Do the static stem in the switching area have a function?
Back in the early Riboswitch labs I made an observation that a static stem would turn up in a huge amount of the winners. I started to speculate about that the static stem was necessary. That it had a function on its own.
For background see the section No Static Stem.
Particularly in the Exclusion NG 2 lab did this stand out. In our lastest riboswitch lab (101), roughly 95% of all the winners have the static stem right next to the aptamer gate.
http://www.eternagame.org/game/browse/6369184/?filter1_arg1=6456051&filter1=Id&filter1_arg2=…
I ended up doing some experiments, where the space for the static stem got deleted. All designs I did this to across labs, ended up with a lower score than the original designs except in one case.
Here are the two small loop labs that are equivalent to the Exclusion NG 2 lab. All these designs are based on winning Exclusion NG 2 designs, but without space for and the sequence of the static stem. They all took a score hit.
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Omei’s insight + mine = Is the Static Stem in the switching area doing Coaxial stacking?
What I’m really interested in now is getting something specific tested.
Omei has earlier brougth up that stems when being next to a sequence that would bind up with an outside input, were doing coaxial stacking and helping the input bind with the sequence next to the
static stem.
Intro to flush stacking energy
I have started to wonder if not the static stem in the switching area of a riboswitch, when next to the aptamer or MS2 is doing coaxial stacking.
Combining these two ideas
- Static stems are (often) necessary in the switching area
- A coaxial stacking aids the binding of the sequence next to it
And it would pretty much make sense that static stems do have a function.
Static stems seem necessary at specific spots and those specific spots are somewhere where coaxial stacking will help the fold.
Potentially allowing for a coaxial stacking of the static stem with the aptamer gate and as such potentially aiding the bind of the FMN molecule.
The Nature of Static Stems
I basically think static stems are a bit like mushrooms. If there are enough bare soil, more will pop up. So if there are excess bases not in use or needed for the switching area itself, a static stem will come in handy.
If there aren’t excess bases, a static stem isn’t needed. If there are lots of excess bases, more static stems are needed.
I also think that if there is space for two shorter static stems, that they will be better than one real long static. Basically RNA seems to not be too happy about all too long stems. Unless some GU or mismatches are stuck into them. Also if coaxial stacking is occouring, then two static stems would mean two energy bonuses. 
Additional experiment proposals
While I have gotten closer to have my experimental starter designs put up, I realized that in some labs, the aptamer took so much place or the switch elements were placed in such a way, that I can only run 1 out of 4 experiments. Thus I have 90 slots to spend for other experiments.
What I’m thinking of is to use them on a design with 1 static stem. And do something like change the position of the static stem, so it in 30 designs will be next to the aptamer gate, in 30 be next to the MS2 and in the last 30 be inbetween.
It could also be interesting having frequency experiments where the static stem gradually gets moved between being next to the aptamer gate to being next to the MS2. In a systematic manner. Like the ones Omei has done and I show in this intro to using eterna spreadsheets.
In particular in the CRISPR/FMN NG labs, this should be interesting to test as we can literally stick in past winners. And then move around the static stem.
Get creative…
