[Strategy Market] [Switch] Complementary Zipper Style - MS2/FMN Turnon labs

Strategy Intro

This strategy is in courtesy of Nando and Brourd. Nando for his explanations of RNA switch zipping and Brourd for origin of pattern.

I noticed that a specific part of the MS2 hairpin stem very often gets mirrored in the stem of the aptamer gate in MS2 turn on labs and that even something related turns up in the MS2 gate in the microRNA turnon lab. So I suspect that this pattern are going to turn up strongly across turn on labs in general.

Special section in the MS2 hairpin


Greatly reward when the aptamer gate contains this sequence CAUG following reading direction (5’ to 3’) and in both aptamer gate strands.

If aptamer gate is early, reward if this stem sequence is at the first 4 base pairs.

Early aptamer gate

If the aptamer gate is late, reward if the stem sequence is placed like this, at the 2-5 base pairs after the aptamer.

Late aptamer gate

While I do think of this pattern as beneficial, I do not wish to on penalizing the less similarity the design has to this specific pattern, since there are other ways of solving. So I will rather just reward this if present and avoid penalizing if not to not rule out otherwise legal solves.

Strategy background

I have noticed that among the turn on labs, that direct complementarity between MS2 and aptamer gate is often put in play as solving main strategy, to a far bigger degree than in turnoff labs. Exclusion 2 seems to be main exception for now in the turnoff labs, but I expect this lab to get better solves next round, and perhaps lands in a spectrum more close to its peer labs and with less complementarity.

In turn on labs the MS2 don’t need a next door MS2 turnoff sequence, rather they by far prefer sequence around the MS2 that doesn’t pair with itself or anything else. So turnon labs can take a more direct route to complementarity between MS2 and FMN. What they very often do is make 4 identical strands in two stems. Which means the capability of making two different sets of stems - while identical - with strands complementary to each other.

The pattern generally originates from a specific stretch in the MS2 hairpin and getting mirrored on the aptamer gate (the switching end of the aptamer)

Since I caught this pattern in both same state 1, same state 2 and even in the microRNA sensor 208a lab, I consider it of importance. Not all winners contain it, however I have seen it enough times to think of it as a general beneficial as a thing to be rewarded, hence this strategy.

Same State 1: Salish mod of one of Brourd’s designs.

salish99_ss1_r3_093, Score 94%


Same State 2: Salish mod of one of Brourd’s designs

salish99_SS2_r3_015, score 100%


1 Like

Dear Eli Fisker, 

Your strategy has been added to our implementation queue and we should have it completed within the next two to three weeks. You can check the status of the implementation here.

We will also be uploading the code used to write your strategy on this page if you are interested in reading it later.

After implementing your idea, we will post the direct link to the code here. Then, we will optimize the parameters, and test it. At that point, we will tell you the correlation of how good your strategy was and what the new optimized parameters are.

Thanks for sharing your idea!

Vineet Kosaraju
The EteRNA Team

Dear Eli Fisker,

I am pleased to announce that a preliminary version of your strategy has been implemented with 61 lines of code. The code might slightly change in the future to remove bugs, but you can check the current version here. We will soon work on optimizing your parameters and testing the strategy.

Thank you again for sharing your switch strategy!

Vineet Kosaraju
The EteRNA Team