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

[vineetsk1]

Original Author: Eli Fisker Original Link: https://getsatisfaction.com/eternagame/topics/-strategy-market-switch-how-microrna-likes-to-bind-turn-on-labs

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! :)

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...

[vineetsk1]

Implemented with 45 lines of code.