DesignOfRibocomputingDevices/Fig 8 - Sample NUPACK code for a six-input OR gate RNA.txt at main · AlexGreenLab/DesignOfRibocomputingDevices · GitHub

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# Sample NUPACK Code for a Six-Input OR Gate RNA

material = rna1999
temperature = 37.0
trials = 10

# target structure: six toehold switch structures separated by 12-nt spacers followed by the linker and output gene
structure gate = U3 U12 D9 (U3 D6 U12 U3) U12 U12 D9 (U3 D6 U12 U3) U12 U12 D9 (U3 D6 U12 U3) U12 U12 D9 (U3 D6 U12 U3) U12 U12 D9 (U3 D6 U12 U3) U12 U12 D9 (U3 D6 U12 U3) U50

domain switch_A = GUAAUGAAUUGUAGGCUUGUUAUAGUUAUGAAACAGAGGAGACAUAACAUGAACAAGCCU
domain switch_B = AUAGAUUUGAUGGCUAUUUGUACGUGUUCGAAACAGAGGAGACGAACAAUGACAAAUAGC
domain switch_C = CGAAUAAGACUGAGGCUGGGUAUGGUUAGAAAACAGAGGAGAUCUAACAUGACCCAGCCU
domain switch_D = AUCACUUAUUGUCGUCUUUGUAUGUCUGUAAAACAGAGGAGAUACAGAAUGACAAAGACG
domain switch_E = ACAAAGAUUGGUCGUUUCAUUACCGUUAGAAAACAGAGGAGAUCUAACAUGAAUGAAACG
domain switch_F = AAUUGGAUGAAGGCGGUAAGUAUGAUUGUAAGACAGAGGAGAUACAAUAUGACUUACCGC

#linkers between switch modules
domain linkerA1 = NNNNNNNNNNNN
domain linkerA2 = NNNNNNNNNNNN
domain linkerA3 = NNNNNNNNNNNN
domain linkerA4 = NNNNNNNNNNNN
domain linkerA5 = NNNNNNNNNNNN

domain preG = GGG
domain linker21 = AACCUGGCGGCAGCGCAAAAG
domain output_gene = AUGCGUAAAGGAGAAGAACUUUUCACUGG #first 29 nt of GFP

# thread sequence domains onto target structures
gate.seq = preG switch_A linkerA1 switch_B linkerA2 switch_C linkerA3 switch_D linkerA4 switch_E linkerA5 switch_F linker21 output_gene

# specify stop condition for normalized ensemble defect
gate.stop = 10

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