Digest and ligate can also be done by copying and pasting sequences. Please see cloning by copy and paste to learn how.
To access the Assembly Wizard, first open a sequence file. Look to the bottom of your screen and find Assembly Wizard next to Split Workspace. Click Assembly Wizard > Create New Assembly.
Select Digest and Ligate.
Start by opening the sequence for your backbone in Benchling and clicking on Backbone panel in the Assembly Wizard modal. Click on the restriction enzyme site of interest, hold shift, and click on the second restriction enzyme site. Right click and select Invert Selection to highlight the larger backbone piece. Your selection should look similar to the image below. In the Assembly Wizard, finally click Set from Selection.
To attach the insert, click on the Insert panel in the Assembly Wizard. Navigate to your insert sequence in Benchling and click on the first cut site and then shift-click the second cut site. Click Set from Selection.
Benchling will check that the sticky ends of the two sequences match and will display error messages in the Assembly Wizard. Reversing the orientation could help with sequence alignment.
If there are 0 errors or warnings, select the check box in the Wizard panel, name your assembly and click Assemble. You'll then be prompted to select a folder you want to store this new construct.
When the new sequence opens, open the history panel on the right and click the Lineage tab. You’ll see lineage information about your assembly.