Agarose gel - (Feb/11/2008 )
I made an 0.7% agarose gel with ethdium bromide. Run gel for 40minutes and took pictures.
I saw that the up part of the picture is very bright and the low part of the picture is so dark that it blocks some bands of the dna.
Does anybody know what happened to my gel?
Were the settings in the camera/imager unchanged? Could you show the gel pic.
EtBr runs to the negative side opposite to DNA. The brightest in the up side is because the EtBr is more concentrated and the bottom side is dark and bands are less brilliant because there are less amount of EtBr.
You can re-stain in EtBr and wash for seen the smaller bands or run a little bit more to see the big bands clearer.
This happens to me as well, the EthBr migrates in the gel.
You can eliminate this problem by adding a few ul of EtBr (or sybrsafe, which is what we use) to the positive buffer reservoir.
I'll try that. Do you not submerge your whole gel in buffer? I don't really have a positive buffer reservoir - just one big reservoir Should I be using less buffer?
Our gels run just barely submerged, so I guess in theory you could say there is one reservoir, but the gel really is between a positive and negative relatively high volume of buffer in two deeper wells.