How do I create and configure an agarose gel simulation?
Start the Simulate Agarose Gel tool
To create a gel simulation, click menu Tools → Simulate Agarose Gel....
Alternatively, to start the gel with selected inputs, select one or more input files in the Project folder side panel and click Simulate Agarose gel....
If required, use the dialog to add sequences to the gel simulation.
If required, select one or more sequences in the list and use the arrow buttons to set the order of the sequences.
Enter a name for the new gel, then click OK to create a gel file.
Set the MW Marker
If you are not using the default ladder then select the MW lane on the gel, or in the list, and choose a new "MW Marker" via the drop-down menu. If the ladder you have used is not in the default list then see Customise the MW marker List.
Add Additional Sequences to the Gel
- To choose a lane, click a number above the gel, or click the lane number in the list
- Click the dropdown to choose a sequence for the selected lane.
- Alternatively, use the Choose DNA sequences button to select 1 or more sequences to the gel.
To reorder lanes after they have been added see Rearrange the Gel Lanes.
View the Gel
Initially, all sequences will be displayed as uncut 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.
SnapGene accurately simulates relative migration rates of supercoiled (covalently closed circular) DNA. See How does SnapGene estimate supercoiled DNA migration rates in an agarose gel simulation?
Generate a PCR Product Fragment
- Select a lane with a sequence that has annotated primers.
- 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, ensure "Show Primers" is toggled on in the side toolbar and click on first primer then shift-click on the second primer to set the primer pair.
- The fragment amplified by PCR using 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".
- Specify the enzymes:
- Use the dropdown menus to specify up to 4 enzymes for digestion of the selected sequence, or
- Type the name of the enzyme/s in the fields provided, or
- Select an enzyme site in Map or Sequence view (if enzyme sites are displayed).
- The restriction fragments generated by digestion with the selected enzymes will be shown on the gel, and all fragment sizes will be shown in the list.
Optional: Specify the Gel Buffer for Supercoiled Sequences
The migration of supercoiled DNA relative to linear DNA varies 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.
