Restriction Enzyme Fragment Calculator
Calculate expected DNA fragment sizes from restriction enzyme digestion. Enter total plasmid or DNA size and cut positions to predict gel electrophoresis band pattern.
Formula & Reference
| Variable | Symbol | Formula | Units |
|---|---|---|---|
| Restriction Enzyme Fragment Calculator | — | fragments = positions between cuts | bp |
Step-by-Step Examples
pUC19 (2686 bp) cut with EcoRI at position 396.
- Cut at 396 bp
- Fragment 1: 396 bp (from start to cut)
- Fragment 2: 2686-396 = 2290 bp
- Two bands on gel: 396 bp and 2290 bp
5000 bp plasmid cut at positions 1200 and 2800.
- Sorted cuts: 1200, 2800
- Fragment 1: 1200 bp
- Fragment 2: 2800-1200 = 1600 bp
- Fragment 3: 5000-2800 = 2200 bp
- Check: 1200+1600+2200=5000 ✓
pBR322 (4361 bp) cut with BamHI at 375 and PvuI at 3607.
- Fragment 1: 375 bp
- Fragment 2: 3607-375 = 3232 bp
- Fragment 3: 4361-3607 = 754 bp
- 3 bands on gel at expected positions
Real-World Applications
Common Mistakes to Avoid
Circular plasmid: one cut gives 1 linear fragment. Two cuts give 2 fragments. Linear DNA: one cut gives 2 fragments from start. Account for topology.
Restriction enzyme databases list recognition site positions; the actual cut may be within or offset from recognition site. Always use the exact cut position, not recognition start.
Fragments within 10-20% of each other on gel may not resolve well. Use gel percentage accordingly: 1% for large fragments, 2-3% for small.