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We had a dream about fully standardized parts

So far all the RBS parts were measured with GFP. We assumed that the strength of RBS is standard – does not depend on the expressed protein. But it turns out that the world is not as perfect as we would like it to be: it was during the 2010 iGEM competition that we came across the first sings that something is wrong. To investigate this problem further, this year we measured several RBS parts with various fluorescent proteins. Unfortunately, we were right.

The Problem
Variances in strength of RBS parts are caused by different mRNA fold. The beginning of every protein influences mRNA fold, which in turn makes the RBS sequence more or less accessible for the ribosome. If the RBS becomes a part of a secondary structure, ribosome is less likely to bind to it and the protein expression is limited or even impossible.