Enzyme Selection
Find Enzymes by Cut Frequency
from Bio import SeqIO from Bio.Restriction import Analysis, CommOnly, AllEnzymes
record = SeqIO.read('sequence.fasta', 'fasta') seq = record.seq
analysis = Analysis(CommOnly, seq)
Enzymes that cut exactly once (good for linearization)
once_cutters = analysis.once_cutters()
Enzymes that cut exactly twice (good for excision)
twice_cutters = analysis.twice_cutters()
Enzymes that don't cut (good for cloning insert)
non_cutters = analysis.only_dont_cut()
All enzymes that cut (any number of times)
all_cutters = analysis.only_cut()
Find Non-Cutters for Insert
from Bio.Restriction import Analysis, CommOnly
Find enzymes that don't cut your insert
insert_seq = record.seq analysis = Analysis(CommOnly, insert_seq)
non_cutters = analysis.only_dont_cut() print('Enzymes that do not cut the insert:') for enzyme in non_cutters: print(f' {enzyme}')
Find Compatible Enzyme Pairs
from Bio.Restriction import EcoRI, BamHI, BglII, XhoI, SalI
Check if enzymes produce compatible overhangs
def find_compatible_enzymes(enzyme): '''Find enzymes with same overhang''' compatible = enzyme.compatible_end() print(f'{enzyme} is compatible with: {compatible}')
find_compatible_enzymes(BamHI) # Compatible with BglII find_compatible_enzymes(XhoI) # Compatible with SalI
Filter by Overhang Type
from Bio.Restriction import CommOnly, Analysis
analysis = Analysis(CommOnly, seq) cutters = analysis.only_cut()
Filter by overhang type
blunt_cutters = [e for e in cutters if e.is_blunt()] five_prime = [e for e in cutters if e.is_5overhang()] three_prime = [e for e in cutters if e.is_3overhang()]
print(f'Blunt cutters: {len(blunt_cutters)}') print(f'5' overhang: {len(five_prime)}') print(f'3' overhang: {len(three_prime)}')
Filter by Recognition Site Length
from Bio.Restriction import AllEnzymes, CommOnly
6-cutters (most common for cloning)
six_cutters = [e for e in CommOnly if len(e.site) == 6]
8-cutters (rare cutters, good for large constructs)
eight_cutters = [e for e in CommOnly if len(e.site) == 8]
4-cutters (frequent cutters)
four_cutters = [e for e in CommOnly if len(e.site) == 4]
print(f'4-cutters: {len(four_cutters)}') print(f'6-cutters: {len(six_cutters)}') print(f'8-cutters: {len(eight_cutters)}')
Find Enzymes with Specific Overhang
from Bio.Restriction import CommOnly
def find_by_overhang(overhang_seq): '''Find enzymes that produce a specific overhang''' matching = [] for enzyme in CommOnly: if hasattr(enzyme, 'ovhgseq') and enzyme.ovhgseq == overhang_seq: matching.append(enzyme) return matching
Find enzymes with AATT overhang (like EcoRI)
aatt_enzymes = find_by_overhang('AATT') print(f'Enzymes with AATT overhang: {aatt_enzymes}')
Find Unique Cutters in Multiple Sequences
from Bio import SeqIO from Bio.Restriction import Analysis, CommOnly
records = list(SeqIO.parse('sequences.fasta', 'fasta'))
Find enzymes that cut once in each sequence
common_once_cutters = None
for record in records: analysis = Analysis(CommOnly, record.seq) once = set(analysis.once_cutters().keys())
if common_once_cutters is None:
common_once_cutters = once
else:
common_once_cutters &= once
print('Enzymes that cut once in all sequences:') for enzyme in common_once_cutters: print(f' {enzyme}')
Select Enzymes for Directional Cloning
from Bio.Restriction import Analysis, CommOnly
def find_cloning_pairs(vector_seq, insert_seq): '''Find enzyme pairs for directional cloning'''
# Analyze both sequences
vec_analysis = Analysis(CommOnly, vector_seq)
ins_analysis = Analysis(CommOnly, insert_seq)
# Enzymes that cut vector once
vec_once = set(vec_analysis.once_cutters().keys())
# Enzymes that don't cut insert
ins_non = set(ins_analysis.only_dont_cut())
# Candidates: cut vector once, don't cut insert
candidates = vec_once & ins_non
# Group by overhang type for pairs
five_prime = [e for e in candidates if e.is_5overhang()]
three_prime = [e for e in candidates if e.is_3overhang()]
blunt = [e for e in candidates if e.is_blunt()]
print(f'Candidate enzymes: {len(candidates)}')
print(f" 5' overhang: {[str(e) for e in five_prime[:5]]}")
print(f" 3' overhang: {[str(e) for e in three_prime[:5]]}")
print(f" Blunt: {[str(e) for e in blunt[:5]]}")
return candidates
Usage
candidates = find_cloning_pairs(vector_seq, insert_seq)
Check Commercial Availability
from Bio.Restriction import CommOnly, AllEnzymes, EcoRI
Check if enzyme is commercially available
def is_commercial(enzyme): return enzyme in CommOnly
print(f'EcoRI commercial: {is_commercial(EcoRI)}')
List all commercial enzymes
print(f'Total commercial enzymes: {len(CommOnly)}')
Find Isoschizomers
from Bio.Restriction import EcoRI, HpaII
Isoschizomers: same recognition, may have different cuts
isoschizomers = EcoRI.isoschizomers() print(f'EcoRI isoschizomers: {isoschizomers}')
Neoschizomers: same recognition, different cut position
neoschizomers = HpaII.neoschizomers() print(f'HpaII neoschizomers: {neoschizomers}')
Check Methylation Sensitivity
Some enzymes are blocked by DNA methylation (Dam, Dcm in E. coli). Important when digesting genomic DNA from bacteria.
from Bio.Restriction import DpnI, DpnII, Sau3AI, MboI
Check if enzyme is sensitive to methylation
def check_methylation(enzyme): dam = enzyme.is_dam_methylable() dcm = enzyme.is_dcm_methylable() print(f'{enzyme}: Dam={dam}, Dcm={dcm}')
check_methylation(DpnI) # Requires Dam methylation to cut check_methylation(DpnII) # Blocked by Dam methylation check_methylation(Sau3AI) # Not affected by Dam check_methylation(MboI) # Blocked by Dam methylation
from Bio.Restriction import CommOnly, Analysis
Find enzymes not affected by common methylation
def find_methylation_insensitive(seq): analysis = Analysis(CommOnly, seq) cutters = analysis.only_cut()
insensitive = [e for e in cutters
if not e.is_dam_methylable() and not e.is_dcm_methylable()]
print(f'Methylation-insensitive cutters: {len(insensitive)}')
return insensitive
Usage for genomic DNA from E. coli
insensitive = find_methylation_insensitive(seq)
Type IIS Enzymes for Golden Gate Cloning
Type IIS enzymes cut outside their recognition site, enabling scarless assembly.
from Bio.Restriction import BsaI, BbsI, BsmBI, SapI
Type IIS enzymes cut outside recognition sequence
BsaI: GGTCTC(N)1 - cuts 1bp after recognition
BsmBI: CGTCTC(N)1
def type_iis_info(enzyme): print(f'{enzyme}:') print(f' Recognition: {enzyme.site}') print(f' Overhang: {enzyme.ovhg} bp ({enzyme.ovhgseq if enzyme.ovhgseq else "variable"})') print(f' Cuts outside: {enzyme.fst3cut}, {enzyme.fst5cut}')
type_iis_info(BsaI) type_iis_info(BsmBI)
from Bio.Restriction import BsaI, BsmBI from Bio.Seq import Seq
Golden Gate assembly: design parts with compatible overhangs
BsaI creates 4-bp overhangs that can be designed for specific fusion
def find_golden_gate_sites(seq, enzyme=BsaI): '''Find Type IIS sites and their overhang positions''' sites = enzyme.search(seq)
if not sites:
print(f'No {enzyme} sites found - sequence is Golden Gate compatible')
return []
print(f'{enzyme} sites found at: {sites}')
print('These sites must be removed for Golden Gate cloning')
return sites
Check if insert is free of BsaI sites
insert_seq = Seq('ATGCGATCGATCGATCG') find_golden_gate_sites(insert_seq, BsaI)
Common Type IIS enzymes for Golden Gate/modular cloning
from Bio.Restriction import BsaI, BsmBI, BbsI, SapI, BtgZI
golden_gate_enzymes = [BsaI, BsmBI, BbsI, SapI, BtgZI]
for enzyme in golden_gate_enzymes: print(f'{enzyme}: site={enzyme.site}, overhang={enzyme.ovhg}bp')
Enzyme Properties Reference
from Bio.Restriction import EcoRI
Get all properties
print(f'Site: {EcoRI.site}') print(f'Cut: {EcoRI.fst3cut}, {EcoRI.fst5cut}') print(f'Overhang: {EcoRI.ovhg} ({EcoRI.ovhgseq})') print(f'Blunt: {EcoRI.is_blunt()}') print(f'5' overhang: {EcoRI.is_5overhang()}') print(f'3' overhang: {EcoRI.is_3overhang()}') print(f'Ambiguous: {EcoRI.is_ambiguous()}') print(f'Defined: {EcoRI.is_defined()}')
Related Skills
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restriction-sites - Find where selected enzymes cut
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restriction-mapping - Map selected enzyme sites
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fragment-analysis - Predict fragments from selected enzymes