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As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any factors to consider when introducing eukaryotic RNA in prokaryotes? Is it possible to predict the proper shape and folding upon introduction to a prokaryotic cell?

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Interesting question. Ionic concentrations and temperature will certainly affect RNA folding. There may well be other constraints as well. –  terdon Jul 18 '13 at 17:41
    
RNA chaperones will be different as well. I'm not sure how much the relevant ion concentrations vary, but Mg concentration is certainly a very important factor in RNA folding. And are you asking about secondary or tertiary structure by the way? –  Mad Scientist Jul 18 '13 at 18:11
    
@MadScientist, in my specific case I was more interested in secondary structure, but an answer addressing tertiary would be ideal –  LanceLafontaine Jul 19 '13 at 14:23
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