Editing Gel electrophoresis (section)

===Nucleic acids===
{{Main|Gel electrophoresis of nucleic acids}}

[[File: Pcr gel.png|thumb|An agarose gel of a [[Polymerase chain reaction|PCR]] product compared to a DNA ladder.]]

In the case of nucleic acids, the direction of migration, from negative to positive electrodes, is due to the naturally occurring negative charge carried by their [[sugar]]-[[phosphate]] backbone.<ref name=Lodish>{{cite book|author = Lodish H|title = Molecular Cell Biology|edition = 5th|publisher = WH Freeman: New York, NY|year = 2004|url = https://archive.org/details/molecularcellbio00harv|isbn = 978-0-7167-4366-8|author2 = Berk A|author3 = Matsudaira P|url-access = registration}}</ref>

Double-stranded DNA fragments naturally behave as long rods, so their migration through the gel is relative to their size or, for cyclic fragments, their [[radius of gyration]]. Circular DNA such as [[plasmid]]s, however, may show multiple bands, the speed of migration may depend on whether it is relaxed or supercoiled.  Single-stranded DNA or RNA tends to fold up into molecules with complex shapes and migrate through the gel in a complicated manner based on their tertiary structure. Therefore, agents that disrupt the [[hydrogen bond]]s, such as [[sodium hydroxide]] or [[formamide]], are used to denature the nucleic acids and cause them to behave as long rods again.<ref>Troubleshooting DNA agarose gel electrophoresis. Focus 19:3 p.66 (1997).</ref>

Gel electrophoresis of large [[DNA]] or [[RNA]] is usually done by agarose gel electrophoresis. See the "[[chain termination method]]" page for an example of a polyacrylamide DNA sequencing gel. Characterization through ligand interaction of nucleic acids or fragments may be performed by mobility shift [[affinity electrophoresis]].

Electrophoresis of RNA samples can be used to check for genomic DNA contamination and also for RNA degradation. RNA from eukaryotic organisms shows distinct bands of 28s and 18s rRNA, the 28s band being approximately twice as intense as the 18s band. Degraded RNA has less sharply defined bands, has a smeared appearance, and the intensity ratio is less than 2:1.