= Agarose gel electrophoresis
<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.<Five Main Nucleic Acid Gel Electrophoresis Steps by Thermo Fisher Scientific>[Step 1, Selection and gel preparation; Recommended percentage of agarose gels for separation of DNA fragments]{ref} A compact circular <DNA> <molecule> need not migrate like linear <DNA> of the same <length>: geometry affects passage through the mesh.<Five Considerations for the Nucleic Acid Gel Electrophoresis Process by Thermo Fisher Scientific>[Effects of conformation, Figure 1: nicked circular, linear and supercoiled forms of the same DNA]{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>.<Agarose Gel Electrophoresis by Addgene>[Equipment; Pouring a Standard 1% Agarose Gel, steps 1–7; Loading Samples and Running an Agarose Gel, steps 1–9; Analyzing Your Gel]{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.<Five Main Nucleic Acid Gel Electrophoresis Steps by Thermo Fisher Scientific>[Step 1, Figure 3 and caption: same DNA ladder at three agarose percentages under the same conditions, including run time]{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>.
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