RNA gel problems - (Sep/26/2005 )
Hi,
I'm having trouble with my Northern gels. I extracted total RNA from mouse brains using Trizol reagent and am running 30ug on a 1% formaldehyde gel. This has always worked nicely in the past but recently my 18s and 28s bands when visualised under UV are running at different heights relative to the other samples. Any suggestions? I didn't transfer these Northerns as i thought the RNA that I would be probing will also be at different levels 
Hi,
I am not sure what really is your problem.
Is the concentration of RNA accurate?
If ETBR is in your gel, larger amouts of RNA
run faster because they consume more EtBR as
they run in the gel.
Also, if you load 30ug of RNA, the bands
may be too bright and it is hard to tell 18s and 28s
bands. If you want to visualyze total RNA, 1ug is
more than enough.
slab
I am not sure what really is your problem.
Is the concentration of RNA accurate?
If ETBR is in your gel, larger amouts of RNA
run faster because they consume more EtBR as
they run in the gel.
Also, if you load 30ug of RNA, the bands
may be too bright and it is hard to tell 18s and 28s
bands. If you want to visualyze total RNA, 1ug is
more than enough.
slab
I agree. And for a RNA testgel you can leave out the formaldehyde. This will give sharper bands which allows better to compare the amount of RNA.
Just autoclave the agarose and make your equepment RNAse-free with H2O2