Gel Electrophoresis Migration Calculator

Estimate DNA migration distance in gel electrophoresis using log-linear relationship: log(size) vs migration. Predict band positions, interpolate unknown sizes, or determine optimal gel percentage.

🧬 Molecular Biology📐 log(size) = a - b x migration🧬 Biology
Fragment 1 size (bp) from ladder
Fragment 1 migration (mm)
Fragment 2 size (bp) from ladder
Fragment 2 migration (mm)
Unknown migration distance (mm)
Please enter valid values.

Formula & Reference

VariableSymbolFormulaUnits
Gel Electrophoresis Migration Calculator—log(size) = a - b x migrationbp

Step-by-Step Examples

Example 1
Size Determination

Ladder: 1000bp at 30mm, 500bp at 45mm. Unknown band at 38mm.

  • log(1000)=3.0 at 30mm; log(500)=2.699 at 45mm
  • Slope = (2.699-3.0)/(45-30) = -0.020 log/mm
  • Unknown: log(size) = 3.0 + (-0.020)(38-30) = 3.0 - 0.16 = 2.84
  • Size = 10^2.84 = 692 bp
✓ Unknown fragment ≈ 692 bp
Example 2
Gel Percentage Selection

1% agarose: good for 200-5000bp. 2%: 100-2000bp. 3%: 50-500bp.

  • For a 150 bp PCR product: use 2% or 3% gel
  • For 5kb insert: use 0.8-1% gel
  • Higher % gives better resolution of small fragments
✓ Use gel % appropriate for fragment size
Example 3
Linear vs Circular DNA

Supercoiled plasmid migrates faster than linear of same size. Open circular migrates slowest.

  • Supercoiled: most compact, fastest
  • Linear: intermediate speed
  • Relaxed (open circular): slowest, largest apparent size
  • All three bands visible in undigested plasmid prep
✓ Migration: supercoiled > linear > open circular

Real-World Applications

🧬
Diagnostic Restriction Digest
Confirm expected band pattern after plasmid restriction digest.
🧪
PCR Product Verification
Verify amplicon size before sequencing or cloning.
📊
RFLP Genotyping
Restriction fragment length polymorphism analysis for genotyping.
🏥
Clinical Diagnostics
PCR-based diagnostics use gel electrophoresis to confirm pathogen detection.

Common Mistakes to Avoid

⚠️
Using logarithmic interpolation outside ladder range

Standard curve only applies between the smallest and largest ladder bands. Extrapolation gives inaccurate size estimates.

⚠️
Running gel at wrong voltage

High voltage: fast but poor resolution and band distortion. Optimal: 5-8 V/cm of gel length. For a 20cm gel: 100-160 V.

⚠️
Forgetting ethidium bromide or SYBR safety

EtBr is mutagenic — handle with gloves and dispose properly. SYBR Green/Safe alternatives are less hazardous but also require care.

Frequently Asked Questions

How does DNA migrate in gel? ▾
DNA is negatively charged (phosphate backbone). In electric field, migrates toward positive electrode. Smaller fragments migrate through gel matrix faster than larger ones.
Why is migration logarithmic with size? ▾
Larger DNA requires more energy to snake through gel pores. Migration distance correlates linearly with log10(size) due to the sieving mechanism through agarose matrix.
What is TAE vs TBE buffer? ▾
TAE (Tris-Acetate-EDTA): better for large DNA, cheaper. TBE (Tris-Borate-EDTA): better resolution, higher conductivity. TAE is standard for most gel electrophoresis.
What is the smallest fragment I can see on gel? ▾
Depends on staining: with EtBr, ~100 bp with strong staining. SYBR Green can detect even smaller. For fragments < 50 bp, use polyacrylamide gel electrophoresis (PAGE).
What staining options are available? ▾
EtBr (classic, mutagenic), SYBR Green/Safe (non-mutagenic, sensitive), GelRed (non-mutagenic, similar sensitivity to EtBr), silver staining (most sensitive, used in PAGE).

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