How do I determine sizes/lengths on Northern blots?

Gys de Jongh Gys_nospam_deJongh at
Wed Jul 16 12:11:01 EST 2003

"Peter Frank" <peter_frankde at> wrote in message
news:bvvahvk4lhdv2odf7nauatejf00cgdlh30 at
> Which is the best method to determine sizes/lengths of RNA bands on
> Northern blots? After all, lengths of RNA marker bands cannot be
> "seen" directly on the blot.
> I can think of two methods:
> * The RNA marker lane is cut off the gel before blotting and stained
> with EtBr and photographed. The relative migration distances are used
> to determine lengths on the blots.
> * In "Molecular Cloning" (Maniatis et al.) they say that RNA can be
> stained on blots by using a special methylene blue solution. So, the
> RNA marker lane could be blotted together with the rest of the gel and
> then the RNA marker lane could be cut off to be stained with methylene
> blue.

methylene blue (do NOT use bromophenol blue!!) is positively charged. It colors
any neg macro molecule , like RNA . You can just dip your BLOT in a methylene
blue solution and take a photograph with your standard equipment using daylight
instead of UV. The washing buffers in the protocol contain SDS which is neg
charged. This soap will remove the pos charged methylene blue very effectively.
So no cutting.
Works great for me.


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