RNA electrophoresis - (Feb/18/2009 )
When I perform RNA electrophoresis in a standard formaldehyde agarose gel, I often observe uneven distribution of rRNA band intensity across the gel lanes. These bands are much more intense at the edges than in the centre of the lanes. Please see the attached gel picture. Kate
Are these different RNA samples? The difference across different lanes are likely due to different RNA yield or concentration of the different preps. Are you asking why there is a line breaking up the band? Could it be possible that the teeth of your comb make two wells within one well?
If you ask why RNA only appear at edge of each lane/well, I think it may due to your gel.
Are you sure your gel completely solidify?
When extraction did you use carrier to bring down RNA? if your carrier cannot move well in gel it will make RNA run in strange way.
How much RNA you load into your well?
If you just want to see is RNA OK or not, 0.8% regular agarose gel will do fine.
There are 6 samples of Triticale in 2 concentrations (left and right on the picture). I'm sure, that everything was allright with the comb. Problem is, as you've sad, a line breaking up the band.