def add_scaffold_crossovers(design: sc.DNADesign):
crossovers = []
# scaffold interior
for helix in range(1, 23, 2):
crossovers.append(
sc.Crossover(helix1=helix,
helix2=helix + 1,
offset1=152,
forward1=False))
# scaffold edges
for helix in range(0, 23, 2):
crossovers.append(
sc.Crossover(helix1=helix,
helix2=helix + 1,
offset1=8,
forward1=True,
half=True))
crossovers.append(
sc.Crossover(helix1=helix,
helix2=helix + 1,
offset1=295,
forward1=True,
half=True))
design.add_crossovers(crossovers)
def add_precursor_staples(design: sc.DNADesign):
staples = [
sc.Strand(
[sc.Domain(helix=helix, forward=helix % 2 == 1, start=8, end=296)])
for helix in range(24)
]
for staple in staples:
design.add_strand(staple)
def add_staple_crossovers(design: sc.DNADesign):
for helix in range(23):
start_offset = 24 if helix % 2 == 0 else 40
for offset in range(start_offset, 296, 32):
if offset != 152: # skip crossover near seam
design.add_full_crossover(helix1=helix,
helix2=helix + 1,
offset1=offset,
forward1=helix % 2 == 1)
def add_toeholds_for_seam_displacement(design: sc.DNADesign):
for helix in [2, 17]:
staples_5p = design.strands_starting_on_helix(helix)
# remove scaffold
staples_5p = [st for st in staples_5p if len(st.domains) <= 3]
staples_5p.sort(key=lambda stap: stap.offset_5p())
for stap_5p in staples_5p:
toe_ss = sc.Domain(helix=1 if helix == 2 else 18, forward=helix == 2,
start=stap_5p.first_domain().start, end=stap_5p.first_domain().end)
design.insert_domain(stap_5p, 0, toe_ss)
def add_deletion_in_range(design: sc.DNADesign, helix: int, start: int, end: int, deletion_offset: int):
#Inserts deletion somewhere in given range.
#`offset` is the relative offset within a column at which to put the deletions.
#If negative, chooses first available offset.
candidate_offsets = []
for candidate_deletion_offset in range(start, end):
if valid_deletion_offset(design, helix, candidate_deletion_offset):
candidate_offsets.append(candidate_deletion_offset)
if len(candidate_offsets) == 0:
raise ValueError(f"no pair of Substrands found on Helix {helix} "
f"overlapping interval [{start},{end})")
if deletion_offset < 0:
# pick offset furthest from edges of interval
candidate_offsets.sort(key=lambda offset: min(offset - start, end - offset))
deletion_absolute_offset = candidate_offsets[0]
else:
deletion_absolute_offset = start + deletion_offset
design.add_deletion(helix, deletion_absolute_offset)
def add_domains_for_barrel_seam(design: sc.DNADesign):
top_staples_5p = design.strands_starting_on_helix(0)
top_staples_3p = design.strands_ending_on_helix(0)
bot_staples_5p = design.strands_starting_on_helix(15)
bot_staples_3p = design.strands_ending_on_helix(15)
# remove scaffold
top_staples_5p = [st for st in top_staples_5p if len(st.domains) <= 3]
top_staples_3p = [st for st in top_staples_3p if len(st.domains) <= 3]
bot_staples_5p = [st for st in bot_staples_5p if len(st.domains) <= 3]
bot_staples_3p = [st for st in bot_staples_3p if len(st.domains) <= 3]
top_staples_5p.sort(key=lambda stap: stap.offset_5p())
top_staples_3p.sort(key=lambda stap: stap.offset_3p())
bot_staples_5p.sort(key=lambda stap: stap.offset_5p())
bot_staples_3p.sort(key=lambda stap: stap.offset_3p())
for top_5p, top_3p, bot_5p, bot_3p in zip(top_staples_5p, top_staples_3p,
bot_staples_5p, bot_staples_3p):
ss_top = sc.Domain(helix=0,
forward=False,
start=top_5p.first_domain().end,
end=top_3p.last_domain().start)
ss_bot = sc.Domain(helix=15,
forward=True,
start=bot_3p.last_domain().end,
end=bot_5p.first_domain().start)
design.insert_domain(bot_5p, 0, ss_top)
design.insert_domain(top_5p, 0, ss_bot)
def add_angle_inducing_insertions_deletions(design: sc.DNADesign):
# insertion followed by deletion
start = 59
end = start + (32 * 12)
for helix in [1, 5, 7, 11, 13]:
for offset in range(start, end, 32):
design.add_insertion(helix, offset, 1)
design.add_deletion(helix, offset + 16)
# deletion followed by insertion
for helix in [2, 4, 8, 10, 14]:
for offset in range(start, end, 32):
design.add_deletion(helix, offset)
design.add_insertion(helix, offset + 16, 1)
def move_top_and_bottom_staples_within_column_boundaries(design: sc.DNADesign):
top_staples = design.strands_starting_on_helix(0)
bot_staples = design.strands_starting_on_helix(15)
bot_staples.remove(design.scaffold)
for top_staple in top_staples:
current_end = top_staple.domains[0].end
design.set_end(top_staple.domains[0], current_end - 8)
for bot_staple in bot_staples:
current_start = bot_staple.domains[0].start
design.set_start(bot_staple.domains[0], current_start + 8)
def valid_deletion_offset(design: sc.DNADesign, helix: int, offset: int):
domains_at_offset = design.domains_at(helix, offset)
if len(domains_at_offset) > 2:
raise ValueError(f'Invalid DNADesign; more than two Substrands found at '
f'helix {helix} and offset {offset}: '
f'{domains_at_offset}')
elif len(domains_at_offset) != 2:
return False
for ss in domains_at_offset:
if offset in ss.deletions:
return False # already a deletion there
if offset in (insertion[0] for insertion in ss.insertions):
return False # already an insertion there
if offset == ss.start:
return False # no 5' end
if offset == ss.end - 1:
return False # no 3' end
return True
def add_crossovers(design: sc.DNADesign):
# staples interior
for offset in range(84, 1246, 42):
design.add_full_crossover(helix=0,
helix2=1,
offset=offset,
forward=False)
design.add_full_crossover(helix=3,
helix2=4,
offset=offset,
forward=True)
for offset in range(56, 1246, 42):
design.add_full_crossover(helix=1,
helix2=2,
offset=offset,
forward=True)
design.add_full_crossover(helix=4,
helix2=5,
offset=offset,
forward=False)
for offset in range(70, 1246, 42):
design.add_full_crossover(helix=2,
helix2=3,
offset=offset,
forward=False)
design.add_full_crossover(helix=5,
helix2=0,
offset=offset,
forward=True)
for offset in range(49, 1245,
42): # extra crossovers 5 - 0 for some reason
design.add_full_crossover(helix=5,
helix2=0,
offset=offset,
forward=True)
# staples edges
design.add_half_crossover(helix=0, helix2=1, offset=42, forward=False)
design.add_half_crossover(helix=3, helix2=4, offset=42, forward=True)
design.add_half_crossover(helix=0, helix2=5, offset=1245, forward=False)
design.add_half_crossover(helix=2, helix2=3, offset=1245, forward=False)
# scaffold interior
crossovers = []
for offset in range(58, 1250, 42):
crossovers.append(
sc.Crossover(helix=0, helix2=1, offset=offset, forward=True))
for offset in range(30, 1250, 42):
crossovers.append(
sc.Crossover(helix=1, helix2=2, offset=offset, forward=False))
for offset in range(54, 1250, 42):
crossovers.append(
sc.Crossover(helix=2, helix2=3, offset=offset, forward=True))
for offset in range(26, 1250, 42):
crossovers.append(
sc.Crossover(helix=3, helix2=4, offset=offset, forward=False))
# scaffold edges
crossovers.append(
sc.Crossover(helix=0, helix2=1, offset=16, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=2, helix2=3, offset=12, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=4, helix2=5, offset=19, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=0, helix2=1, offset=1275, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=2, helix2=3, offset=1271, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=4, helix2=5, offset=1278, forward=True, half=True))
design.add_crossovers(crossovers)
def add_nicks(design: sc.DNADesign):
design.add_nick(helix=5, offset=399, forward=False) # scaffold
for offset in range(56, 1246, 42):
design.add_nick(helix=0, offset=offset, forward=False)
design.add_nick(helix=3, offset=offset, forward=True)
for offset in range(70, 1246, 42):
design.add_nick(helix=1, offset=offset, forward=True)
design.add_nick(helix=4, offset=offset, forward=False)
for offset in range(84, 1246, 42):
design.add_nick(helix=2, offset=offset, forward=False)
design.add_nick(helix=5, offset=offset, forward=True)
def add_twist_correct_deletions(design: sc.DNADesign):
# I choose between 3 and 4 offset arbitrarily for twist-correction deletions for some reason,
# so they have to be hard-coded.
for col, offset in zip(range(4, 29, 3), [4, 3, 3, 4, 3, 3, 3, 3, 3]):
for helix in range(0, 16):
design.add_deletion(helix, 16 * col + offset)
def adjust_helix_grid_and_positions(design: sc.DNADesign):
design.grid = sc.Grid.none
for helix in design.helices.values():
helix.grid_position = None
position3d = idx_to_position(helix.idx)
helix.position3d = position3d
def export_idt_plate_file(design: sc.DNADesign):
for strand in design.strands:
if strand != design.scaffold:
strand.set_default_idt(use_default_idt=True)
design.write_idt_plate_excel_file(use_default_plates=True)
def add_deletions(design: sc.DNADesign):
for helix in range(24):
for offset in range(27, 294, 48):
design.add_deletion(helix, offset)
def add_scaffold_nicks(design: sc.DNADesign):
for helix in range(1, 24):
design.add_nick(helix=helix, offset=152, forward=helix % 2 == 0)
def add_staple_nicks(design: sc.DNADesign):
for helix in range(24):
start_offset = 32 if helix % 2 == 0 else 48
for offset in range(start_offset, 280, 32):
design.add_nick(helix, offset, forward=helix % 2 == 1)
