Hi Mark

1) Try to make fresh buffers. (TAE+ running buffer)

2) You can try resolving the product in 2% agarose gel. 

I hope it helps

This is the glow of the ethidium bromide in the gel.  EtBr runs in the opposite direction to the DNA.  Given long enough all the EtBr would electrophorese out of the gel

the etbr concentration is way too high. You should dilute your etbr with destilated water.  and then try again from the start. Try 1/10 dilution.

Hi all!

Thanks for helping me. Actually I'm using GR Safe nucelic acid gel stain (http://www.excellgen.com/protocols/GR_Safe_Protocol.pdf) instead of EtBr. According to the protocol I added 2ul directly into the gel before cast.

Based on your advices I decreased the volume to 0,5ul, but still the same. Another strange fact, that the ladder wich runs into the darker part of the gel (out of the strong background) is much fainter then which stays in the "white cloud".

I don't think it's a matter of gel percentage as Rajesh said, because I got the same result with 1% agarose gel before. I always prepare fresh buffer for each running, but to be honest my 50x TAE buffer stock solution (from Lonza) is a bit old (however it was unopend before I started to use, and the solution is clear without any precipitation in it).

Probably I should decrease the amount of the gel stain further and apply shorter running period (~45min). So the background will decrease and the gel stain won't migrate out of the bottom (darker) part of the gel.

Thoughts?

The binding of the stain to the DNA is a dynamic process.  The association/dissociation of the stain with the DNA in a band passing through the part of the gel that still contains the stain will be in equillibrium and the band will glow with a particular intensity.  Once the band passes into a region of the gel without any stain the DNA will only lose stain and therefore intensity under UV.  So it's really just a matter of balancing the background glow (which will always be there if the stain is present) with band intensity.  If you are trying to observe low weight bands either 1) don't run them in the lower part of the gel or 2) place some dye in the running buffer

Dear Mark,

I would suggest checking the concentration of buffer (if the buffer is of 10X concentration then you won't get expected result) and the amount of sample you have loaded onto the gel..!!!

Thank you all for your useful advices, I'll take them all into consideration. With some optimization I hope I can manage to get nicer gel after electrophoresis.  :)

you should dilute the gel stain, try taking 1 ul of the stain and add 9 ul of destilated water, then take 1 ul of the dilution to 25 ul of agarose. 

If you just want consistency in the gel so you can play around with the intensity of the bands, you can always add a little ethidium bromide to the bottom buffer well of the gel running apparatus so it will replenish what runs out of your gel during the electrophoresis (I usually just add a couple microliters). This really helps to get a more consistent background to help with playing with the contrast/brightness. Also, I noticed some of your bands in the top portion of your gel look like they are overlapping with where your dye is running. If you are having trouble seeing your bands, you might want to consider diluting your dye a bit so the dye front isn't obstructing your ability to see the bands you expect or changing the dyes you use in your solution.

The solution was simple!

I ordered a fresh SYBR SAFE DNA gel stain (because what I used for staining was probably a bit old), and since then it's working like a charm. No "clouds", no intensity differences. :)

Once again thank you all for the valuable suggestions!

We just recently experienced this issue in our laboratory, and after considerable troubleshooting, identified the source of the problem as the agarose used to make the gel. While the lot was well within its shelf-life and had just been unsealed, the agarose inside was denser than usual indicating that it had absorbed moisture. Needless to say, we contacted the vendor for replacement.