Gel Electrophoresis Simulator
Equations in this simulation
| V | Voltage V (volts) | DNA is negatively charged, so it runs from the black electrode (−) toward the red one (+) | |
|---|---|---|---|
| d | distance between the electrodes | 15 cm in this tank; the field E is what matters, so a longer tank needs more volts | |
| E | electric field | about 5 to 8 V/cm for a standard run | |
| v | speed of a band | in cm per hour |
With the current values:
| μ₀ | mobility of DNA in free solution | 3 × 10⁻⁴ cm²/(V·s), the same for every length because charge and friction both grow with length | |
|---|---|---|---|
| L | length of the fragment (bp) | the gel is a sieve: long fragments are held back more | |
| T | Agarose T (% w/v) | a denser gel has smaller pores, separating small fragments better and large ones worse | |
| L* | the length the gel slows to half speed | an empirical fit; above about 20 kb in a 1% gel every fragment runs at the same limiting speed and they pile up in one band |
With the current values:
| a, b | the standard curve | a straight line fitted to the ladder bands; reading an unknown band off it gives its size | |
|---|---|---|---|
| R² | how well the line fits | it falls when ladder bands near the top or bottom leave the range the gel separates well |
With the current values:
| σ | width of a band | the band starts as wide as the well and spreads by diffusion; a long, slow run gives fuzzier bands, and Joule heating above about 10 V/cm smears them more |
|---|
With the current values:
| R | resistance of the buffer | about 1.6 kΩ for a mini gel in 1× TAE | |
|---|---|---|---|
| P | heating power | warms the gel and the buffer: too much and the gel smiles (the middle lanes run ahead) or melts |
With the current values:
How to use the gel electrophoresis simulator
- Lane 1 holds a ladder of known sizes, lane 2 an uncut plasmid, lane 3 the plasmid cut once, lane 4 the plasmid cut with two enzymes, lane 5 a PCR product and lane 6 any sizes you type. The gel starts running at once: the DNA moves from the black electrode toward the red one, with the blue loading dyes running ahead.
- Watch the run time and the dye front, and stop when bromophenol blue is about three quarters of the way down, before small fragments run off the end. Change the agarose percentage to see a dense gel separate small fragments and a dilute one separate large ones; turn the voltage up to run faster, and past about 10 V/cm see the bands smear and smile as the gel heats.
- Read the band sizes under the picture: the simulation fits a straight line of log size against distance to the ladder bands and reads each other band off it, with a question mark where a band is outside the ladder. The chart shows that standard curve. To pour the gel, use the Agarose Gel Calculator; to size bands from a real gel, the Gel Band Size Estimator.
Frequently asked questions
Why does DNA move through the gel?
Its phosphate backbone carries one negative charge per base, so in an electric field DNA moves toward the positive electrode. Charge and drag in free solution both grow with length, so every fragment would move at the same speed; the agarose mesh is what separates them, by holding back long molecules more than short ones.
Why does uncut plasmid give more than one band?
A plasmid straight from the cell is mostly supercoiled, twisted tightly on itself, which makes it compact and lets it run ahead of linear DNA of the same length. Plasmids with a break in one strand relax into an open circle that drags through the gel and runs behind. Cut once, the plasmid becomes a single linear band at its true length.
Which agarose percentage should I use?
About 0.7% for fragments of 5 to 20 kb, 1% for 0.5 to 10 kb, 1.5% for 0.2 to 3 kb, and 2 to 3% for 50 bp to 1 kb. Small fragments run together in a dilute gel, and in a dense gel large ones barely enter it. Above about 20 kb all fragments in an ordinary gel move at the same limiting speed and pile up in one band; pulsed-field gels are used for them.
How accurate is reading a band size from the ladder?
Within about 5 to 10% when the band lies between ladder bands in the middle of the gel, where log size falls in a nearly straight line with distance. It gets worse near the top and bottom of the gel and outside the ladder's range, and supercoiled or nicked plasmid cannot be sized against a linear ladder at all.
It says WebGL is turned off.
The 3D view needs WebGL, which every current browser has. It can be switched off by hardware acceleration being disabled in the browser settings, or by a very old graphics driver. Turn hardware acceleration on, or try another browser.
Is anything uploaded?
No. The simulation is drawn by your own browser with WebGL; nothing is sent anywhere, and it keeps working offline once the page has loaded.