The focus of this post will be about bases 20 and 44 in the 1st state.
Base 20
Base 44
As can be seen by the SHAPE data, both bases tend to be shown as protected in the 1st state for many of the designs. It is true that as long as a base shifts 0.1, it will score a full point. However, it is easier for a base to score a full point if it has not already in the state it is supposed to be when the molecule is introduced. Plus, if a design has only one base shifting the 0.1, that means the complementary base in the pair will not get a full point.
This data contributes to the ultimate conclusion that the 2nd state or a similar intermediary shape may be forming before the molecule is introduced, and not the multiloop we want.
Base 20
Base 44
As can be seen by the SHAPE data, both bases tend to be shown as protected in the 1st state for many of the designs. It is true that as long as a base shifts 0.1, it will score a full point. However, it is easier for a base to score a full point if it has not already in the state it is supposed to be when the molecule is introduced. Plus, if a design has only one base shifting the 0.1, that means the complementary base in the pair will not get a full point.
This data contributes to the ultimate conclusion that the 2nd state or a similar intermediary shape may be forming before the molecule is introduced, and not the multiloop we want.
Posted 7 years ago
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