gel analysis of large RNA products - (Dec/28/2004 )
I have a large RNA (~6kb) comes from in vitro transcription and labeled with 32P. I runned it by polyacrylmide gel, however, I found that it still stayed in the sample well after I runned at 10mA for 3 h. I also tried to run it on agrose gel and transfer then exposured to x-ray film but without any luck. Did anyone have experience to deal with such large RNA before? What is the best way to visualize it? Thanks.
Did you use formamide-containing agarose gel?
Try etanol precipitation before loading, it is possible that something prevent RNA motility
Thanks for your kindly reply. I do use the 4% denatured gel. But the bands above 5000 bp of my RNA ladder also stayed in the sample well. Do you think use acrylamide-agrose gel would be helpful? Thanks
Please indicate all conditions of the electrophoresis you perform. May be agarose was too concentrated?