Agarose Gel Percentage & Recipe Calculator

Understanding the agarose gel calculator — concept and principle

This calculator tells you how much agarose powder to weigh for a gel of a given percentage and volume, and suggests a gel percentage for the DNA fragment size you want to separate. It is used daily to check PCR products and restriction digests.

Grams of agarose = % × volume ÷ 100; pick the % from the DNA size you need to see.

How it is calculated

Gel percentage is weight per volume (w/v): grams of agarose per 100 mL of buffer.

Agarose (g) = % × V ÷ 100, where V is the gel volume in mL of 1× TAE or 1× TBE.
Suggested % follows the fragment size: above 5,000 bp → 0.5–0.7%; 1,000 to 5,000 bp → 0.8–1%; above 300 and below 1,000 bp → 1.2–1.5%; 300 bp or less → 2–3%.

The principle

Molten agarose sets into a mesh of polysaccharide fibres. DNA is negatively charged, so in an electric field it moves towards the positive electrode, and the mesh acts as a sieve: small fragments slip through quickly, long ones are slowed more. A higher percentage gives a tighter mesh, which spreads out small fragments but traps large ones near the well; a lower percentage does the opposite. Choosing the percentage is therefore about placing the sizes you care about in the part of the gel where migration changes most with size.

Worked example

Defaults: gel % = 1, volume = 50 mL, fragment size = 1,000 bp.
Agarose = 1 × 50 ÷ 100 = 0.5 g.
Suggested %: 1,000 bp falls in the 1,000–5,000 bp band → 0.8–1%, so the default 1% gel is a good match.
Note that 1 kb sits exactly on the boundary; a 1% gel also resolves it well, so the 1% default is a reasonable choice for a mix of fragments around 1 kb.

Each point is the calculator re-run with only “Gel %” changed; the gold point is the default example. Change the inputs above and this chart follows your numbers.

Gel %	Agarose (g)
0.25	0.125
0.5	0.25
0.75	0.375
1	0.5
1.25	0.625
1.5	0.75
2	1

How to read the result

Weigh the agarose into the buffer, heat until fully clear, replace water lost by evaporation, cool to about 50–60 °C, add stain if your protocol uses an in-gel stain, and pour. For a typical mini-gel tray, 30–60 mL is common. Always run a DNA ladder whose size range brackets your fragments, and compare band positions with the ladder rather than with distance alone.

Common mistakes

Dissolving agarose in water instead of buffer, which gives no conductivity and poor runs.
Not dissolving completely, leaving lumps that distort bands.
Using different buffers for the gel and the running tank.
Expecting a 2–3% gel to separate fragments of several kb.

Keep in mind: The suggested ranges are typical starting points for standard agarose and linear double-stranded DNA. Supercoiled plasmids, RNA, low-melting agarose and pulsed-field methods behave differently, and microwaved agarose can boil over, so use heat-resistant gloves and follow your lab's protocol.

Frequently asked questions

How long can I keep a poured gel?

Wrapped and refrigerated, gels are often kept for a few days, but fresh gels give the most reliable results.

Why do my bands smile or smear?

Common causes are excessive voltage, overloaded wells, degraded DNA or buffer that is too concentrated or exhausted.

Can I reuse running buffer?

TAE has a lower buffering capacity and is best replaced often; TBE can be reused a few times for short runs.

Sources: Green M.R. and Sambrook J., Molecular Cloning: A Laboratory Manual, 4th ed., Cold Spring Harbor Laboratory Press, 2012 · Lee P.Y. et al., Agarose gel electrophoresis for the separation of DNA fragments, Journal of Visualized Experiments, 2012

Checked 8 Nov 2026. Standard textbook formulas in SI units, computed in your browser. For learning and estimates — real designs must follow your local codes and be checked by a qualified engineer.

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