DesignOfRibocomputingDevices/Fig 4 - Sample NUPACK code for the AND-computing toehold switch type I.txt at main · AlexGreenLab/DesignOfRibocomputingDevices · GitHub

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#Sample NUPACK Code for the AND-Computing Toehold Switch (ACTS) Type I

material = rna1999
temperature = 37.0
trials = 10

# target structures

structure switch = U3 U16 D12 (U3 D6 U14 U3) U50
structure target = U3 D8 U6 U3 U28 U3 U47
structure complex = U3 D8 U6 U3 D28 (U3 U47 + U3) U6 U12 U14 U12 U50

# sequence domains
domain T7_term = UAGCAUAACCCCUUGGGGCCUCUAAACGGGUCUUGAGGGGUUUUUUG
domain linker21 = AACCUGGCGGCAGCGCAAAAG

#first 29 nt of GFP
domain output_gene = AUGCGUAAAGGAGAAGAACUUUUCACUGG

domain preG = GGG
domain targ_stem = N8
domain targ_loop = N6
domain targ_spacer1 = N3
domain targ_spacer2 = N3

domain toehold = N16
domain stem1 = N12
domain stem2 = N3
domain stem3 = NNNNNN
domain loop  = NNNAACAGAGGAGA
domain stem2_star = AUG #start codon

switch.seq = preG toehold stem1 stem2 stem3 loop stem3* stem2_star stem1* linker21 output_gene
target.seq  = preG targ_stem targ_loop targ_stem* targ_spacer1 stem1* toehold* targ_spacer2 T7_term
complex.seq = preG targ_stem targ_loop targ_stem* targ_spacer1 stem1* toehold* targ_spacer2 T7_term preG toehold stem1 stem2 stem3 loop stem3* stem2_star stem1* linker21 output_gene

# specify stop conditions for normalized ensemble defect
# Stop condition is increased to 10 to accommodate terminator
# and output gene non-ideal secondary structure

switch.stop = 10
target.stop = 10
complex.stop = 10

#
# prevent sequence patterns
#

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