Editing Agarose gel electrophoresis (section)

===Staining and visualization===
[[Image:AgarosegelUV.jpg|thumb|Agarose gel with UV illumination: DNA stained with [[ethidium bromide]] appears as glowing orange bands.]]

DNA as well as RNA are normally visualized by staining with [[ethidium bromide]], which intercalates into the major grooves of the DNA and fluoresces under UV light. The intercalation depends on the concentration of DNA and thus, a band with high intensity will indicate a higher amount of DNA compared to a band of less intensity.<ref name=":0" /> The ethidium bromide may be added to the agarose solution before it gels, or the DNA gel may be stained later after electrophoresis. Destaining of the gel is not necessary but may produce better images. Other methods of staining are available; examples are [[MIDORI Green]], [[SYBR Green I|SYBR Green]], [[GelRed]], [[methylene blue]], [[brilliant cresyl blue]], [[Nile blue]] sulfate, and [[crystal violet]].<ref>{{cite web |url=http://www.ncbe.reading.ac.uk/ncbe/protocols/DNA/PDF/DNA14.pdf |title=DNA revealed |work=National Centre for Biotechnology education |publisher=University of Reading |url-status=dead |archive-url=https://web.archive.org/web/20120304065032/http://www.ncbe.reading.ac.uk/ncbe/PROTOCOLS/DNA/PDF/DNA14.pdf |archive-date=2012-03-04 }}</ref> SYBR Green, GelRed and other similar commercial products are sold as safer alternatives to ethidium bromide as it has been shown to be [[mutagenic]] in [[Ames test]], although the [[carcinogenicity]] of ethidium bromide has not actually been established. SYBR Green requires the use of a blue-light transilluminator. DNA stained with crystal violet can be viewed under natural light without the use of a UV transilluminator which is an advantage, however it may not produce a strong band.

When stained with ethidium bromide, the gel is viewed with an [[ultraviolet]] (UV) transilluminator. The UV light excites the electrons within the aromatic ring of ethidium bromide, and once they return to the ground state, light is released, making the DNA and ethidium bromide complex fluoresce.<ref name=":0" /> Standard transilluminators use wavelengths of 302/312-nm (UV-B), however exposure of DNA to UV radiation for as little as 45 seconds can produce damage to DNA and affect subsequent procedures, for example reducing the efficiency of [[Transformation efficiency|transformation]], ''in vitro'' [[Transcription (genetics)|transcription]], and [[Polymerase chain reaction|PCR]].<ref>{{cite journal | vauthors = Gründemann D, Schömig E | title = Protection of DNA during preparative agarose gel electrophoresis against damage induced by ultraviolet light | journal = BioTechniques | volume = 21 | issue = 5 | pages = 898–903 | date = November 1996 | pmid = 8922632 | doi=10.2144/96215rr02| doi-access = free }}</ref>  Exposure of DNA to UV radiation therefore should be limited. Using a higher wavelength of 365&nbsp;nm (UV-A range) causes less damage to the DNA but also produces much weaker fluorescence with ethidium bromide. Where multiple wavelengths can be selected in the transilluminator, shorter wavelength can be used to capture images, while longer wavelength should be used if it is necessary to work on the gel for any extended period of time.

The transilluminator apparatus may also contain image capture devices, such as a digital or polaroid camera, that allow an image of the gel to be taken or printed.

For gel electrophoresis of protein, the bands may be visualised with [[Coomassie brilliant blue|Coomassie]] or [[silver stain]]s.
[[File:Cutting of the agarose gel.jpg|thumb|Cutting out agarose gel slices. Protective equipment must be worn when using UV transilluminator.]]