FMN Switch 2.0 Thoughts Pt 1

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  • Updated 7 years ago
In the next few forum posts, I will post my thoughts about the results of the 2 rounds for the FMN Switch 2.0 lab puzzle we have so far. To start off, here are some screenshots of the results.





The focus of this first part will be on base pair 13-57 in the 1st state.



In most of the synthesized designs so far, base 13 is blue, indicating that it is protected and a part of a base pair, yet, base 57 in all but 9 of the designs, is yellow, indicating that it is accessible. This means that this base is not a part of the pair that is supposed to form at 13-57.

Since we have no data for bases 58-60, we assume that since the bases across from it are blue, that this means those bases are pairing as well. However, if base number 57 is any indication of that stack in the 1st state, it would appear that bases 10-12 may instead be pairing with their complementary bases from the 2nd state, and that the base at 13 could be interacting with the base at 51.

In terms of scoring, this base does not matter in the end, for as long as there is a shift of 0.1 in the SHAPE data, it recieves a full point. However, in most designs, this base does not shift to a lighter color in the 2nd state, therefore, it does not get a point. In addition, while it may not matter in the end if one base does not get a point, I believe that this base not being protected is indicative of the 2nd state forming 1st, or a state similar to the 2nd.

In the next few posts, I will point out other patterns in the SHAPE data that suggest it may be the 2nd state forming 1st in manyof the synthesized designs.
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Brourd

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Posted 7 years ago

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