Does anyone else have problems with the negative control mimics?
Typically, negative control mimics are designed computationally to have no perfect seed-sequence matches to the transcriptome of the species you work with. Unfortunately, our knowledge of miRNA targeting is so incomplete, they only cover the most basic canonical base pairing. We already know that other bases are important, but no solid rules have as yet been defined. I suspect that due to the interplay with RNA binding proteins and mRNA folding, there may not even EXIST specific all-encompassing rules.
In addition, good R&D companies also perform microarray or RNA-seq experiment following transfection of their negative control candidates. While this screens against obviously bad sequences, there is no guarantee that:
(1) the miRNA does not affect its target only at the translational level, so invisible to microarrays etc.
(2) the specific experimental system is expressing all the potential targeted mRNAs in the first place.
Very few negative mimics are tested on the proteomic level.
What problems exactly are you having? I have seen and resolved quite a bunch, you may be lucky and I could save you some work?
Good luck,
Anna
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