[Strategy Market] [Switch] Obligate switching bases versus additional switching bases

I got inspired from the discussion with Omei and Vineet. (See the Strategy on obligate switching base pairs) So I made a new strategy. :slight_smile:

Strategy Intro

Generally I think it smarter to lock up areas of a switch to make it a partial switch, so a smaller area is doing the switching. I think it a more effective way of hitting a winner. This is one of the things I can see EternaBot is lacking in knowledge, when I took a look at its first solves. It has no idea of when it pays better of locking certain sections of the design, in order to control where the switching happens.

Which is the motivation of this strategy. The intention is to get the bot to focus primarily on the main areas of importance - having switching happening specifically in the obligate switching area and then in relation to it. It doesn’t have to involve all of the bases in the obligate switching area, just some.

I wish these obligate switching base pairs/bases to be the majority. There should be far fewer alternative switching bases, than obligate switching bases. The obligate switching bases should be the majority. Else there are too much switching going on elsewhere in the design, that really isn’t necessary. So if main part of the switching goes on outside of the obligate switching area, the switch is making too big and unnecessary changes, and only a minority of these fuller moving switches will make it through to work.


There should be more bases in the obligate switching area involved in active switching, than additional switching bases.

Reward designs that has as low as 1/5 additional switching bases compared to the number of active bases from the obligate switching area. Steadily decrease reward. Start penalize when the amount of additional bases becomes more than half of the amount of obligate switching bases, and penalize heavily when there are more additional switching bases than obligatory switch bases.


Obligate bases (orange) additional switching bases (light blue)


Maximum amount of possible obligatory switching bases are 25. (Turnoff labs) 19 from MS2 and 6 from aptamer closing end. Same state designs can have longer aptamer gates, so perhaps adjustments in the future will be needed for EternaBot between turnoff and turn on labs. They have similar rules in many areas, but different rules in specific cases. Such as same state don’t need a MS2 turnoff, but turnoff labs mostly do. And that aptamer gate length differ between turnoff and turn on.  

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 37 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