If the backbone is flexible enough, the thought goes, it can wiggle around to get into the right position to interact with the SHAPE probe if the the backbone is being held rigidly, the SHAPE probe can not get access to the reaction site. So when we interpret the lab data, we are actually making inferences about the configuration of the backbone.Īs a first approximation, the generally accepted explanation is that the rate at which the SHAPE chemical (or SHAPE probe, as it is often called) reacts at each base is an indication of how flexible the backbone is at that base.
The Nucleic Acid base itself (A, U, G or C) plays no role in the chemical reaction. The data we get back from the lab (the SHAPE data) comes from measuring the rate at which the SHAPE chemical (specifically 1-methyl-7-nitroisatoic anhydride, or 1M7) interacts with the backbone at each base position. In the lab, though, the situation is very different. That is, you can mutate any base that hasn't been "locked", but you can't actually move a given base to a different position in the puzzle. The backbone has minimal significance for Eterna puzzles, where its only role is to "string together" the bases. The Significance of the Backbone in Eterna
4 Backbone Units: Nucleotides versus Suites.2 Specifying the Backbone Configuration: Torsion Angles.
1 The Significance of the Backbone in Eterna.
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