What is a restriction enzyme?

A restriction enzyme (endonuclease) is a protein that recognizes a specific short DNA sequence (recognition site) and cuts the double-stranded DNA at or near that site. They are essential tools in recombinant DNA technology and cloning.

What does the cut position number mean?

The position reported is the 1-based index of the first nucleotide of the recognition sequence on the input strand. The actual cleavage may occur within or outside the recognition sequence depending on the enzyme.

How are degenerate bases handled?

IUPAC ambiguity codes (R, Y, S, W, K, M, B, D, H, V, N) in the recognition sequences are expanded to all matching bases during the search, so degenerate motifs like RGATCY are correctly matched.

What does "unique cutter" mean?

A unique cutter cuts the sequence exactly once. These sites are especially useful for linearizing circular DNA or for inserting a single fragment at a defined position.

Are both strands searched?

Yes. The tool searches both the forward strand and its reverse complement, but palindromic recognition sequences (most common enzymes) produce the same positions on both strands, so they are deduplicated.

Why might a familiar enzyme not appear in the results?

Either the recognition sequence is absent from your input, or the enzyme is not yet in the built-in library. The library currently covers 40+ widely used enzymes; rare cutters may be missing.

Restriction Enzyme Finder

Name: Restriction Enzyme Finder
Availability: InStock
Author: Nham Vu

Paste a DNA sequence to find all restriction enzyme cut sites from a library of 40+ common enzymes.

Enter DNA Sequence

0 bp

Filter Enzymes

Common Cloning 6-Cutters 4-Cutters Rare Cutters (8 bp)

Cut Site Results

Enzyme	Recognition Seq	Cuts	Positions (1-based)

Paste a DNA sequence above to find restriction sites.

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Summary

Paste a DNA sequence to find all restriction enzyme cut sites from a library of 40+ common enzymes.

How it works

Paste or type your DNA sequence into the input box.
Select which enzyme groups to include — popular cloning enzymes are checked by default.
The tool scans the sequence and lists every enzyme that cuts, along with the number of cut sites and their positions.
Click any enzyme row to see the cut positions highlighted in the sequence.
Use the filter to search for a specific enzyme by name.
Copy the results table to your clipboard for use in a lab notebook.

Use cases

Screen a cloning insert for compatible restriction sites.
Design a restriction digest map for gel verification.
Identify unique (single-cut) sites for linearizing a plasmid.
Find enzymes that do NOT cut your insert before cloning.
Quickly verify a published sequence by checking expected cut sites.
Select compatible cohesive ends for directional ligation.
Teach restriction enzyme biology with a hands-on visual tool.

Frequently Asked Questions

Related tools

Reverse Complement Tool Sequence Gc Content Tm Primer Calculator Orf Finder Codon Table Lookup

Last updated: 2026-05-29 · Reviewed by Nham Vu