Hello Angelica

The two dark zone may be due to the loading dye (bromophenol blue, xylene cyanol). Try to reduce the concentration of the dye. Also check whether you are getting those zones in a well where you add nothing (just for confirmation).

Hello Angelica

The two dark zone may be due to the loading dye (bromophenol blue, xylene cyanol). Try to reduce the concentration of the dye. Also check whether you are getting those zones in a well where you add nothing (just for confirmation).

i agree with Nithin it is the blue dyes. you could also use orange G dye which is saller and less visible in the gel

In our lab, we are using Midori Green instead of EtBr, and it works great.

Dear Angelica

The two dark zone are the loading dye: 1) bromophenol blue, 2) xylene cyanol

if you change your method or dye concentration can help you.

The tracking dyes cause darkening of the EtBr stained gel, so reduce the conc of both Xylene cyanol and Bromophenol Blue in loading solution. One may stain the gel with EtBr after the run also.

Dear Angelica,

I am in agreement with the other answers. The dark zones are the dyes.  I make my 6X  dye minus the Bromophenol blue and another minus the xylene cyanol.  I then customize the dye used according to the DNA size.  The marker is missing these dark zones, which is due to either less dye being used or a different dye.  I do agree that ethidium bromide runs from negative to positive, but this does not seem to be your problem.

Cheers,

Evelyn Prugar

DNA negatively charged (phosphate GRP), phosphate groups transfers or moves towards positive pole during electrophoresis. This results in appearance of DARK ZONE in the agrose gel when we analyze it (gel) under the UV transilluminator.