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Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of degrading (or just inactivating) them.

This scenario seems more likely in eukaryotes, as they have capped 5' UTRs and a polyA tail at 3' UTRs that lend to RNA stability. How quickly and how much will an uncapped RNA degrade? What about the lack of a polyA tail?

Since prokaryotes lack these structures, I am restricted to the use of UTR regions in my particular instance. Is there any similar mechanism, whether in general or for specific proteins, that will allow me to exploit a UTR region for RNA inactivation in prokaryotes? Please keep in mind adding synthetic sequences to these UTR regions is certainly a possibility.

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You can use riboswitches. Small RNAs have been shown to affect RNA stability in prokaryotes too but i think they have a stabilizing role in contrary to that of eukaryotes. –  WYSIWYG Sep 6 '13 at 5:45
The polyA tail has a different function in bacteria than in eukaryotes, in bacteria the polyA tail seems to trigger RNA degradation, not prevent it. I've never tried to transform bacteria with mRNA, but I've injected lots of mRNA into mice, and the cap and tail are critical for expression, if they are absent the RNA is usually degraded too quickly to detect protein, at least in my bioluminescent imaging assay. –  user137 13 hours ago

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