Problems doing Northern Blot with small probes (oligo, riboprobe, PCR and random primed)

[Sharon]

Dear All,

I am having problems doing a Northern Blot with small probes. I am 
able to do a great Northern Blot with a random primed probe that is 
500 bp or longer. However, when I try to do a blot with a 200 bp or 
shorter probe I get no signal. I am using radiolabeled probes. I have 
tried kinased oligo probes, Starfire probes (IDT), riboprobes, PCR'd 
probes and random primed probes. I wonder if the problem is that my 
message is rare and I don't get enough signal - maybe the random 
primed larger probe concatamerizes and increases signal that way, but 
I just don't know. I am using Expresshyb (clontech) or Ultrahyb 
(ambion) with no difference (no signal). When I decrease 
hybridization or washing temperature/stringency I still haven't 
gotten a signal (down to 37C with high stringency (2x SSC) wash 
buffer only. I can't imagine what I'm doing wrong (I expect it's 
something silly and obvious). I would appreciate any advice, 
questions, etc.

Thanks in advance,
Sharon