The clone by copy and paste method allows you to set up an assembly from digested fragments in Benchling. As an overview, you will need to do the following in order to use this method:
- Make a copy of your plasmid for the assembly
- Select your enzymes
- Copy the insert sequence from your fragment and past it into the copy of the plasmid
Steps to clone by copy and paste
- Open a plasmid sequence, and open the History icon, click onto the version you want to clone, and then click Clone version
- Click into the Metadata tab of the new sequence and click the edit icon to edit the name of the sequence, ideally the name should reflect the assembled state
- In your fragment, copy the bases flanked by your restriction sites by clicking the name of the first restriction site and shift clicking the second restriction site
- Click Copy from the toolbar and confirm that you want to copy the DNA sequence
- In your copied plasmid sequence, shift select your two restriction sites then paste the insert into the sequence
- Press enter to confirm that that you want to insert the pasted bases
Note: Benchling will automatically reverse the fragment, if needed, and handle ligating sticky ends. Annotations and translations from first sequence should also have been brought along.