Restriction Enzyme Mapper
A free online restriction enzyme mapper that searches 50+ common restriction enzymes in any DNA sequence. Visualize cut site positions on a linear map, predict fragment sizes for single or double digests, filter enzymes by overhang type (5', 3', blunt), and plan cloning strategies — all computed in your browser with no DNA data uploaded.
Select Enzymes
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What is a Restriction Enzyme Mapper?
A restriction enzyme mapper identifies recognition sequences (restriction sites) within a DNA molecule and predicts where specific endonucleases will cut. Restriction enzymes are proteins that cut DNA at specific 4-8 base pair palindromic sequences, producing fragments used in molecular cloning, DNA fingerprinting, and genetic engineering. The mapper shows cut positions, predicts fragment sizes, and helps plan restriction digests for cloning strategies.
How to Use This Tool
- Enter or paste your DNA sequence in the input field (only A, T, G, C characters)
- Select one or more restriction enzymes from the list (use filters to narrow by overhang type)
- Click Find Cut Sites to identify all recognition sites
- View the linear map showing cut positions along the sequence
- Check the fragment sizes table for gel electrophoresis planning
Frequently Asked Questions
What are the most commonly used restriction enzymes?
The most commonly used restriction enzymes in molecular biology are EcoRI (GAATTC), BamHI (GGATCC), HindIII (AAGCTT), XhoI (CTCGAG), NdeI (CATATG), and NotI (GCGGCCGC). These are Type II restriction endonucleases that recognize specific palindromic sequences and are widely used in cloning, subcloning, and DNA analysis.
What is the difference between 5' overhang, 3' overhang, and blunt ends?
When a restriction enzyme cuts DNA, it can produce three types of ends: 5' overhang (sticky end with a protruding 5' strand, e.g., EcoRI), 3' overhang (sticky end with a protruding 3' strand, e.g., KpnI), or blunt end (both strands cut at the same position, e.g., SmaI). Sticky ends are preferred for cloning because complementary overhangs can base-pair and ligate more efficiently.
How are fragment sizes used in gel electrophoresis?
After restriction digestion, DNA fragments are separated by agarose gel electrophoresis based on size. Smaller fragments migrate faster through the gel matrix. Comparing observed band patterns with predicted fragment sizes from a restriction map confirms the identity and integrity of DNA constructs. Standard DNA ladders provide size references for accurate estimation.
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