Restriction Enzyme Cut Site Finder
Paste your DNA sequence and select restriction enzymes to find recognition sites, cut positions, and predicted fragment sizes. Use results for molecular cloning and designing inserts into vectors for microfluidic diagnostic panels.
DNA Sequence
Cleaned sequence: 44 bp · AMASMDGAATTCGATATCGGATCCAAGCTT...
Analysis
EcoRIGAATTC
| Fragment | Size (bp) | % |
|---|---|---|
| #1 | 7 | 15.9 |
| #2 | 37 | 84.1 |
BamHIGGATCC
| Fragment | Size (bp) | % |
|---|---|---|
| #1 | 19 | 43.2 |
| #2 | 25 | 56.8 |
HindIIIAAGCTT
| Fragment | Size (bp) | % |
|---|---|---|
| #1 | 25 | 56.8 |
| #2 | 19 | 43.2 |
About Restriction Enzymes
Restriction enzymes (restriction endonucleases) are molecular scissors that recognize specific DNA sequences and cut them at precise locations. Each enzyme has a unique recognition sequence, typically 4 to 8 base pairs long. They are indispensable tools in molecular cloning, genetic engineering, and diagnostics.
How They Work
A restriction enzyme scans the DNA sequence looking for its recognition site. When found, the enzyme makes a double-strand break at or near that site, producing fragments. Some enzymes create blunt ends, while others create sticky (cohesive) ends with short single-stranded overhangs, which are useful for directional cloning.
Microfluidic Applications
In microfluidic diagnostic panels, restriction enzymes are used to digest DNA inserts for cloning into vectors. Knowing the exact cut positions and fragment sizes allows precise design of on-chip cloning workflows, multiplexing of restriction digests, and validation of genetic constructs in compact, integrated devices.
Sticky vs. Blunt Ends
Enzymes like EcoRI and BamHI produce sticky (cohesive) ends, which are useful for directional cloning because they are sequence-specific. Other enzymes like PstI and SmaI produce blunt ends, which are less specific but can be ligated to any compatible fragment. Mixing enzymes with different end types allows for complex multi-insert constructs.
Design a custom microfluidic cloning device?
Integrate restriction digestion, ligation, and transformation into a single chip. From rapid prototyping to production-scale devices in COC and COP.