i m continuousely facing a problem while runnig RNA gel. Problem is that the bands run in opposite direction. I mean when i run the gel both dyes (xylene and bromophenol blue) run along the gel but when i view the gel under UV the bands are in opposite direction (almost at the end of -ve termini and are about to go into buffer). If i run it for longer time they goes out of the gel into the buffer. ( i checked my termini they are always at right position)
I repeated the procedure for several times with fershly isolated RNA. Used DEPC H2O wherever required. used 1.2% agarose and for some times 1.5%
plz tell me is it possible that these orange golden bands in the opposite direction are either RNA or it is only EtBr that is shining.
Another problem that is facing by a friend of mine is :her RNA bands are not resolved into 28s and 18s. Moreover she is using DNA ladder as markers and marker bands are also not resolving (she has no option other than using DNA marker).