[Strategy Market] [Switch] How MicroRNA likes to bind: Turn on labs

Strategy Market Strategy Market - Switches
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Intro

It is not just switches that are different from static designs, also switches involving microRNA are different from the regular MS2/aptamer switch designs. Therefore a specific strategy for turnon microRNA labs.

Strategy

  • Give +1 for each the first 19 of the 22 mir bases that are paired up complementary.

  • Give 1⁄2 if the last 3 are also paired up.

  • Give -1 for each of the base pairings that do not use the strongest possible match (eg a GU when a GC is possible or a GU when an AU is possible. Except at two first and two last of the base pairs from each end of the microRNA. These ends are allowed to pair weaker. So give only 1⁄2 penalty there.

MicroRNA bases that should preferably pair up with the design: All of them! :slight_smile:

Background

The majority solve types have most of the microRNA bound up with a complementary stretch right after the MS2 turnoff sequence. They even solve in an almost identical way when it comes to structure. There is a potential of 22 microRNA bases pairing. The trend is toward the more of them pairing, the better. The 2 state majority solves generally have a MS2 gate (5 base pairs) and then there is the MS2 hairpin. (7 base pairs) 22+5+7=34

The winners seems to have base pairs in a range of 28 to 33 base pairs.

Background articles

https://getsatisfaction.com/eternagam…
https://getsatisfaction.com/eternagam…
https://docs.google.com/document/d/1A…

2 Likes
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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

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Dear Eli Fisker,

I am pleased to announce that a preliminary version of your strategy has been implemented with 45 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