page_title: Agarose gel electrophoresis
section_title: Staining and visualization
hierarchical_section_title: Agarose gel electrophoresis / General procedure / Staining and visualization
caption_attribution_description: English: Agarose gel following Agarose gel electrophoresis on UV light box Gel from a research project on hepatitis B virus Regulatory genomics research group at the University of Otago [1] Čeština: Agarózový gel po proběhlé DNA elektroforéze: pod UV lampou jsou patrné fluoreskující DNA „bandy“. Z výzkumného projektu viru hepatitidy B na University of Otago [2]
context_page_description: Agarose gel electrophoresis is a method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. The proteins may be separated by charge and/or size, and the DNA and RNA fragments by length. Biomolecules are separated by applying an electric field to move the charged molecules through an agarose matrix, and the biomolecules are separated by size in the agarose gel matrix.
  Agarose gel is easy to cast, has relatively fewer charged groups, and is particularly suitable for separating DNA of size range most often encountered in laboratories, which accounts for the popularity of its use. The separated DNA may be viewed with stain, most commonly under UV light, and the DNA fragments can be extracted from the gel with relative ease. Most agarose gels used are between 0.7–2% dissolved in a suitable electrophoresis buffer.
context_section_description: 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. 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 SYBR Green, GelRed, methylene blue, brilliant cresyl blue, Nile blue sulphate, and crystal violet. 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. 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, in vitro transcription, and PCR.  Exposure of the DNA to UV radiation therefore should be limited. Using a higher wavelength of 365 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 transillumintor, the shorter wavelength would be used to capture images, while the 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 or silver stains.
caption: The gel with UV illumination: DNA stained with ethidium bromide appears as glowing orange bands.
exif: {"Image Make": "Panasonic", "Image Model": "DMC-LZ5", "Image Orientation": "0", "Image XResolution": "72", "Image YResolution": "72", "Image ResolutionUnit": "Pixels/Inch", "Image Software": "Ver.1.0", "Image DateTime": "2007:03:09 01:32:59", "Image YCbCrPositioning": "Co-sited", "Image ExifOffset": "418", "Image PrintIM": "[80, 114, 105, 110, 116, 73, 77, 0, 48, 50, 53, 48, 0, 0, 14, 0, 1, 0, 22, 0, ... ]", "Thumbnail Compression": "JPEG (old-style)", "Thumbnail XResolution": "72", "Thumbnail YResolution": "72", "Thumbnail ResolutionUnit": "Pixels/Inch", "Thumbnail JPEGInterchangeFormat": "7077", "Thumbnail JPEGInterchangeFormatLength": "3148", "EXIF ExposureTime": "1/8", "EXIF FNumber": "14/5", "EXIF ExposureProgram": "Program Normal", "EXIF ISOSpeedRatings": "200", "EXIF ExifVersion": "0220", "EXIF DateTimeOriginal": "2007:03:09 01:32:59", "EXIF DateTimeDigitized": "2007:03:09 01:32:59", "EXIF ComponentsConfiguration": "YCbCr", "EXIF CompressedBitsPerPixel": "4", "EXIF ExposureBiasValue": "0", "EXIF MaxApertureValue": "3", "EXIF MeteringMode": "Pattern", "EXIF LightSource": "Unknown", "EXIF Flash": "Flash did not fire, compulsory flash mode", "EXIF FocalLength": "61/10", "EXIF FlashPixVersion": "0100", "EXIF ColorSpace": "Uncalibrated", "EXIF ExifImageWidth": "480", "EXIF ExifImageLength": "417", "Interoperability InteroperabilityIndex": "R98", "Interoperability InteroperabilityVersion": "[48, 49, 48, 48]", "EXIF InteroperabilityOffset": "6953", "EXIF SensingMethod": "One-chip color area", "EXIF FileSource": "Digital Camera", "EXIF SceneType": "Directly Photographed", "EXIF CustomRendered": "Normal", "EXIF ExposureMode": "Auto Exposure", "EXIF WhiteBalance": "Auto", "EXIF DigitalZoomRatio": "0", "EXIF FocalLengthIn35mmFilm": "37", "EXIF SceneCaptureType": "Standard", "EXIF GainControl": "Low gain up", "EXIF Contrast": "Normal", "EXIF Saturation": "Normal", "EXIF Sharpness": "Normal", "EXIF ImageUniqueID": "874e666d031ad3508d86040517f798fd"}