Agarose Gel Calculator
Recommend agarose percentage by DNA size and calculate gel preparation.
Agarose Gel Concentration Reference
| Gel % | Separation range (kb) | Optimal (kb) |
|---|---|---|
| 0.5% | 1–30 kb | 10–30 kb |
| 0.7% | 0.8–12 kb | 5–10 kb |
| 1% | 0.5–10 kb | 3–7 kb |
| 1.2% | 0.4–7 kb | 2–5 kb |
| 1.5% | 0.2–4 kb | 0.5–3 kb |
| 2% | 0.1–3 kb | 0.2–1.5 kb |
| 3% | 0.05–1 kb | 0.1–0.5 kb |
Learn more
What it does
The agarose gel calculator works in two directions: given a target DNA size it recommends a gel percentage and shows the effective separation range, and given a percentage and volume it calculates how much agarose powder and buffer to weigh out. A reference table of concentrations against resolvable size ranges, based on standard molecular cloning practice, sits alongside. It answers the two questions asked most often at the bench, namely which gel to pour and how much powder to add. Both calculations are simple arithmetic, but getting the concentration wrong means bands either run together or leave the gel entirely, so keeping them on one page removes a round of manual conversion.
How it works
Agarose forms a hydrated mesh whose pore size shrinks as the concentration rises, and DNA migrating through that mesh moves at a rate that decreases roughly with the logarithm of fragment length — larger fragments travel more slowly, and differences between long fragments get compressed. Low percentage gels, around 0.5%, have wide pores and keep fragments of 1 to 30 kilobases distinguishable; high percentage gels, up to 3%, have narrow pores and resolve small fragments from about 50 to 1000 base pairs. Outside its range a gel either lets fragments run together near the front or stacks them close to the well without separating them, and changing the concentration helps far more than running the gel longer. Gel preparation is a straightforward weight-for-volume calculation: the percentage is weight per volume, meaning grams of agarose per 100 millilitres of gel solution, so agarose mass in grams = percentage x volume in millilitres / 100. A 1% gel is 1 gram of agarose per 100 millilitres of running buffer. Because the powder contributes negligible volume, the buffer volume is simply taken as the gel volume. In practice, weigh the powder into the buffer, heat until fully dissolved with no lens-shaped particles remaining, cool to about 60 degrees Celsius, then add nucleic acid stain and pour — hotter solution degrades the stain, cooler solution starts to set before you pour.
Worked example
In recommendation mode, enter a target size of 0.3 kilobases — a 300 base pair colony PCR product — and the calculator recommends a 1.5% gel with an effective separation range of 0.2 to 4 kilobases; if you need to tell 300 from 350 base pairs apart, going to 2% or 3% sharpens resolution at the small end. Enter 9 kilobases and the recommendation is 0.7%, because that size sits inside the optimal window of a 0.7% gel, which is 5 to 10 kilobases; a 1% gel usually still runs it, but 9 kilobases is close to that gel upper limit and the band sits lower in the resolving range. In preparation mode, entering 1.5% and 70 millilitres gives 1.5 x 70 / 100 = 1.05 grams of agarose dissolved in 70 millilitres of 1x TAE or TBE, which is the most common small-tray format. The classic 1% 100 millilitre gel returns exactly 1 gram from the same arithmetic. For a thicker gel with wider wells, intended for gel extraction, scale the volume to 150 millilitres and add powder in the same proportion, which at 1.5% means 2.25 grams.
When to use it
Screening colony PCR products of a few hundred base pairs works best on a 1.5 to 2% gel, which keeps the target band clearly separated from the primer dimer front; the default 1% gel tends to crowd them together. Checking a restriction digest of a plasmid whose fragments span several kilobases calls for 0.7 to 1%, which resolves the large fragments instead of stacking them near the well. Judging whether a ligation worked is easier at low percentage, where the few hundred base pairs between vector and insert show up as a visible shift. When a band has to be cut out for extraction, preparation mode gives the powder and buffer for a thicker, larger-volume gel that tolerates wide wells and a clean excision. For Southern blotting or long-fragment analysis, a low percentage gel run at reduced voltage for longer keeps large fragments from compressing into each other. In teaching labs a 1% gel with a standard ladder is the usual way to show the logarithmic relationship between migration distance and fragment length.
FAQ
- What agarose percentage should I use for a 500 bp fragment?
- 1.5% to 2% is the usual choice: both resolve fragments of a few hundred base pairs and run in a reasonable time. A 1% gel still shows the band, but neighbouring sizes are harder to tell apart, so raise the concentration whenever closely spaced small fragments have to be distinguished.
- How much agarose powder do I need for a 1% 100 mL gel?
- One gram, because the percentage here is weight per volume, so 1% means 1 gram per 100 millilitres. Weigh the powder into the buffer rather than the reverse, heat until fully dissolved with no visible lens-shaped particles, and let the solution cool to about 60 degrees Celsius before adding stain and pouring.
- Why do large DNA fragments run poorly on a high-percentage gel?
- Because the pores are too small for a large molecule to migrate efficiently. Fragments beyond a gel effective range all move very slowly and pile up near the well as one unresolvable band. The fix is a lower percentage gel; for fragments above roughly 30 kilobases, also reduce the voltage, extend the run time, or switch to pulsed-field electrophoresis.
- Should I use TAE or TBE buffer for agarose gels?
- TAE has weaker buffering capacity but gives better resolution and mobility for large fragments, and interferes less with downstream enzymatic reactions after gel extraction, which makes it the default for cloning work. TBE buffers more strongly and resolves small fragments better in long or high-voltage runs, but residual borate can inhibit enzymes in subsequent steps.
- How much agarose do I need for 70 mL of a 1.5% (w/v) gel?
- 1.05 grams. The percentage is weight per volume, so the mass is percentage times volume divided by 100, which here is 1.5 x 70 / 100 = 1.05 grams of agarose powder dissolved in 70 millilitres of 1x TAE or TBE. The same formula gives 1 gram for a 1% 100 millilitre gel and 0.7 grams for a 0.7% 100 millilitre gel. The powder contributes negligible volume, so no correction is needed for it.
- What gel percentage should I use for a 9 kb DNA fragment?
- 0.7% is the best choice: 9 kilobases falls inside the optimal window of a 0.7% gel, which is 5 to 10 kilobases, and that gel resolves fragments from 0.8 to 12 kilobases overall. A 1% gel will usually still run it, but 9 kilobases sits near that concentration upper limit, so the band travels further into the compressed part of the range. Avoid 1.5% and above for a fragment this size — those concentrations are meant for small fragments and would leave the band close to the well.
- How much agarose powder do I need for 50 mL of a 1.2% gel?
- 0.6 grams. The percentage is weight per volume, so mass = percentage × volume ÷ 100 = 1.2 × 50 ÷ 100 = 0.6 g of agarose dissolved in 50 mL of 1× TAE or TBE. A 1.2% gel is a convenient small-tray volume for checking a restriction digest; the same arithmetic returns 1 g for a standard 1% 100 mL gel. Weigh the powder into the buffer, swirl to disperse it before heating, and dissolve completely — visible lens-shaped particles mean it is not ready to pour.
- How does the agarose percentage affect resolution?
- Higher percentages produce a finer mesh that separates short fragments better; lower percentages give a looser mesh that keeps long fragments apart. A 0.7% gel is best for 5–10 kb, 1% for 0.5–10 kb, 1.5% for 0.2–3 kb and 2–3% for very small fragments of 50–500 bp. Within a single percentage, resolution can be improved by running the gel longer at a lower voltage and by loading less DNA per lane, but changing the concentration is usually far more effective than running longer.