What type of Northern Blot should be used for smaller transcripts? - (Jun/25/2013 )

I am trying to figure out how to look at RNA transcripts which are between 200-500bp in length. Most protocols are either for full length transcripts, 1-2kbp, or miRNA, ~20bp, and the protocols vary dramatically for these 2 types. Is there a special type of gel I should use for looking at a transcript between these 2 sizes? I was thinking about simply increasing the concentration of my agarose gel and follow the protocol for full lengths transcripts. Anyone have any ideas about whether or not this will work?

Thank you for your help!

Yes, that should work. A 1.5 -2% gel would work in this instance. The protocols for full length vs miRNA only really differ in the probe sizes used. Typically for larger transcripts, probes of about 100 bp or more are used, but you can vary this and alter the annealing temp and times to suit.

Thank you!