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Agarose gel electrophoresis uses a porous agarose polymer network. For linear double-stranded DNA within a suitable separation range, shorter fragments generally move farther in a fixed run. Raising the agarose concentration changes the mesh and the range of sizes that can be resolved.^[ref] A compact circular DNA molecule need not migrate like linear DNA of the same length: geometry affects passage through the mesh.^[ref]

A concrete laboratory example is Addgene's documented DNA separation protocol. Its standard 1% gel contains 1 g of agarose in 100 mL of TAE buffer. Dissolved agarose sets in a casting tray around a comb; removing the comb leaves sample wells. The gel is covered with the same buffer solution in a box connected to a voltage source. Loading buffer contains glycerol to increase sample density and a tracking dye to show run progress. A DNA ladder occupies a separate lane beside the samples. With wells near the negative cathode, DNA migrates toward the positive anode. After separation, bound stain makes the DNA visible by fluorescence under a UV transilluminator. The DNA ladder supplies the size reference; the tracking dye monitors migration but does not identify sample DNA.^[ref]

In the manufacturer's controlled comparison, the same DNA ladder runs in 1%, 2%, and 3% agarose gels with the same run time and other stated conditions. The changed gel band spacing shows why a calibration belongs to its particular gel conditions, rather than establishing a universal distance law.^[ref]

In interpreting an unknown sample, a blank lane tests for detectable background or carryover in that blank, while the DNA ladder checks migration and detection of its known fragments. An empty sample lane cannot by itself distinguish absent DNA from unsuccessful loading or insufficient detection. These controls answer different questions; neither makes matching migration a proof of matching nucleotide sequence.

Separation of charged molecules through a gel in an electric field. Denaturing conditions suppress folded structures, helping compare RNA lengths; matching migration alone does not establish an identical nucleotide sequence or identical covalent bonds. In the ribozyme experiments, labelled RNA was detected after separation by exposing photographic film.

In DNA agarose gel electrophoresis, the backbone phosphate groups carry negative electric charge under the usual mildly alkaline buffer solution conditions. DNA therefore moves toward the positive anode, away from the negative cathode.^[ref]

The electric field points the other way: the electric force $\mathbf{F}=q\mathbf{E}$ reverses direction when $q<0$. The apparatus is driven by an external source of electric potential difference; the positive anode convention here belongs to that operating mode. Direction follows electric charge, so it is not a rule that all molecules move toward the same electrode.

The useful result is a spatial comparison: a mixture becomes separated gel bands, which can be compared with a DNA ladder or recovered for subsequent analysis. Agarose gel electrophoresis of linear double-stranded DNA, gel electrophoresis of denatured RNA, and SDS-PAGE of proteins use different conditions to make migration informative about chain size. An electric field supplies motion; the gel supplies a porous obstacle course.