Biotechnology Index Glossary

Virtual Lab: Agarose Gel Electrophoresis of Restriction Fragments

The program running below is a simulation of an agarose gel electrophoresis setup that allows you to understand how restriction enzyme digests are analyzed. To get the best appreciation for this technique, it would be best to review the sections on Agarose Gel Electrophoresis of DNA and Restriction Mapping if you have not done so already.

NOTE: This program requires a browser that supports Java Version 1.1 or greater, which means Netscape 4.x or Internet Explorer 4. It will not run under earlier versions of those browsers.

To set up and run a gel:

  • Choose a DNA to digest from the drop down box on the upper left - a map of the DNA will appear in the scrolling window on the left.
  • Set the type of restriction digest to load in each of the first 4 lanes using the drop down boxes in the lower left panel.
  • Load the desired lanes by clicking appropriate "Load Lane" buttons. The 5th lane is set to contain molecular weight standards.
  • Click the Turn ON Power

There are several controls (buttons) you can use:

  • Turn ON Power and Turn OFF Power start and stop the electrophoresis. Once you start the power on a gel, you cannot load additional lanes.
  • Turn ON UV and Turn OFF UV toggles between seeing the gel under visible and ultraviolet light. The two bands seen under visible light are xylene cyanol (cyan) and bromophenol blue (blue), whereas under UV light, you see ethidium bromide-stained fragments of DNA. If you are using UV light and turn off the power, the molecular weight markers become labeled.
  • RESET clears the current gel DNA. This button is only active when the power is OFF.

One thing you will observe in the simulation is also important in the real world: if two fragments of DNA differ in size by only a small amount (say less than 100 bp for fragments larger than about 1 kb), they will run sufficiently close to one another to appear as a single band. In the real world, you can sometimes handle this kind of situation for a particular set of bands by altering the agarose concentration.

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Back to the index of Gel Electrophoresis of DNA and RNA

Last updated on January 8, 2000
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