How do I determine sizes/lengths on Northern blots?

Michael L. Sullivan mlsulliv at
Wed Jul 16 14:02:37 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 usually run my Northerns with EtBr in the gel, so it's already 
stained after the run.  I then poke the gel with a pasture pipette at 
the position of each marker band.  Following blotting the gel (and 
before separating the gel and the membrane, you can flip the 
gel/membrane combo so the gel side is up and run your finger over the 
gel surface which will reveal the places you poked the gel.  You can 
use a pencil to mark the position of each marker hole you made in the 
gel onto the membrane.  Post hybridization and imaging, you can line 
up the blot with the film or image and estimate the sizes of your 
bands of interest.


Michael L. Sullivan, Ph.D
Research Plant Molecular 
U.S. Dairy Forage Research Center
1925 Linden Drive West
Madison WI, 53706

(608) 264-5397 Phone
(608) 264-5147 Fax

More information about the Methods mailing list