Restriction site finder
Paste a DNA sequence and see every common enzyme that cuts it, how many times and where — or pick one enzyme to get its fragment sizes and the kind of ends it leaves. Circular plasmids are searched across the joint between the end and the start of the sequence.
Runs in your browser: nothing you enter is sent anywhere.
How to use it
- Paste the DNA sequence. FASTA and numbered GenBank-style text work.
- Choose linear or circular DNA.
- Leave “All enzymes” to see every cutter with its positions, the single cutters at a glance and the enzymes that do not cut. Or choose one enzyme for its fragments and ends.
How it works
Every site in the list is a palindrome — it reads the same on both strands 5′ → 3′ — so one search of the top strand finds all sites. For each match the cut position is the start of the site plus the enzyme’s offset (EcoRI: 1). In circular mode the end of the sequence is joined to its start, so a site spanning the joint is found too. Fragments are the distances between consecutive cuts.
Worked example
AAGAATTCAAGAATTCAA (18 bp) has GAATTC at bases 3–8 and 11–16. EcoRI cuts after bases 3 and 11. As linear DNA that gives fragments of 8, 7 and 3 bp; as a circle, 10 and 8 bp.
The default sequence is built like a plasmid multiple cloning site: 17 enzymes cut it, among them single cutters BamHI (after base 37), HindIII (7), PstI (23), SalI (25), XbaI (31), KpnI (50) and SacI (56).
Tips
- Single cutters for cloning. An enzyme that cuts a plasmid once, inside the cloning site, opens it without losing a piece.
- Compatible ends. BamHI, BglII and MboI all leave GATC overhangs that can be ligated to each other.
- Near the ends. Many enzymes cut poorly when the site is only a few bases from the end of a PCR product; add extra bases to primers.
Frequently asked questions
Which enzymes are included?
41 widely used type II enzymes with palindromic recognition sites and no ambiguous bases, from AatII to XmaI, including EcoRI, BamHI, HindIII, NotI, XhoI, NdeI and the 4-cutters AluI, HaeIII, MspI, TaqI, RsaI and MboI. Sites and cut positions follow REBASE and NEB.
What does G^AATTC mean?
The caret marks where the enzyme cuts the top strand: EcoRI cuts between G and A. Because the site is a palindrome, the bottom strand is cut at the mirror position, leaving a four-base AATT overhang on each 5′ end.
Why do SmaI and XmaI give different positions for the same site?
They are neoschizomers: both recognise CCCGGG, but SmaI cuts in the middle (CCC^GGG, blunt ends) and XmaI after the first base (C^CCGGG, 5′ overhangs). The finder reports where each one cuts.
How are fragments of a circular plasmid counted?
A circle cut n times gives n fragments, the last one running across the joint from the last cut back to the first. One cut just opens the circle into a single linear molecule of full length. A linear molecule cut n times gives n + 1 fragments.
Does it consider methylation?
No. Some sites are blocked by Dam or Dcm methylation in DNA from common E. coli strains (MboI, for example, does not cut Dam-methylated GATC). Check the enzyme’s sensitivity before you plan a digest.