Create an Agarose Gel

How do I create and configure an agarose gel simulation?

Open the "Simulate Agarose Gel" Dialog

To open the Simulate Agarose Gel dialog, click Tools → Simulate Agarose Gel....

Select One or More Input Sequences

Select the sequences to display on the gel by one or a combination of the following methods:

  1. Select then drag and drop one or more files into the "Simulate Agarose Gel" window.
  2. Click  Choose DNA Sequences → Choose Sequence Files to browse to and select files on your computer.
  3. Click Choose DNA Sequences → Choose Open Sequences to select files currently open in SnapGene.

Select one or more sequences and click Remove to remove sequences.

Note that if you do not add any sequences and click OK then an "empty" gel will be created. You can add sequences after a gel is created.

Set the Order of the Input Sequences

Select one or more sequences and use the arrow buttons to reorder the sequences.

Name The Gel File

SnapGene 6.0 and later allow you to save agarose gel files.

Enter an appropriate name for the new gel file.

Click OK to create the gel.

Choose a MW Marker

If you are not using the default ladder then select Lane 1 on the gel, or in the list, and choose a new MW marker via the drop-down menu.

Add Additional Sequences to the Gel

To choose a lane, click a number above the gel, or click the lane number in the list, then click the dropdown to choose a sequence for the selected lane.

Alternatively, drag and drop a sequence file into the gel to add it to the selected lane.

To reorder lanes after they have been added see the lesson Rearrange the Gel Lanes.

View the Gel

SnapGene 5.2 and later can accurately simulates relative migration rates of supercoiled (covalently closed circular) DNA.

Prior to specifying digestion with restriction enzymes, SnapGene will simulate the migration of a circular sequence as supercoiled DNA. Uncut supercoiled sequences will be marked as such in the list.

Initially, all sequences will be displayed as uncut DNA. Circular sequences will be displayed as supercoiled fragments.

Choose a PCR Product

Select a lane/sequence with annotated primers and use the dropdown to choose "Amplify by PCR". Alternatively, click on a primer in Map or Sequence view to automatically switch to the "Amplify by PCR" option.

Set the primer pair for PCR using the dropdown menus in the lower panel, or in Sequence or Map view, click on first primer then shift-click on the second primer to set the primer pair.

The PCR product generated by the selected primer pair will be shown on the gel.

Digest a Sequence

Select a lane/sequence for digestion, by default the lane will be set to "cut with".

Use the dropdown menus to specify up to 4 enzymes for digestion of the selected sequence.

Alternatively:

  • Type the name of the enzyme/s in the fields provided
  • Select an enzyme site in Map or Sequence view (if enzyme sites are displayed).

The fragments generated by digestion with the selected enzymes will be shown on the gel.

Optional: Specify the Gel Buffer for Supercoiled Sequences

The migration of supercoiled DNA relative to linear DNA differs significantly depending on the electrophoresis buffer.

If you wish to change the electrophoresis buffer used for simulating the migration of supercoiled DNA, click the blue buffer indicator to open SnapGene Preferences.

Choose the new desired buffer, then close the Preferences window.