Virtual Lab: Agarose Gel Electrophoresis of Restriction Fragments

This program was formerly placed online by Dr. Richard Bowen of Colorado State University who has graciously allowed us to repost the simulator to use in our class.

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 Electrophoresis Concepts section of Experiment 10 if you have not done so already.

NOTE: You have two choices for running this simulation: go to the lab computers and do the simulation there or figure out how to get the simulation to run on your own computer. (It is highly probable that it will be easiest to use the lab computers.) If you have a PC, you can try going to Control Panel, Java, Security Tab, and click "Medium". (If the medium security level is not available, you have a version of Java that is too new and you are out of luck. Go to the lab.) Then in the Exception Site List, add http://baskaufs.github.io/virtual-gel/virgel.html to the list. Open a Firefox browser (not using Firefox? Again, you are out of luck. Go to the lab.) Then reload this page. You will get a series of warnings or dialog boxes. Do something like this: click on Activate Java, then Allow, then Later. Then click Run. If you are extremely lucky, you will see the electrophoresis simulator at the bottom of the page. If not, you are out of luck - go do the assignment on one of the lab computers. If you have a Mac… good luck, you are on your own!

Follow each step of these instructions carefully or it won't work!

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.


Sorry, but your browser is not Java-enabled.
This program will not be visible.
Last updated on January 8, 2000