| - | Micro RNAs regulate the translation of their target genes by binding to regions in the 3’ UTR that we call miRNA binding sites (ref). This miRNA binding site (BS) consists of a Xbp seed region that is perfectly matched to the miRNA, and surrounding regions that matched partially. The seed region is defined as being the minimal required basepairing at the 5’ end of the miRNA that can regulate the mRNA. Apart from the seed region, binding can be unspecific, creating bulges between miRNA and mRNA (fig). The position and properties of the bulges seem to play a role in miRNA binding and therefore knockdown efficiency. <br>
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| - | One goal of the iGEM Team Heidelberg 2010 was to test the effects of changes in BS sequence and thereby characterize miRNA BS. To standardize our measurements of knockdown according to BS specificity, we had to come up with a new standard that is independent from the endogenous cell machinery. We decided to bring in synthetic miRNAs and engineer BS for them, simulating naturally occurring miRNAs and miRNA BS without having to worry about the effect of endogenous targets. Of course there are also differences that arise through the availability of the enzymes involved in the miRNA pathway that may differ slightly from cell to cell. Therefore, we also measured the knockdown achieved by the perfect binding site and set this as 100% knockdown efficiency. (still, this will not happen in the same cell. Problem??)
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| - | The main idea of our measurement standard, miMeasure, was to express two nearly identical but discernable proteins, one of them tagged with a BS, the other one unregulated. These two reporters were expressed by a bidirectional CMV promoter to make sure their expression rate is identical. We used a stablilized version of GFP, dsGFP by Clontech (ref) and a dsBFP that was derived from the same sequence. Thus, we could make sure that both proteins exhibit the same synthesis and degradation properties, making them directly comparable. We included a BBB standard site into our plasmid, which allows to clone BS behind the GFP. If co-transfected with the corresponding shRNA, GFP will be downregulated, while BFP expression is maintained. The ratio of GFP to BFP expression (measured how?) can be used to conclude the knockdown efficiency (in percent, compared to perfect binding site=100% and no binding site=0%) of the BS. Having destabilized marker proteins with a turnover time of ?hours enables us not only to avoid accumulation of marker proteins, which would make the knockdown harder to observe, but also to conduct time-lapse experiments. In the future, this could be for example a way to observe the activity patterns of endogenous miRNAs (even in vivo… that would be really cool. Is that possible? It would be like, blinking signal? Not in mouse, obviously, but in fish or flies :D)
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