[Strategy Market] [Switch] Base pair difference between states for MS2/FMN switches


Another thing that matters a great deal for how easy it is to make a switch switch well, is that there isn’t too big a difference in the amount of base pairs per state.

Switch designs that have a very big difference in numbers of base pairs between states, are generally harder to solve. Meaning that it is generally easier to solve a switch by making a smaller and partial switch than making all the base pairs switch between states. It is more typical for the bots to solve as full moving switches, because they don’t know, when to make tail bases pair up, how to make the one end of the aptamer stable or make the stem long enough for it to be stabilizing.


Reward designs that keeps the amount of switching base pairs not too different between states.

  • Give + 3 to designs that has less than 5% difference in amount of base pairs between the states

  • Give + 2 to designs that has less than 10% difference in amount of base pairs between the states

  • Give +1 to designs that has less than 15 % difference in amount of base pairs between the states  

  • Start penalize for designs that has a bigger than 15% difference in amount of base pairs between the states and penalize increasingly.

This goes for both turn on and turnoff labs. Either state included.

MicroRNA’s are excluded since they obviously :slight_smile: needs a big difference of switching base pairs between states, due to need to switch between no microRNA in one state and pairing up with most of a 22 nucleotide long sequence in next.

Background article

Different types of switches

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 then 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 12 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