In addition to the approaches listed by Dasaradhi above...check also the possibility of using hari-pin primer based qRT-PCR.........but i feel Northern blotting is still very much ...like a gold standard...for small RNA analysis......
We routinely use Real-Time PCR with Taqman probe in our lab, to verify induction or repression of microRNA in various condition. At the biological level, to verify the effect of microRNA we use microRNA mimics and inhibitors. We also use RT-PCR to verify if the microRNA mimics or inhibitors worked properly.
Thanks everybody for the suggestions. Even I am thinking of proceeding with qRT-PCR qith Taqman probe, but I am not sure whether this system is worked out in prokaryotes, as I was not able to find any reference.
Other doubt I have- in the hairpin primers, the stem loop part is designed and commercially available for eukaryotes, but what if I want to design for prokaryotes, any non-specific sequence is enough with similar melting behaviour, or some other strategy is involved for the primer design