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?
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.
Before DNA sequencing was used to deduce the sequence of cloned or reverse-transcribed RNA molecules, slower and more cumbersome direct sequencing of RNA was performed using the method of Sanger et al. (Sanger, F., Brownlee, G. G. and Barrel B. G. (1965) J. Mol. Biol. 13, pp. 373–398). This used ribonucleases in a manner somewhat similar to pre-Edmann protein sequencing.
Because of its abundance and ease of purification ribosomal RNA was a suitable species for this approach, and Carbon et al reported the complete sequence of E. coli 16S rRNA in 1978 (Carbon P., Ehresmann C., Ehresmann, B. and Ebel J.P. (1978) FEBS Letters 94, pp. 152-156).
Sigh! How little do modern molecular biologists know about the history of their subject.