on your imager plate. No fair cleaning it first.
Since your ladder is pretty clear, there should be something wrong in your PCR master mix or sample. Try changing the master mix !
It appears in other samples too. In digested or undigested plasmids too