Navigate to Virtual Gel and Set Parameters
To simulate gel electrophoresis, navigate to the “PCR” tab in the top banner and select “Virtual Gel”, this will open the gel creation modal box.
The “Create virtual gel” modal box is split up into three sections. On the left you can select your gel’s agarose percentage and select which products to run across which lanes. In the center is the gel visualization where you can see the simulated gel, here you can also set the run time. In the right section you can see a preview of the file that is modified and run across the gel.
Start by setting the agarose percentage of your gel. You will see in the “Lanes” section that the first lane is automatically filled with a ladder, by default the Thermo Fisher High DNA Mass Ladder is selected, if you wish to change the ladder, select the dropdown and choose your ladder of choice (most commercially available ladders are available if you have a ladder you would like to add please contact us at info@fearlessleague.com). To add more lanes to your gel use the “+ Add lane” button. For each lane, click the “Select” dropdown and choose between “Restriction digest”, “PCR” or another ladder.
Simulating Gel Electrophoresis for Restriction Digestion
If you would like to simulate the gel for a restriction digestion, use the select dropdown next to the desired lane. Then choose “Restriction digest” > “Select file”. This will open the file selection modal box and you will be able to choose a file in your library. Once selected use the “Select” button to load this file into the selected lane.
For restriction digest you will see a new section under the “Lanes” section called “Digest” here you can select an enzyme group (unique cut, dual cut, unique/dual cut or show all), once this is selected you can use the “Select enzyme” dropdown to search for the desired enzyme name or to scroll and select the desired enzyme. If you would like to digest with multiple enzymes this is also possible, simply select the “+ Add enzyme” button and repeat the procedure to add another enzyme. Once your enzymes have been selected you will see the fragment(s) appear on your gel visualization interface in the center, additionally you will see in the region below called “Select region” the different fragments and the ranges of the original plasmid that they encompass. You can also hover over the bands on the gel visualization interface to see the exact size of that fragment.
Simulating Gel Electrophoresis for PCR
It is also possible to simulate the gel electrophoresis of PCR products. To do this start by adding a lane using the “+ Add lane” button. Once you have added the lane use the “Select” dropdown for that lane and select “PCR” > “Select file” this will open the file selection modal box for you to choose a file from your library. Once selected use the “Select” button to load this file into the selected lane. Under you will see the “Lane details” section now contains the PCR simulation tools, these function in the same manner as the tools under “PCR” > “PCR” as described in the guide/manual PCR, Mutagenic PCR and Automated Primer Design. Once you have created primers the resulting PCR product’s band / fragment will be displayed on the gel visualization interface in the respective lane. Again you can hover over the band to see its size.
Once you have finished creating your gel, select “Save” at the bottom right of the modal box. The gel will be saved to your library and the file will open in view mode. If you would later like to edit the gel you can open the file from your library and in view mode select the “Edit gel” button at the top right, this will take you back into the gel creation modal box.
Exporting Virtual Gels
Once you have finished creating your gel, you can export it as PNG, JPG or PDF format. This action can be performed in both the view mode as well as the gel creation modal box. Find the “Export” dropdown and select the desired export format. If using cloud the file will be downloaded directly to the download folder, if you are using the desktop application then you can choose a destination on your device and rename the file if desired.
