def create_design():
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=0, end=16)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=0, end=16)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=16, end=32)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=16, end=32)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=0, end=16)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=0, end=32)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=16, end=32)
scaf = sc.Strand(domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right], is_scaffold=True)
# whole design
design = sc.Design(strands=[scaf, stap_left, stap_right], grid=sc.square)
# deletions and insertions added to design so they can be added to both strands on a helix
design.add_deletion(helix=0, offset=11)
design.add_deletion(helix=0, offset=12)
design.add_deletion(helix=0, offset=24)
design.add_deletion(helix=1, offset=12)
design.add_deletion(helix=1, offset=24)
design.add_insertion(helix=0, offset=6, length=1)
design.add_insertion(helix=0, offset=18, length=2)
design.add_insertion(helix=1, offset=6, length=3)
design.add_insertion(helix=1, offset=18, length=4)
return design
def main():
# helices
helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)]
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=8, end=24)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=8, end=24)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=24, end=40)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=24, end=40)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
stap_right.set_modification_5p(mod.biotin_5p)
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=8, end=24)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=8, end=40)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=24, end=40)
scaf = sc.Strand(domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right], is_scaffold=True)
# whole design
design = sc.DNADesign(helices=helices, strands=[scaf, stap_left, stap_right], grid=sc.square)
# deletions and insertions added to design are added to both strands on a helix
design.add_deletion(helix=1, offset=20)
design.add_insertion(helix=0, offset=14, length=1)
design.add_insertion(helix=0, offset=26, length=2)
# also assigns complement to strands other than scaf bound to it
design.assign_dna(scaf, 'AACGT' * 18)
return design
def main():
ss_f = sc.Domain(helix=0, forward=True, start=0, end=10)
loop = sc.Loopout(length=5)
ss_r = sc.Domain(helix=0, forward=False, start=0, end=10)
hairpin = sc.Strand([ss_f, loop, ss_r])
design = sc.DNADesign(strands=[hairpin], grid=sc.square)
design.assign_dna(hairpin, 'AAAAACCCCCTGCAT')
return design
def create_design() -> sc.Design:
ss_f0 = sc.Domain(helix=0, forward=True, start=0, end=8)
hairpin0 = sc.Loopout(length=5)
ss_r0 = sc.Domain(helix=0, forward=False, start=0, end=8)
crossover_like_loopout = sc.Loopout(length=5)
ss_f1 = sc.Domain(helix=1, forward=True, start=0, end=8)
long_range_loopout = sc.Loopout(length=10)
ss_r2 = sc.Domain(helix=2, forward=False, start=16, end=24)
hairpin2 = sc.Loopout(length=20)
ss_f2 = sc.Domain(helix=2, forward=True, start=16, end=32)
hairpin2_2 = sc.Loopout(length=1)
ss_r2_2 = sc.Domain(helix=2, forward=False, start=24, end=32)
strand = sc.Strand([
ss_f0, hairpin0, ss_r0, crossover_like_loopout, ss_f1,
long_range_loopout, ss_r2, hairpin2, ss_f2, hairpin2_2, ss_r2_2
])
design = sc.Design(strands=[strand], grid=sc.square)
t5 = 'TTTAC'
t10 = 'TTTACTTACG'
t20 = 'TTTTTTTTTTACGTTGCAGG'
design.assign_dna(
strand, f'ACGACGAC '
f'{t5} '
f'???????? '
f'{t5} '
f'GACGACGA '
f'{t10} '
f'CACGACGA '
f'{t20} '
f'???????? '
f'ACGACGAC '
f'T')
return design
def main():
# helices
helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)]
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=8, end=24)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=8, end=24)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=24, end=40)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=24, end=40)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=8, end=24)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=8, end=40)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=24, end=40)
scaf = sc.Strand(
domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right],
is_scaffold=True)
# geometry
geometry = sc.Geometry(rise_per_base_pair=0.2,
helix_radius=1.2,
inter_helix_gap=1.0)
# whole design
design = sc.DNADesign(helices=helices,
strands=[scaf, stap_left, stap_right],
grid=sc.square,
geometry=geometry)
# deletions and insertions added to design are added to both strands on a helix
design.add_deletion(helix=1, offset=20)
design.add_insertion(helix=0, offset=14, length=1)
design.add_insertion(helix=0, offset=26, length=2)
# also assigns complement to strands other than scaf bound to it
design.assign_dna(scaf, 'AACGT' * 18)
return design
def add_hairpins(design, hairpin_locations, hairpin_lattice):
"""Given the design, the hairpin lattice, and the hairpin locations, adds the hairpins to the hairpin lattice and crossovers to the seed"""
seed_domain = range(len(hairpin_locations))
hairpin_domain = range(len(hairpin_locations),
len(hairpin_locations) + len(hairpin_lattice))
#creates the hairpins, included the loopout crossover
for i in range(len(hairpin_domain)):
helix = hairpin_domain[i]
for j in range(len(hairpin_locations[helix - len(seed_domain)])):
left_offset = hairpin_locations[helix - len(seed_domain)][j]
right_offset = left_offset + 8
index = 6 * (i - 1) + j
pin_seq = non_random_hairpin_sequence(index)
staple = sc.Strand([
sc.Domain(helix=helix,
forward=True,
start=left_offset,
end=right_offset),
sc.Loopout(length=4),
sc.Domain(helix=helix,
forward=False,
start=left_offset - 2,
end=right_offset)
],
dna_sequence=pin_seq)
design.add_strand(staple)
#add nicks on staple strands to be able to connect the hairpins
for helix in seed_domain:
forward = sc_general.forward_strand(helix, 'staple')
for nick in hairpin_locations[helix]:
design.add_nick(helix=helix, offset=nick, forward=forward)
#crossovers between the main helices and the hairpins
crossovers = []
for helix in seed_domain:
helix2 = hairpin_domain[helix]
forward = sc_general.forward_strand(helix, 'staple')
for pin in hairpin_locations[helix]:
if forward == True:
forward_pin_offset = pin - 1
reverse_pin_offset = pin
else:
forward_pin_offset = pin
reverse_pin_offset = pin - 1
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=forward_pin_offset,
offset2=pin,
forward=forward,
forward2=True,
half=True))
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=reverse_pin_offset,
offset2=pin - 2,
forward=forward,
forward2=False,
half=True))
design.add_crossovers(crossovers)
def main():
helices = [
sc.Helix(max_offset=64),
sc.Helix(max_offset=64),
sc.Helix(max_offset=64)
]
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=0, end=16)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=0, end=16)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=16, end=32)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=16, end=32)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=0, end=16)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=0, end=32)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=16, end=32)
scaf = sc.Strand(
domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right],
is_scaffold=True)
ss_extra1 = sc.Domain(helix=1, forward=True, start=32, end=48)
ss_extra2 = sc.Domain(helix=1, forward=True, start=48, end=64)
ss_extra3 = sc.Domain(helix=2, forward=False, start=32, end=48)
ss_extra1b = sc.Domain(helix=1, forward=False, start=32, end=48)
ss_extra2b = sc.Domain(helix=1, forward=False, start=48, end=64)
ss_extra3b = sc.Domain(helix=2, forward=True, start=32, end=48)
ss_extra4 = sc.Domain(helix=2, forward=True, start=16, end=32)
ss_extra5 = sc.Domain(helix=2, forward=True, start=0, end=16)
s_extra1 = sc.Strand(domains=[ss_extra1])
s_extra2 = sc.Strand(domains=[ss_extra2])
s_extra3 = sc.Strand(domains=[ss_extra3])
s_extra4 = sc.Strand(domains=[ss_extra4])
s_extra5 = sc.Strand(domains=[ss_extra5])
s_extra1b = sc.Strand(domains=[ss_extra1b])
s_extra2b = sc.Strand(domains=[ss_extra2b])
s_extra3b = sc.Strand(domains=[ss_extra3b])
# whole design
design = sc.DNADesign(helices=helices,
strands=[
scaf, stap_left, stap_right, s_extra1, s_extra2,
s_extra3, s_extra4, s_extra1b, s_extra2b,
s_extra3b, s_extra5
],
grid=sc.square)
# deletions and insertions added to design so they can be added to both strands on a helix
design.add_deletion(helix=0, offset=11)
design.add_deletion(helix=0, offset=12)
design.add_deletion(helix=0, offset=24)
design.add_deletion(helix=1, offset=12)
design.add_deletion(helix=1, offset=24)
design.add_insertion(helix=0, offset=6, length=1)
design.add_insertion(helix=0, offset=18, length=2)
design.add_insertion(helix=1, offset=6, length=3)
design.add_insertion(helix=1, offset=18, length=4)
# DNA assigned to whole design so complement can be assigned to strands other than scaf
design.assign_dna(scaf, 'AACT' * 18)
design.assign_dna(s_extra1, 'AACT' * 4)
design.assign_dna(s_extra2, 'GGTA' * 4)
return design
