RNA Isolation - Fragmented RNA (Mar/22/2007 )
I've had a bizarre experience with RNA isolation. After isolating RNA from brain in Trizol, i've loaded RNA sample in gel loading dye (Sigma), probably bromophenol blue and xylene cyanol. I've found taht a couple of samples turn green instead of blue when mixed with gel loading solution. These give a prominent smear in agarose gel. Does anybody have any explainations??
Bromphenol blue is an indicator, and you are dramatically changing the pH of the mixed loading dye/RNA. Likely there is some carryover of an acidic compound from the isolation. Add more loading dye, improve your isolation, or neutralize the RNA. I'd guess that the smear is an independent (but possibly related) problem.