Pattern/cloud appearing on agarose gel - (Oct/11/2012 )

It's about 3-4 months that we are having serious problem with our gels as a smear/pattern/cloud appears on top of the gel right below the wells. See the photo please. Does anybody know what this is? This time it looks like a painting!

It is like the pattern moves along all lanes and it is always at the top. The picture below is our PCR product. It doesn't matter if the TAE buffer is fresh or old, these patterns are always there.

Is the pattern always the same or does it change with each gel?

it changes, like clouds

Now, I have never seen this before so I'm spitballing.
Is that ethidium bromide stained gels? How are you making up the working solution of ethidium bromide? Have you tried fresh stain?

Tell you what, it's very pretty. Enter for the next Tate Prize. I'd vote for it.

This looks as if it is an artifact of the gelling of the agarose. I suspect that you have changed the way you are mixing or cooling the agarose before pouring the gel, and that some of it is setting more rapidly than other parts, leading to non-uniformity of the gel. Make sure the agarose is well mixed and sufficiently warm before pouring the gel. The solution should be crystal clear before pouring the gel.

we tried fresh and old etbr, the cloud is still there. if you look at the photo the cloud is only over the PCR products. the ladder is clean.

phage434 on Thu Oct 11 11:47:00 2012 said:

I agree with phage434. This pattern you see is exactly what I've seen on the surface of gels that were poured too hot (and not well mixed) by a student in our lab recently.

Also, how much PCR product are you adding, and what is your template? Coz it looks overloaded to me.
Do you add the EtBr to the whole gel? Or to the samples themselves?

Well, yes, it does look somewhat similar to the swirly patterns you get in a gel that's been poured too hot but I'd be concerned about the fact that the sample lanes are lighting up in their entirety. I'm not sure that pouring a gel too hot would cause all that's being seen, You more often get deformations in bands and that's not happening.

Have you tried running PCR product that you know is very good (maybe from a sister lab) and comparing how your gels look?
Have you had someone else pour a gel?

I attached two more gel photos below. The first gel is digested plasmids. We already know if the DNA concentration is too high the bands won't look good, but in here we loaded equal amount of plasmid in each well. The gel looks like a painting of a night with clouds and stars.

The second gel is for different samples: digested pCIneo which is cut from the gel, undigested plasmid, and some other purified PCR products. You can't see the cloud in gel purified PCR samples. But clearly there is something stock in the wells of digested pCIneo.