[Strategy Market] [Switch] Elements: How to turn off MS2

[vineetsk1]

Original Author: Eli Fisker Original Link: https://getsatisfaction.com/eternagame/topics/-strategy-market-switch-elements-how-to-turn-off-ms2

Intro

I mentioned that EternaBot didn’t always had an idea of which elements in the RNA designs are important and why. How to turn off MS2 effectively is one of them.

Strategy for turnoff labs

• Reward designs where MS2 (with a FMN in front of it at a max 0-2 bases distance), that is followed by a sequence of 4-6 bases that are complementary to a stretch in the MS2.
• Reward designs where MS2 (that has max a 0-2 bases distance from a FMN after it) that is followed by a sequence of 4-6 bases that are complementary to a stretch in the MS2.
• Give +2 if the first base in the turnoff sequence is not complementary to the MS2 base it is “across”, if it is single - like forming a 1-1 loop or if it bind is weak - like forming a GU.
• Give + 1 for each C in this turnoff sequence, up to two.
• Give + 1 for each U in the turnoff sequence, up to two.

Strategy for turnon

For the same state labs, FMN or aptamer gates are used for turnoff.

• Reward if the MS2 bases pairs up with one of the FMN sequences.
• Double reward if they pair up with both FMN’s.
• Also reward if the MS2 C’s pair up with one of the aptamer gates with G’s in it.

(In the mir 208 turnon lab, the majority of the solves behaves as turnoff labs, with turnoff sequence of 8 bp after the MS2.)

Background article

https://getsatisfaction.com/eternagam...

[vineetsk1]

Implemented with 83 lines of code.