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Methods:Gel Electrophoresis

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To separate analytes, whether nucleic acids or protein, based on size (1D) and Isoelectric point (2D).

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Materials Needed

  • Depends on the type of gel you intend to run, different analytes will require different gels.
  • Basic necessities:
    • Gel
    • Gel Electrophoresis apparatus(gel box and power source)
    • Analyte (DNA, RNA or protein)
    • Way to visualize your results after the gel is finished(staining)


  • Make the gel solution and pour it into the gel block, insert gel comb so wells form
    • allow gel to solidify
  • Mix dye with the sample and standards, separate from stock solutions
    • most wells cannot contain volumes greater than 20μL, so 10μL of 2X Dye and 10μL or less of analyte (depending on analyte concentration)
      • Analyte concentration will determine band intensity, bands can be too intense.
  • remove the comb from the solidified gel, orient the gel properly in the gel block and add appropriate electrophoretic buffer until wells are submerged.
  • Inject analyte/dye solution into wells (write down what was injected into each well!)
  • Place lid on gel box, connect to power source, and run until dye front is near the bottom of gel
    • Do not let dye front run off the end of the gel, as this could result in loss of analyte
  • Remove gel carefully to avoid tearing the gel and use selected visualization technique.



Agarose gel for DNA

University of Utah interactive slide show


User notes

2D gel visualization [1]

Way to improve visualization[2]

Molecular Weight[3]

Gel Gradients[4]


See Help:References for how to manage references in EcoliWiki.

  1. Van Belle, W et al. (2006) Adaptive contrast enhancement of two-dimensional electrophoretic protein gel images facilitates visualization, orientation and alignment. Electrophoresis 27 4086-95 PubMed EcoliWiki page
  2. Mohamed, MA et al. (1989) Polyacrylamide gel miniaturization improves protein visualization and autoradiographic detection. Anal. Biochem. 177 287-90 PubMed EcoliWiki page
  3. Weber, K & Osborn, M (1969) The reliability of molecular weight determinations by dodecyl sulfate-polyacrylamide gel electrophoresis. J. Biol. Chem. 244 4406-12 PubMed EcoliWiki page
  4. Muyzer, G & Smalla, K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73 127-41 PubMed EcoliWiki page