Restriction digest simulator
A restriction digest simulator predicts where a given set of restriction enzymes will cut a DNA sequence, and what fragments result, before you set up the reaction at the bench. Talindrew's runs against enzyme data from REBASE across eleven predefined enzyme sets, applies host methylation sensitivity, and maps every cut site onto the circular and linear views of your sequence. Fragment sizes feed directly into the gel simulator so you can check that two bands will actually resolve before pouring a gel.
Specifications
| Enzyme source | REBASE |
|---|---|
| Enzyme sets | 11 predefined |
| Set types | All commercial, non-redundant, NEB, Thermo/Fermentas |
| Cutter-type sets | Unique cutters, unique dual cutters, 6+ cutters, Type IIS, Golden Gate, nicking |
| Methylation models | Dam, Dcm, EcoKI |
| Per-enzyme detail | Recognition site, cut positions, overhang, isoschizomers, compatible ends |
| Reference data | Vendor availability, NEB buffer activity, incubation temperature |
| Topology | Circular and linear, origin-aware |
| Price | Free |
Why does methylation matter in a digest?
A digest that looks clean on paper can fail at the bench because the host strain methylated the site. Most laboratory E. coli strains carry Dam methylase, which methylates the adenine in GATC, and Dcm methylase, which methylates the internal cytosine in CCWGG. Enzymes blocked by that methylation will not cut plasmid DNA prepared from those strains, even though the recognition sequence is present. The simulator applies Dam, Dcm and EcoKI sensitivity to the scan and flags blocked sites rather than silently reporting them as cuttable.
What a digest simulation tells you
Running the digest before the bench answers the questions that otherwise cost a failed gel.
- Whether an enzyme cuts your construct once, several times, or not at all.
- Whether the two enzymes in a double digest have compatible buffer and temperature conditions.
- Whether any site is blocked by host methylation.
- What fragment sizes to expect, and whether they will separate on your gel percentage.
- Whether a vector and insert will produce directional, non-religatable ends.
Diagnostic digests
The most common use is verifying a clone. Pick an enzyme pair that produces a distinctive fragment pattern for the correct construct and a visibly different one for the empty vector or a wrong-orientation insert, then check the simulated gel before committing. Because cut sites are overlaid on the plasmid map, it is quick to see which pair gives the largest size difference.
Frequently asked questions
- Is this restriction digest tool free?
- Yes. The restriction digest simulator runs in the browser with no install and no licence. You can paste a sequence or import a GenBank, FASTA or SnapGene file and run a digest immediately.
- Which restriction enzymes are supported?
- Enzyme data comes from REBASE, organised into eleven predefined sets covering all commercial enzymes, a non-redundant set, and vendor-specific sets for NEB and Thermo/Fermentas, plus cutter-type sets for unique cutters, unique dual cutters, six-plus cutters, Type IIS enzymes, Golden Gate enzymes and nicking enzymes.
- Does it account for Dam and Dcm methylation?
- Yes. Dam, Dcm and EcoKI methylation sensitivity is applied during the scan, so sites that would be blocked in a standard laboratory E. coli strain are flagged instead of being reported as cuttable. This is the most common reason a digest that looks fine in software fails at the bench.
Related
Try it on your own sequence.
Free to use. No download required. Works in any modern browser.