Restriction Enzyme Database
Search, filter and compare 300+ restriction enzymes by site, buffer, temperature and supplier.
Learn more
What it does
The restriction enzyme database is a searchable catalog of more than 300 Type II restriction endonucleases used in molecular cloning. Look up any enzyme to see its recognition sequence, cut position, overhang type, optimal buffer and temperature, methylation sensitivity, supplier catalog numbers, and known isoschizomers. Filter the list by recognition-site length, buffer, temperature, methylation class, or whether a commercial supplier stocks it, and sort to compare enzymes quickly. It is aimed at cloning planners who need the right enzyme without opening a printed catalog.
How it works
Each enzyme is defined by a short recognition site, most often 4, 6 or 8 bases, that reads the same on both strands. The tool stores the site, the top-strand cut offset, and the bottom-strand cut offset, then draws the cut diagram and decides whether the enzyme leaves a 5′ overhang, a 3′ overhang, or a blunt end. The listed temperature is the supplier's optimal incubation temperature, usually 37°C but ranging from 25°C for some enzymes to 65°C for thermostable ones. Buffer conditions are grouped into generic categories, so you do not have to match a specific vendor's catalogue name.
Worked example
Open the database and search EcoRI. The record shows the 6 bp site GAATTC cut between G and A on the top strand (G^AATTC), giving a 5′ overhang of AATT. Its recommended buffer condition is the universal single-buffer category and the temperature is 37°C, and it is blocked by Dam and Dcm methylation in some hosts. Compare with BamHI, site GGATCC, also a 5′ overhang but a different sequence, so the two enzymes cannot be ligated directly. Filter by 6 bp and 37°C to see all enzymes that might pair in a single digest.
When to use it
Use the database when choosing enzymes for a cloning plan, checking whether two enzymes leave compatible sticky ends, or finding an alternative when your first choice is blocked by methylation. Watch for pitfalls: isoschizomers cut the same site but may need different buffers, and star activity at high glycerol or wrong salt makes an enzyme cut elsewhere. If you need a single digest, filter for enzymes sharing one buffer and temperature; for rare-cutters, set the length filter to 8+ bp.
FAQ
- How many restriction enzymes are in the database?
- The catalog holds more than 300 Type II restriction endonucleases, the workhorses of molecular cloning, and the list is filtered live as you type. Each record stores the 4, 6 or 8 bp recognition site, the cut offset, optimal buffer and temperature, methylation sensitivity, and supplier catalog numbers for NEB and Thermo Fisher. Filter by site length to narrow 300+ entries to the handful that match your construct.
- What is an isoschizomer and why does it matter?
- An isoschizomer is a different enzyme that recognizes the same DNA sequence as another. EcoRI and its isoschizomers all cut GAATTC, but they may need different buffers, optimal temperatures, or show different methylation sensitivity. The database lists known isoschizomers so you can swap an enzyme that is blocked or out of stock for one that cuts the same site under friendlier conditions without redesigning your primers.
- What does methylation sensitivity mean for a digest?
- Many enzymes are blocked when a base in their site is methylated. Dam methylation at GATC and Dcm at CCWGG in E. coli can protect sites, while CpG methylation blocks others in mammalian DNA. DpnI instead cuts only methylated GATC, which is why it removes templates from dam+ PCR products. The methylation filter flags each enzyme so you can pick one that cuts your template given its host strain.
- What is star activity and when should I worry?
- Star activity is relaxed cutting at non-specific sites when an enzyme is stressed: glycerol above about 5%, too little or wrong salt, high enzyme-to-DNA ratio, or prolonged incubation. EcoRI is a classic offender, cutting NNNNNAATTNN rather than GAATTC. The database flags star-prone enzymes so you can keep reactions short, use the recommended buffer, and avoid over-digesting when clean fragments matter.