def assign_dna_to_unzipper_toeholds(design: sc.Design) -> None:
uz_toes = [sc.wc(seq) for seq in uz_toes_wc]
strands_h1 = design.strands_starting_on_helix(1)
strands_h1.sort(key=lambda _strand: _strand.first_domain().offset_5p())
strands_h1.reverse()
strands_h18 = design.strands_starting_on_helix(18)
strands_h18.sort(key=lambda _strand: _strand.first_domain().offset_5p())
for strand, toe in zip(strands_h1 + strands_h18, uz_toes):
seq = toe + sc.DNA_base_wildcard * (strand.dna_length() - 8)
design.assign_dna(strand, seq)
def add_tiles_and_assign_dna(design: sc.Design) -> None:
# left tiles
left_left = 11
left_right = 32
for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
bot_helix = top_helix + 1
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=left_left,
end=left_right)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=left_left,
end=left_right)
idt = sc.IDTFields(name=f'tile-left-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
tile = sc.Strand(domains=[ss_bot, ss_top],
color=sc.Color(0, 0, 0),
idt=idt)
design.add_strand(tile)
design.assign_dna(tile, seq)
# right tiles
right_left = 480
right_right = 501
for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
bot_helix = top_helix + 1
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=right_left,
end=right_right)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=right_left,
end=right_right)
idt = sc.IDTFields(name=f'tile-right-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
tile = sc.Strand(domains=[ss_bot, ss_top],
color=sc.Color(0, 0, 0),
idt=idt)
design.add_strand(tile)
design.assign_dna(tile, seq)