Strategy for MS2/FMN labs
Turnoff labs
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Give +2 for each base, if the FMN sequence involved in the switching is the one closest to the MS2 sequence
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Give +4 for each base, if the FMN sequence involved in the switching is the FMN1 bit.
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Give +2 for each of the twin G’s in the FMN sequence, which pairs up with a C base in the MS2 turnoff sequence.
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Give +1 for each U base in the MS2 turnoff base that is paired with an A base base in the FMN sequence.
Turnon labs
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Give +2 if FMN1 is targeted
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Give +1 if FMN2 is targeted
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Give +4 if both FMN1 and FMN2 is targeted
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Give +1 if aptamer gate (the moving end) is involved in the switch with MS2.
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Give +2 for each MS2 base that pairs up with FMN1 and FMN2
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Give +1 for each MS2 base that pairs with an aptamer gate base. (The aptamer gate being around 4-5 basepairs long)
Background article