Separation by Size
Gel electrophoresis is the workhorse technique of molecular biology — virtually every genetics lab runs gels daily to verify PCR products, check restriction digests, and analyze DNA quality. The principle is elegant: DNA's uniform negative charge drives it through a porous agarose matrix under an electric field, with smaller fragments migrating faster than larger ones. The result is a pattern of discrete bands, each representing fragments of a specific size, that can be visualized with fluorescent dyes.
The Agarose Matrix
Agarose — a polysaccharide extracted from seaweed — forms a gel with pore sizes determined by concentration. At 0.5%, pores are large enough for fragments up to 30 kb to migrate. At 2%, the tight network resolves fragments as small as 100 bp but traps anything larger than 2 kb. Choosing the right concentration is the first decision in any electrophoresis experiment. This simulation models the pore network and shows how fragment size interacts with gel concentration to determine migration distance.
Voltage, Time & Resolution
Migration distance increases with both voltage and time, but these parameters also affect band sharpness. High voltage causes heating (Joule effect) that can melt the gel and cause band smearing. The optimal field strength is 5-8 V/cm for standard applications. Longer run times improve separation between similarly-sized fragments but risk running small fragments off the gel. The simulation lets you balance these tradeoffs and see how different conditions affect both migration distance and band resolution.
Reading the Gel
Interpreting a gel image is a fundamental skill in molecular biology. Sharp, bright bands indicate clean, concentrated DNA of uniform size. Smearing suggests degradation. Multiple unexpected bands may indicate non-specific amplification or star activity in restriction digests. The DNA ladder provides the size reference — plotting log(size) versus migration distance yields a straight line (Ferguson plot) from which unknown fragment sizes can be interpolated. This simulation includes a standard ladder lane for comparison.