From Eterna Wiki


This entry won't develop much into a blog post. I'm just throwing ideas in the context of a discussion I'm having with Brourd about mimics.


1FMN stacking pattern.png Sarcin-ricin stacking pattern.png
FMN Sarcin-ricin (15 nts)


The top half is structurally quite similar, but the bottom differs a bit. Specifically, it is undeniable that the FMN molecule offers a much larger stacking area than the A+A platform in motif IL_85647.3


1FMN stacking pattern.png Sarcin-ricin (reduced) stacking pattern.png
FMN Sarcin-ricin (13 nts)


A possible way to compensate the difference would be to use a reduced form of the loop, with an additional cWW pair, like in motif IL_49493.4



By the way, this canonical pairs mimic...

Mimic 1.png Mimic 2.png

I'm counting -11.9 kcal, much more than the -4.9 that we're supposed to mimic...

I understand that the mimic is only meant to give us an idea of whether a particular switch has a chance to work or not, but overshooting that much will probably give us a lot of false positives...

Mimic 3.png Mimic 4.png

This is much less, ΔG -2.4 kcal, which possibly undershoots a bit, but at least we'd have solid reasons to be more confident that the switches passing that test will actually work with the real FMN experiment.

Mimic 5.png Mimic 6.png
Mimic 7.png Mimic 8.png

Another example, with a predicted ΔG -3.2 or -4.1 kcal, depending on the base pair that precedes.




Based on Brourd's constructs, a few tests we could run:

FMN-Sarcin mimic project 1.png


FMN-Sarcin mimic project 2.png


These are not perfect, but at least, the EteRNA model thinks these folds are even money...

The idea is to compare the stability of the unbound FMN binding site against various sarcin-ricin loops. If the model is correct, the 16-21 and 28-33 segments should display roughly the same SHAPE protection signal, something around 50%. If the hypothesis that the sarcin-loop is nearly as stable as a bound FMN site is correct, a strong difference should be visible between those 2 segments.


FMN-Sarcin mimic project 3.png


It seems easier to stabilize the design when using 5 nts long stems, instead of 6.