Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects

I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the interaction of the MS2 protein to the hairpin placed upstream of a ORF cause any translational repression?

  • $\begingroup$ Why don't you place the MS2L downstream of the ORF? What exactly is the experiment you want to do? $\endgroup$ – Gergana Vandova Feb 25 '14 at 19:45

I assume you are talking about the mTAG visualization technique for mRNAs (1). You are probably familiar with it, but the OFR of interest is tagged with MS2L sequence downstream of it and upstream of the 3'UTR. There is also a modified version, in which you can visualize both the mRNA of interest, and the protein that is translated, see the figure below (2). Haim and colleagues found that yeast expressing mCherry and MS2L tagged ATP2 grew on glycerol-containing media, which would require efficient translation of ATP2.

enter image description here

So I would assume that there is no translational repression if you tag the mRNA downstream of the ORF. Unless you have a very good reason to tag the ORF of interest with MS2 upstream of the start codon, I wouldn't do it, because these stem-loop structures would most probably stall translation, as mRNA secondary structure has been implicated in translation initiation efficiency.

  • $\begingroup$ The idea would actually be to repress translation via the mecahnism that you suggest. Hence, the rationale of putting the MS2 hairpin upstream of the ORF. $\endgroup$ – bobthejoe Mar 3 '14 at 21:07
  • $\begingroup$ Oh I see now... Interesting idea. Worth exploring. Why don't you use Cas9? $\endgroup$ – Gergana Vandova Mar 3 '14 at 21:34
  • $\begingroup$ Probably because I asked this question back in 2012 and was more of a curiosity question rather than an actual experimental question. More specifically, I'm concerned more about generating a tuneable analog type of repression system where you can generate a range of repress rather than perform a complete knockdown using CRISPR. $\endgroup$ – bobthejoe Mar 4 '14 at 23:17

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