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Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli, suggests that it uses DNA to find the sequence. Would it be possible to isolate the rRNA and derive the sequence from that?

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I’m venturing a guess: probably not, due to the complex tertiary structure. I’ve just had a discussion today where it was mentioned that this is actually done for some small ncRNAs but that it isn’t done for tRNA (which is an ncRNA) due to its structure. –  Konrad Rudolph Jul 19 '12 at 12:31
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As far as I know it'spossible to reverse transcribe a rRNA gene, you may not get the best yields though. The secondary / tertiary structures will be a problem, however, there are reverse transcriptase's commercially available that can handle secondary structure: Thermo-X™ Reverse Transcriptase from Invitrogen or Sensiscript™ from Qiagen.

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Weirdly enough, Thermo-X is discontinued according to the website … –  Konrad Rudolph Jul 20 '12 at 12:55
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@KonradRudolph: Oh perhaps these can be used as alternatives then Thermoscript or Affinity Script –  GWW Jul 21 '12 at 20:27
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