DesignOfRibocomputingDevices/Fig 6 - Sample NUPACK code for a four-input AND RNA network.txt at main · AlexGreenLab/DesignOfRibocomputingDevices · GitHub

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#Sample NUPACK Code for a Four-Input AND RNA Network

material = rna1999
temperature = 37.0
trials = 10

#ACTS_TypeI_N2 switch with extended loop domain, which does not include GFP
domain switch = GGGAUCUAUGUUCAAUUCUAUUCGUCGUCUCAUGAGUAUAGGAGCCGAAACAGUAAACA
        GAGGAGAUAUACUAUGGAGACGACGAAUAACCUGGCGGCAGCGCAAAAG
#ACTS_TypeI_N2 trigger:   GGGACCGGUCUUUGCAGAGACCGGUGUA GAGACGACGAAUAGAAUUGAACAUAGAU AAG
#              structure: ...(((((((((....)))))))))... [   switch binding region  ] ...

#L00 contains the reverse complement of the 5' half of the trigger. The sequence should
#appear in the switch.
domain L00 = NNN CUAUUCGUCGUCUC
domain L01 = NNNNNNNNNNNNNNNNNNNNN
domain L02 = NNNNNNNNNNNNNNNNNNNNN
domain L03 = NNNNNNNNNNNNNNNNNNNNN
domain L04 = NNN AAUUGAACAUAGAU #This is the 3' half of the trigger
# 3-nt spacers are added on to the half trigger domains in L00 and L04 to facilitate
# binding of multi-input multi-arm junction complex to the switch

structure input_01 = U38
structure input_02 = U42
structure input_03 = U42
structure input_04 = U38
structure complex_01_04 = U38+U38
structure complex_01_02 = U17 D21 + U21
structure complex_02_03 = U21 D21 + U21
structure complex_03_04 = U21 D21 + U17
structure hcomp_02 = U18 D13 (U3 D6 U26 U3) U20 + U42
structure hcomp_03 = U18 D13 (U3 D6 U26 U3) U20 + U42

input_01.seq = L00* L01
input_02.seq = L01* L02
input_03.seq = L02* L03
input_04.seq = L03* L04
complex_01_04.seq = L00* L01 L03* L04
complex_01_02.seq = L00* L01 L01* L02
complex_02_03.seq = L01* L02 L02* L03
complex_03_04.seq = L02* L03 L03* L04

#add switch+input complexes as necessary to specify that particular inputs should not
# interact with the switch
hcomp_02.seq = switch L01* L02
hcomp_03.seq = switch L02* L03

input_01.stop = 1
input_02.stop = 1
input_03.stop = 1
input_04.stop = 1
complex_01_04.stop = 1
complex_01_02.stop = 1
complex_02_03.stop = 1
complex_03_04.stop = 1
hcomp_02.stop = 1
hcomp_03.stop = 1

prevent = AAAA, CCCC, GGGG, UUUU, KKKKKK, MMMMMM, RRRRRR, SSSSSS, WWWWWW, YYYYYY