Agarose Gel Percentage & Recipe Calculator
Pick the agarose percentage for the DNA fragment sizes you need to resolve, or set your own, then get the grams of agarose, buffer stock and water (1× TAE or 0.5× TBE from 50×, 10× or 5× stocks), the DNA stain volume, the running buffer for the tank and the voltage, for any tray size and number of gels.
How it works
grams agarose = % × gel volume (mL) ÷ 100 · gel volume = tray length × width × thickness (cm) × gels · stock volume = gel volume × working strength ÷ stock strength · stain (1:X) = gel volume × 1,000 ÷ X µL (1:10,000 → volume ÷ 10) · ethidium bromide = volume × 0.5 µg/mL ÷ 10 mg/mL · voltage = 5–8 V × cm between electrodes
Agarose forms a porous mesh whose pores shrink as the concentration rises. Small fragments need a dense gel to be slowed and separated, and large fragments need a loose one to move at all. The calculator picks the percentage from the smallest fragment you need to see, then checks that the largest still falls inside that gel’s range. If it does not, it moves to a looser gel that covers both, or tells you to run two gels. You can also force any percentage. A percentage is grams per 100 mL, so the recipe follows directly from the gel volume. Type the volume, or enter the tray’s length, width and casting depth, and set the number of gels. The running buffer must be the same in the gel and the tank, so the ion concentration, current and heating stay uniform. Under More options you can make the tank buffer from the same stock and get the voltage for your electrode spacing. Intercalating stains go in once the melted agarose has cooled enough not to degrade them, but before it sets. The alternative is to soak the gel after the run.
Worked example
To resolve fragments between 500 bp and 3 kb in a 50 mL mini-gel tray, use a 1.0% gel: 1.0 × 50 ÷ 100 = 0.50 g agarose. From 50× TAE, mix 1.0 mL stock with 49.0 mL water, melt, cool to hand-hot, add 5 µL of SYBR Safe and pour. A 10 × 7 cm tray cast 5 mm deep holds 10 × 7 × 0.5 = 35 mL, which needs 0.35 g of agarose. For 300 mL of running buffer, mix 6 mL of 50× TAE with 294 mL of water. With electrodes 20 cm apart, run at 100–160 V.
Sources: miniPCR — Choosing the right agarose percentage · Cold Spring Harbor Protocols — TAE recipe · OpenWetWare (Maloof Lab) — electrophoresis buffers
Frequently asked questions
TAE or TBE?
TAE for routine gels and anything you will gel-extract or clone (borate inhibits ligases and some polymerases); TBE at 0.5× for small fragments, long runs and sharper bands.
Can I re-melt a used gel?
Gels without DNA loaded can be re-melted a couple of times, but each cycle evaporates water (raising the percentage) and degrades stain; weigh and top up, and re-add stain.
How many grams of agarose for a 1% gel?
1 g per 100 mL of buffer: 0.50 g for a 50 mL tray, 0.35 g for 35 mL. For several gels, enter the number of gels and the calculator scales the agarose, buffer and stain together.
How do I work out the gel volume from my tray?
Multiply the tray’s inside length and width by the casting depth, all in cm: a 10 × 7 cm tray cast 0.5 cm deep holds 35 mL. Choose "Enter the tray size" to have it done for you. Most mini gels are 3–5 mm thick.
What voltage should I run my gel at?
About 5–8 V per cm of distance between the electrodes, not the gel length. A mini tank with electrodes 20 cm apart runs at 100–160 V. Higher voltages run faster but heat the gel and smear large fragments.
Related calculators
Standard laboratory formulas and textbook recipes (Sambrook, Bio-Rad, Thermo Fisher protocol conventions). Follow your own kit or instrument manual where it differs, and validate with controls — this tool does not replace lab training or safety procedures.