How it Works
This simulation models vertical gel electrophoresis. Charged DNA fragments are loaded into wells at the top of a gel lane (the cathode end). When voltage is applied, the negatively-charged fragments are pulled downward toward the positive anode. As they move, the gel's polymer mesh acts like a sieve: small fragments slip through pores easily while larger ones are impeded more, so their migration speed falls off with size. Over time, fragments that started together in a well separate into distinct bands ordered from smallest (furthest travelled) to largest (closest to the well).
A ladder lane containing fragments of known standard sizes is run alongside unknown samples. Because migration distance follows an approximately power-law relationship with fragment size in the Ogston sieving regime, plotting log(distance) against log(size) for the ladder gives a nearly straight calibration line. Locating an unknown band's migration distance on that line and reading across lets you estimate its size — exactly how real gels are sized in a lab.
Sieving exponent: n = 0.35 + 0.25·C (steeper for higher gel % C)
Calibration: log(d) ≈ log(k·V/C) − n·log(size)
Band spread (diffusion): σ(t) grows roughly with √t
Frequently Asked Questions
How does gel electrophoresis separate molecules by size?
An electric field pulls charged molecules through a porous gel mesh. The mesh acts as a sieve: larger molecules get tangled and slowed more than smaller ones, so after a fixed run time molecules of different sizes end up spread into separate bands ordered by size.
Why do DNA fragments and most proteins migrate toward the positive electrode?
DNA carries a strong net negative charge from its phosphate backbone, so it is drawn toward the positive anode. Proteins have variable native charge, but in SDS-PAGE they are coated with the negatively-charged detergent SDS, which makes them migrate uniformly toward the anode too.
Why do smaller fragments migrate faster than larger ones?
Smaller molecules slip through the gel's random pore network with less obstruction, while larger molecules must repeatedly squeeze or route around mesh fibers, which slows their net velocity. This size-dependent drag is what turns a single field into a size-separation tool.
What does the % agarose or polyacrylamide concentration control?
Gel concentration sets the average pore size. A higher percentage gel has smaller pores, resolving small fragments well but running slowly, sometimes almost trapping large fragments. A lower percentage gel has larger pores, better for separating large DNA but with poorer resolution among similarly-sized small fragments.
What is a DNA ladder used for?
A DNA ladder is a mixture of fragments of known, standard sizes run in its own lane alongside samples. Plotting log(size) against migration distance for the ladder gives a near-linear calibration line; measuring how far an unknown band travelled and reading its position on that line estimates its size.
Why do bands broaden or blur over long run times?
Even molecules of identical size diffuse randomly as they move, so a band that starts as a sharp line gradually spreads into a wider, fainter zone. Running a gel too long trades resolution for spreading, which is why runs are stopped once the smallest fragments near the gel's far edge.
What are real-world applications of gel electrophoresis?
Gel electrophoresis underlies DNA fingerprinting and forensic profiling, verifying PCR product sizes, SDS-PAGE protein analysis, and the initial separation step in Southern, Northern, and Western blotting workflows used across molecular biology and diagnostics.
What is the difference between agarose and polyacrylamide gels?
Agarose gels have larger, less uniform pores and are typically used for DNA fragments from about 100 bp to tens of kilobases. Polyacrylamide gels have finer, more tunable pores and are used for high-resolution separation of small DNA fragments or proteins, as in SDS-PAGE.
Why is a constant voltage applied during a run?
A steady field keeps the electrophoretic force on each charged molecule constant, so migration speed depends predictably on size and pore structure rather than a changing field. This makes the ladder's calibration line reliable for sizing unknown samples.