[Strategy Market] [Switch] JL’s microRNA fish hook 2: MicroRNA landing spots

Original Author: Eli Fisker Original Link: https://getsatisfaction.com/eternagame/topics/-strategy-market-switch-jl-s-microrna-fish-hook-2-microrna-landing-spots

Intro

This strategy is courtesy to jandersonlee and based on his superior round 1 microRNA design strategy, that ended hitting through among the majority of the winners in the following round too.

Strategy for Turn on labs microRNA positioning

Give +2 for each base of the full microRNA that pairs up in the space between 6 and 28 bases after the MS2.

Penalize designs that makes the main part of the microRNA bases, pair up before the MS2 sequence into oblivion. :)

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Strategy for microRNA turnoff labs

I wish to reward designs that has each end of the microRNA pair up on each side of the MS2 sequence.

MS2 in early half of the RNA sequence

Give +2 for each base of mir 2 sequence (of the last 8 last bases of the microRNA) that pairs up 8-14 bases before the MS2 sequence. (These 6 bases between MS2 and mir pair up leaves room for the MS2 to get a proper turnoff sequence)

Give +2 for each base of the mir 1 (earliest 11 bases of the mir) that pair up after the MS2 sequence. Region for pair up: The last base of the MS2 sequence and the 11 bases after.

Image: https://lh6.googleusercontent.com/1KiirWzsxteXALEzONfv5eqkywDlh5Eq8uhNhmAJTcxkwoqIl9tzhNx7kwkI3xqbmx60-tDiqZcJYpSHvjzWaUqu8uwa2Syc04FZbmZAyk3VbbO1tDqF8ggrBcO93evR5Jur8A

MS2 in late half of the RNA sequence

Give +2 for each base of mir 2 sequence (of the last 8 last bases of the microRNA) that pairs up 2-14 bases before the MS2 sequence

Give +2 for each base of the mir 1 (earliest 11 bases of the mir) that pair up after the MS2. In the region of 6-8 bases after the MS2. (These 6 bases leaves room for the MS2 to get a proper turnoff sequence) Region for pair up between mir and design 6-19 bases after the MS2

Image: https://lh3.googleusercontent.com/s8EDdmKtk-hDQmDRaceJ9XpGzQ-I03p8lfTkOzXMbyzA8C_PO7F4dYiq6fc01w8OhpwhM2_Ykq7kit9D5CMm9K-ecR5OcIaWjB2VRRUSdBPUOxfeDLojnp2oPYtq-h3LCoBS-g

Background articles

Imagining the microRNA labs

https://getsatisfaction.com/eternagame/topics/johan-s-microrna-lab?topic-reply-list[settings][filter...

vineetsk1 / Switch-Strategies

[Strategy Market] [Switch] JL’s microRNA fish hook 2: MicroRNA landing spots #2