Agarose gel percentage guide
Agarose percentage sets the sieving range of a gel: low percentages resolve large DNA, high percentages resolve small. Standard ranges run from 0.5% (1–30 kb) through 1% (0.5–10 kb) — the everyday default — to 2% (50 bp–2 kb). Enter your smallest and largest fragments and the guide picks the tightest gel that resolves both.
Result
Ranges per Sambrook & Russell and vendor electrophoresis guides. For ranges no single gel covers, run two gels or a gradient; below ~100 bp consider polyacrylamide.
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Formula
0.5% → 1–30 kb · 0.7% → 0.8–12 kb · 1.0% → 0.5–10 kb · 1.2% → 0.4–7 kb · 1.5% → 0.2–3 kb · 2.0% → 0.05–2 kb
Source: Sambrook & Russell, Molecular Cloning; vendor electrophoresis guides
Worked example
Given: Diagnostic digest expected to give 0.5 kb and 2 kb bands
- 1.Both fragments must fall inside one gel's range.
- 2.1.5% resolves 0.2–3 kb — covers 0.5 and 2 kb with good separation in the small range.
- 3.1.0% would also cover it but compresses the 0.5 kb end; the guide picks the tighter 1.5%.
Pour a 1.5% agarose gel
How the calculation flows
Units & constants
| Everyday default | 1% — resolves 0.5–10 kb, covers most cloning checks |
|---|---|
| Below ~100 bp | Use 2.5–3% agarose or polyacrylamide |
| Above ~30 kb | Pulsed-field electrophoresis territory |
| High-% pouring tip | ≥ 2% gels need slow, complete melting to avoid lensing |
| Verify in-app | Talindrew's gel simulator predicts band positions for your actual digest |
| Price | Free |
Why does percentage change what a gel resolves?
Agarose forms a pore network that DNA snakes through; pore size shrinks as percentage rises. Large molecules barely enter a tight matrix (they compress at the well in 2%), while small fragments run unretarded through a loose one (they blur at the front in 0.5%). Matching pore size to fragment size is all this choice is.
How do you decide when bands are close together?
Separation matters most where your bands are closest. If you must distinguish 900 bp from 1,100 bp, choose the highest percentage whose range still includes both (1.5%), run longer at lower voltage, and use a ladder with rungs bracketing the gap. Better still, simulate the digest first — Talindrew's gel simulator shows whether the two bands will visibly separate before you pour anything.
Frequently asked questions
- What percentage for a 300 bp PCR product?
- 1.5–2%. At 1% a 300 bp band runs near the dye front with little resolution; 2% places it mid-gel where 50–100 bp differences are visible.
- Can I just always pour 1%?
- For checks of fragments between 0.5 and 10 kb, yes — that is why it is the default. You lose real information outside that window: sub-500 bp bands compress together and > 10 kb fragments crowd the well.
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