agarose gels

David E Bell bell at mari.acc.stolaf.edu
Mon Jun 21 08:32:10 EST 1993


hi there,

can somebody answer me just in a few words about the following 
thoughts concerning (RNA) agarose electrophoresis:

1)	why is the Maniatis et. al. buffer system for RNA gels based on
	MOPS and not on TRIS ??? the pH of 7.0 should be covered by
	TRIS as well ?

2)	what is/are the main reason(s) for running the RNA in formaldehyde?
	is it just unfolding it's secondary structure or additionally
	prevent RNAase gegradation, or...?

3)	somebody before pointed out to load EtBr together with the samples
	onto the gel. we use EtBr mixed gel for DNA and this works fine.
	since the EtBr is running in the opposite direction (to D/RNA), the
	dye is removed from the nucleic acid the longer the gel runs.
	when i started a gel today a big lane of EtBr was running off the
	gel quickly. is this method still effective after long gels ??
	it seems interesting to load EtBr in the lower buffer tank...

thnaks for any ideas

tom
 







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