Agarose gel preparation
Agarose to weigh for a gel, and which percentage resolves your fragment.
1% is 1 g in 100 mL.
TAE or TBE, as the gel is cast in.
Checks the percentage suits it.
Agarose to weigh
Into 100 mL of buffer, for a 1% gel.
What each percentage resolves
- 0.5%1,000 – 30,000 bp
- 0.7%800 – 12,000 bp
- 1.0% — yours500 – 10,000 bp
- 1.2%400 – 7,000 bp
- 1.5%200 – 3,000 bp
- 2.0%50 – 2,000 bp
The bounds are where resolution starts to fail, not hard limits. A fragment just outside still runs; it stops being distinguishable from its neighbours.
mass = percentage (w/v) × volume; 1% w/v = 10 g/L- Agarose percentage and the fragment range it resolves — Journal of Visualized Experiments, 2012
TBE resolves small fragments better and buffers longer; TAE is kinder to DNA you intend to extract from the gel, since borate inhibits several enzymes. Dissolve fully before pouring — undissolved grains scatter light and read as bands — and add stain once the gel has cooled below about 60 °C.
When to use this
Use this to weigh the agarose for a gel, and to check the percentage actually resolves the fragment you are trying to see. The second half matters more — the arithmetic is easy and the choice of percentage is what costs an afternoon.
Worked example
A 100 mL gel to resolve a 500 bp PCR product.
- Gel percentage
- 1.5% (w/v)
- Buffer volume
- 100 mL
- Fragment
- 500 bp
Result
1.5% resolves 200–3000 bp, so a 500 bp band will run well clear of its neighbours.
What people get wrong
- Running a small product on a loose gel. A 500 bp fragment on 0.7% agarose runs near the front and cannot be distinguished from anything else down there.
- Adding stain to gel that is still too hot. Wait until it has cooled to about 60 °C, or the stain degrades.
- Pouring before the agarose has fully dissolved. Undissolved grains scatter light and read as bands under UV.
Questions
+TAE or TBE?
TBE resolves small fragments better and buffers longer. TAE is kinder to DNA you intend to extract, because borate inhibits several downstream enzymes.
+What is 1% w/v in grams?
One gram in 100 mL, which is 10 g/L. The tool accepts the percentage directly and converts.
+What if my fragment is under 100 bp?
Use polyacrylamide. Agarose above about 3% is difficult to pour and still resolves small fragments poorly.
Related tools
- Recipe scaler — Scale a recipe to a different batch size and keep every concentration the same.
- DNA and RNA quantification — Concentration and purity from A260, with the conversion factor made explicit.
- Molarity calculator — Convert between mass, molar concentration and volume for a solution.
Science last reviewed .