@ Sarang : Indeed EtBr does migrate during the gel run as the molecule is positively charged which means it migrates in the opposite direction compared to DNA. Therefore if EtBr is at first included into the gel, the lower part of the gel tends to stain less after the run because of reduced local concentration of EtBr.

Hi there

To avoid this, prepare and run the gel without any EtBr and then incubate the gel in EtBr containing TBE for 15-30 minutes prior UV illumination.

Hi Thanh

Dominique has nice alternative for staining the gel with EtBr, but I would suggest you to check your EtBr stock and the TBE buffer. Sometimes  over reuse of buffers create such problems. Old EtBr stock solution can cause failed staining result.

Please use freshly prepared TBE for making the gel. Moreover it is highly unlikely that EtBr diffuses out of gel. May be your EtBr stock is very old. In addition to normal EtBr induction you can also do the strategy suggested by Dominique. 

@ Sarang : Indeed EtBr does migrate during the gel run as the molecule is positively charged which means it migrates in the opposite direction compared to DNA. Therefore if EtBr is at first included into the gel, the lower part of the gel tends to stain less after the run because of reduced local concentration of EtBr.

@Dominique : thanks a lot for clarifying my misconception .

Thank you all for your answers. It is much appreciated.

@ Dominique: However, my case is not what you usually experience. The top less stained than the bottom in fact. I don't know what has gone wrong as I have changed to a fresh buffer stock but the problem resists.

Photo of my gel for clarification: https://drive.google.com/file/d/0B9Ff3E00Y3QMekZyWVp3WWg2Zlk/view

According to the DNA ladder on the left there is something wrong with migration: DNA ladder bands have hardly migrated and resolution is poor. And the staining is not bad but the background is pretty high...

Hi Dominique. May be the ladder is not separating properly because I ran it too short a time?

This one I ran it 70V for 60m and the ladder looks nice but EtBr diffused half out of the gel and the positive bands looked blurred, https://drive.google.com/file/d/0B9Ff3E00Y3QMb0VhOEVncUhvV1E/view?usp=sharing

It seems your ladder is running very slow. The distance is very short... With such condition you would expect the front migration to be at least half way through the gel which is obviously not the case. Are you absolutely sure of the composition of the buufer used for gel preparation and for filling the tank? The other issue might be the power supply...