What is the Restriction Enzyme Finder?
Find restriction enzyme cut sites in DNA sequences instantly in your browser. Scan for EcoRI, BamHI, HindIII, NotI, and 30+ common enzymes with recognition sequences, cut positions, and overhang type. Filter by unique cutters or a single enzyme. Supports FASTA input. Free, private, and no signup.
How to use the Restriction Enzyme Finder
- Paste a DNA sequence (A, T, G, C) or FASTA text.
- Choose All enzymes, Unique cutters only, or a Selected enzyme.
- Review the enzyme summary table and per-site cut positions.
- Check overhang type (5′, 3′, or blunt) for cloning plans.
- Copy the summary for lab notes or cloning design.
Common use cases
- Choosing a unique cutter for inserting a gene into a plasmid
- Checking whether a PCR product has BamHI or EcoRI sites
- Planning a double digest with two compatible enzymes
Frequently asked questions
- What is a restriction enzyme cut site?
- Restriction enzymes recognize specific DNA sequences and cleave the phosphodiester backbone at defined positions, producing sticky or blunt ends useful in molecular cloning.
- What does unique cutter mean?
- A unique cutter is an enzyme that cuts your sequence exactly once. Unique cutters are often preferred for single-site cloning into a vector.
- How are cut positions reported?
- Positions are 1-based on the 5′ strand. The cut position is where the enzyme cleaves between nucleotides on that strand.
- Does it support degenerate recognition sites?
- Yes. Enzymes with IUPAC degenerate bases (e.g. HincII GTYRAC) are matched using standard IUPAC codes.
- Is my sequence uploaded?
- No. All scanning runs locally in your browser.
