Gel Electrophoresis Simulator
Digest DNA, run the gel, read the bands
Cut a plasmid with real restriction enzymes, load the fragments into lanes beside a ladder, and run a gel whose migration is computed from the physics.
The takeaway
Migration distance scales with the log of fragment size, not size itself — which is why a gel resolves 500 bp from 600 bp beautifully and 9 kb from 10 kb not at all.
1 · The DNA
A synthetic plasmid with sites scattered around the whole circle. N cuts → N fragments.
2 · Restriction digest
3 · The gel
Hover or click a band to read its size.
Run conditions
Loaded lanes
How you actually read a gel: the standard curve
Plot the ladder's migration distance against log₁₀(size) and you get a straight line inside the gel's resolving window. To size an unknown band, you measure how far it ran and read its size off that line — that is the entire method, and it is why the ladder is not optional. Hover a band on the gel to place it on this curve.
Why does DNA move at all?
The sugar–phosphate backbone carries one negatively charged phosphate per nucleotide, at any pH you would run a gel at. So every DNA molecule has essentially the same charge-to-mass ratio and every DNA molecule is pulled toward the positive electrode (anode). In free solution they would all move at the same speed — useless. The agarose is the point: it is a mesh, and long molecules snag in it while short ones snake through. Separation comes from the sieve, not from the charge.
Why log₁₀, and why the % matters
Within the resolving window, migration distance falls off linearly with log₁₀(size) — a 10-fold smaller fragment travels a fixed extra distance. That is what this simulator computes. Raising the agarose percentage tightens the mesh: small fragments get resolved beautifully, but everything large jams up near the well. Drop to 0.5% and you can separate 10 kb from 20 kb — while a 300 bp band vanishes off the front. Pick the gel for the size range you care about.
Why some bands are brighter
Intercalating dyes bind along the duplex, so signal tracks mass, not molecule count. A digest gives equimolar fragments — one of each per plasmid — so a 3 kb fragment carries six times the mass of a 500 bp one and glows about that much brighter. This is why faint low-molecular-weight bands are easy to miss, and why a real ladder deliberately spikes reference bands so you can orient yourself instantly.