Gel electrophoresis is a standard molecular biology technique used to separate biomolecules (DNA, RNA, and proteins) based on their size and charge. Have your students learn about DNA gel electrophoresis by doing virtual restriction enzyme digests on Benchling. Best of all, it doesn’t require any experimental setup and can be done entirely in silico.

Simulate gel electrophoresis runs with a virtual restriction digest on Benchling

For any DNA sequence such as a plasmid or PCR product, Benchling can recognize cut sites for restriction enzymes and simulate the expected fragments of DNA after digestion with them. Different digests can be displayed on a virtual gel for students to predict the expected band patterning. Analysis of these simulated gel images prepares students to interpret data from their own experiments.

Try out this exercise below that illustrates varying DNA fragments after digestion of a vector with different restriction enzymes:

  • Copy the pBAD Vector into your own Project. Open and switch the view to Linear Map.
  • Open the Digests button, navigate to New Digest, and specify “NEB” and “Double Cutters” in the settings.
  • Search by the number of cuts, “1”, find and left-click on “AseI” to select this enzyme, and hit Run Digest.
  • Save the digest as “Linearized” and navigate to the Virtual Digest tab to see the simulated gel image.
  • Repeat Steps 3 & 4 with different sets of enzymes, Pair 1: ClaI - HincII and Pair 2: AccI - BglII and then view the Virtual Digest again.
  • Analyze the size of each band by clicking on it and specify a commercial DNA ladder or create your own.
  • Change the order of the lanes on the Virtual Digest by rearranging the digest tabs.

Record your experimental gel electrophoresis analysis in the Notebook

Teach your students how to perform an actual gel electrophoresis run in the lab using this example entry. Afterwards, show them how to use the Notebook to store gel images they acquire. Ask students to compare the acquired images with the simulated gel from the Virtual Digest and see if the results matched their predictions.


What’s next?

Check out this next module and teach your students all about: Molecular Cloning Methods (coming soon)

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