So as to try and reduce sequence specific bias design a number of 150 bp probes spread along the length of the RNA. The guidelines for primer design are the same as for any PCR (Tm around 60 deg, no more than 60% GC (though I like to go lower (40-50%) if possible to increase primer length, hence specificity, hence stringency)). I've never generated cDNA from rRNA so as 23s RNA has quite a strong secondary structure you may need to add DMSO ro help amplification though at 150 bp you really shouldn't have too much of a problem.......perhaps someone who HAS done this can advise.

Thank you Marcus for your suggestion.