PCR primers for ribosomal RNA

Tracy Aquilla aquilla at salus.med.uvm.edu
Tue Jun 14 17:24:00 EST 1994


In Article <mohanish.1.0013731B at pharmdec.wustl.edu>,
mohanish at pharmdec.wustl.edu wrote:
>Hi,
>I wanted to design PCR primers for amplifying all four ribosomal RNAs from 
>rat. Does anyone have any suggestions regarding sites, potential secondary 
>str. problems or optimal PCR conditions for such analysis?
>
>Thanks,
>Mohanish

Hi Mohanish,
    I think you have a very challenging problem. I have designed oligo
probes from rat rRNA before, and the problem is the repetetive nature of
these RNAs. It is difficult to find highly specific primers, although not
impossible. I suggest using a good computer program to help design your
primers (Oligo by NBI is the best) and making them as long as you can. Good
luck.
                                                        Tracy
Tracy Aquilla, Post-doctoral Research Associate
Department of Molecular Physiology and Biophysics
University of Vermont, College of Medicine
aquilla at salus.med.uvm.edu



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