Guides

Gel electrophoresis at home

You can run a DNA gel at home. It takes a gel box with a power supply, agarose and buffer, a DNA stain and a light to see the stain by.

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How a gel sorts DNA

DNA carries a negative charge, so in an electric field it moves toward the positive electrode. The University of Utah's Genetic Science Learning Center explains that the shortest fragments travel farthest.

Agarose sets into a mesh that works like a sieve. A higher percentage of agarose makes smaller pores, which is why the gel you pour depends on the size of the DNA you expect.

Short fragments travel farthest, and the ladder lane turns that distance into a size. The gel moves onto the blue light box after the run; all-in-one units build the light into the base. Open the printable diagram

What a home gel setup includes

Part	What it does	Worth knowing
Gel box and power supply	Holds the gel in buffer and runs current through it	All-in-one units build in the power and the light
Agarose	Sets into the gel	1 g in 100 mL of buffer makes a 1% gel
Buffer, TAE or TBE	Carries the current and keeps the gel wet	TBE gives sharper bands for small fragments
DNA stain	Makes the bands visible	Blue light stains avoid UV and ethidium bromide
Blue light transilluminator	Lights the stain from below	Look for a peak around 470 nm
Micropipette and tips	Loads a few microliters into each well	See how to use a micropipette
DNA ladder	Fragments of known size to read your bands against	Choose one that covers the sizes you expect

Which agarose percentage to use

Agarose gel	Separates fragments of about
0.5%	2,000 to 50,000 bp
1.0%	400 to 8,000 bp
1.5%	200 to 3,000 bp
2.0%	100 to 2,000 bp

Picking a percentage

Pick by the size of the DNA you expect to see. miniPCR bio's guide adds that higher-percentage gels take longer to run and lower-percentage gels tear more easily, so it suggests a 2% gel for beginners.

For very small fragments, NEB says a 50 bp and a 150 bp fragment separate best on a 1.2% TAE gel, and may run together below 1%.

Don't overload the wells. miniPCR bio notes that too much sample smears the bands.

Blue light or UV

Ethidium bromide, the classic DNA stain, glows under UV light. miniPCR bio notes that it is hazardous, needs special disposal and is banned in many schools.

Blue light stains glow under a blue LED instead. miniPCR bio says blue light avoids the risks of UV and damages DNA less, which matters if you plan to clone a band.

Blue stains you can see in ordinary light, such as FlashBlue and CarolinaBLU, cost less. They detect less DNA, and the gel has to soak and rinse for anywhere from 15 minutes to overnight.

Blue light stains compared

Stain	Strength	Drawback
SYBR Safe	Doesn't distort how bands run	Fades quickly under light
GelGreen	Resists fading	Binds DNA strongly and can distort bands
SeeGreen	Sensitive and stable, and works under blue or UV light	Runs in the opposite direction from DNA, so it suits runs under 40 minutes

A gel box with a blue light

Edvotek's M12 Ultra package pairs its electrophoresis chamber with the battery-powered TruBlu Jr. transilluminator, which lights SYBR Safe and GelGreen at 470 nm.

miniPCR bio sells the blueGel direct. It runs a 6 by 6 cm gel at a fixed 60 V with the blue light built in, takes up to 26 samples and runs on USB-C power.

miniPCR bio says a blueGel run separates bands fully in 15 minutes.

Edvotek M12 Ultra electrophoresis chamber and TruBlu Jr. blue light on an oak lab bench by a window

Gel electrophoresis

Edvotek M12 Ultra electrophoresis and blue light package

An electrophoresis chamber with accessories and the battery-powered TruBlu Jr. transilluminator, which lights blue-light dyes such as SYBR Safe and GelGreen at 470 nm.

View on Amazon →

Building your own gel box

The University of Utah publishes step-by-step plans for an acrylic chamber with wire electrodes, run from a 24 V power supply.

The plans use Monel or copper wire. Copper reacts with the buffer and turns it blue, so a copper box needs fresh buffer for every run.

To practice before you have DNA, Utah's colorful electrophoresis activity runs food colors through an agar agar gel in salt water.

When the bands smear

Thermo Fisher's troubleshooting guide lists the usual causes of smeared bands. Most come down to how the gel was poured and loaded.

Too much DNA. Thermo Fisher suggests 0.1 to 0.2 µg per millimeter of well width. Trailing smears and U-shaped bands are signs of an overloaded well.
Damaged wells. Do not push the comb to the bottom of the tray, let the gel set before pulling it out, and keep the pipette tip from puncturing the well as you load.
A thick gel. Thermo Fisher pours horizontal gels about 3 to 4 mm thick; over 5 mm, bands can spread.
Degraded or salty samples. Use gloves and clean, nuclease-free tubes. A sample in a salty buffer can be diluted in nuclease-free water before the loading dye goes in.
The run itself. Too high or too low a voltage, or a run long enough to heat the gel, blurs the bands.
Waiting to look. Small bands spread if the gel sits before you image it.

Switch off before you touch the gel

A gel box runs current through salty buffer. Turn off and unplug the power supply before you open the lid, reach into the buffer or lift the gel out.

Wear gloves and goggles when you handle any DNA stain.

Common questions

Yes. You need a gel box and power supply, agarose, buffer, a DNA stain and a light to see it. All-in-one units such as miniPCR bio's blueGel combine the box, the power and a blue light.

It depends on the size of your DNA. miniPCR bio lists a 1% gel for about 400 to 8,000 bp and a 2% gel for about 100 to 2,000 bp.

Dissolve 1 g of agarose powder in 100 mL of buffer by heating it, then pour it into the gel tray with the comb in place.

miniPCR bio says blue light avoids the hazards of UV. Its stains, such as SYBR Safe and GelGreen, are sold as safer than ethidium bromide, but still wear gloves.

Most often too much DNA in the well, a damaged well or a gel run too hot or too long. Thermo Fisher suggests loading 0.1 to 0.2 µg of DNA per millimeter of well width.

The University of Utah's plans use acrylic sheet, Monel or copper wire electrodes and a 24 V power supply. With copper electrodes, use fresh buffer for every run.

Sources for this page

Compatibility details come from manufacturers' published documentation and can change. Confirm fit in your model's current manual before use.