How do I determine sizes/lengths on Northern blots?

Peter Frank peter_frankde at
Wed Jul 16 11:56:56 EST 2003

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

Which one is more commonly used? Oddly enough, the papers in which
Northern blots were made use of do not mention how the RNA sizes of
bands on a Northern blot was determined. They just say that certain
RNA markers and/or 18S- as well as 28S-rRNA were used as size markers.
That is why I would like to know how it is usually done.


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