Editing Gel electrophoresis (section)

==Applications==
*Estimation of the size of DNA molecules following restriction enzyme digestion, e.g. in [[restriction enzyme|restriction mapping]] of cloned DNA.
*Analysis of [[Polymerase chain reaction|PCR]] products, e.g. in molecular [[Preimplantation genetic diagnosis|genetic diagnosis]] or [[genetic fingerprinting]]
*Separation of restricted genomic DNA prior to [[Southern blot|Southern transfer]], or of RNA prior to [[Northern Blot|Northern transfer]].

Gel electrophoresis is used in [[Forensic chemistry|forensics]], [[molecular biology]], [[genetics]], [[microbiology]] and [[biochemistry]]. The results can be analyzed quantitatively by visualizing the gel with UV light and a gel imaging device. The image is recorded with a computer-operated camera, and the intensity of the band or spot of interest is measured and compared against standard or markers loaded on the same gel. The measurement and analysis are mostly done with specialized software.

Depending on the type of analysis being performed, other techniques are often implemented in conjunction with the results of gel electrophoresis, providing a wide range of field-specific applications.

===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.

===Proteins===
{{Main|Gel electrophoresis of proteins}}

[[File:SDSPAGE.png|thumb|right|'''SDS-PAGE [[autoradiography]]''' – The indicated proteins are present in different concentrations in the two samples.]]
[[Protein]]s, unlike nucleic acids, can have varying charges and complex shapes, therefore they may not migrate into the polyacrylamide gel at similar rates, or all when placing a negative to positive EMF on the sample. Proteins, therefore, are usually [[Denaturation (biochemistry)|denatured]] in the presence of a [[detergent]] such as [[sodium dodecyl sulfate]] (SDS) that coats the proteins with a negative charge.<ref name=Stryer /> Generally, the amount of SDS bound is relative to the size of the protein (usually 1.4g SDS per gram of protein), so that the resulting denatured proteins have an overall negative charge, and all the proteins have a similar charge-to-mass ratio. Since denatured proteins act like long rods instead of having a complex tertiary shape, the rate at which the resulting SDS coated proteins migrate in the gel is relative only to their size and not their charge or shape.<ref name=Stryer />

[[Protein]]s are usually analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis ([[SDS-PAGE]]), by [[Native Gel Electrophoresis|native gel electrophoresis]], by preparative native gel electrophoresis ([[QPNC-PAGE]]), or by [[2-D electrophoresis]].

Characterization through ligand interaction may be performed by [[electroblotting]] or by [[affinity electrophoresis]] in agarose or by [[capillary electrophoresis]] as for estimation of [[binding constant]]s and determination of structural features like [[glycan]] content through [[lectin]] binding.

===Nanoparticles===

A novel application for gel electrophoresis is the separation or characterization of metal or metal oxide nanoparticles (e.g. Au, Ag, ZnO, SiO2) regarding the size, shape, or surface chemistry of the nanoparticles.<ref>{{cite journal | url=https://pubs.acs.org/doi/full/10.1021/nl071615y | doi=10.1021/nl071615y | title=Separation of Nanoparticles by Gel Electrophoresis According to Size and Shape | year=2007 | last1=Hanauer | first1=Matthias | last2=Pierrat | first2=Sebastien | last3=Zins | first3=Inga | last4=Lotz | first4=Alexander | last5=Sönnichsen | first5=Carsten | journal=Nano Letters | volume=7 | issue=9 | pages=2881–2885 | pmid=17718532 | bibcode=2007NanoL...7.2881H }}</ref> The scope is to obtain a more homogeneous sample (e.g. narrower particle size distribution), which then can be used in further products/processes (e.g. self-assembly processes). For the separation of nanoparticles within a gel, the key parameter is the ratio of the particle size to the mesh size, whereby two migration mechanisms were identified: the unrestricted mechanism, where the particle size << mesh size, and the restricted mechanism, where particle size is similar to mesh size.<ref name="Barasinski2020">{{cite journal | last1=Barasinski | first1=Matthäus | last2=Garnweitner | first2=Georg | title=Restricted and Unrestricted Migration Mechanisms of Silica Nanoparticles in Agarose Gels and Their Utilization for the Separation of Binary Mixtures | journal=The Journal of Physical Chemistry C | publisher=American Chemical Society (ACS) | volume=124 | issue=9 | date=2020-02-12 | issn=1932-7447 | doi=10.1021/acs.jpcc.9b10644 | pages=5157–5166| s2cid=213566317 }}</ref>