Make a copy of your plasmid for the assembly

Open a plasmid sequence. From the the History panel on the right (clock icon), select Clone Version. 

Select your enzymes for the assembly

In your new sequence, click the Digests button on the right. Select enzymes for the assembly. Jump to their region on the map. See the finding enzymes in sequences help doc for an in-depth guide. You can always create new lists of enzymes in Benchling by editing your restriction enzyme settings. 

Hit cmd/ctrl + C to copy the region. The cut sites should get highlighted. Benchling will highlight all cut sites with compatible sticky ends.

Open your second sequence files and find the enzyme cut sites. Hit cmd/ctrl + V to paste the region.

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.

What's next? 

After reviewing this tutorial you might want to learn how to clone using the Digest and Ligate, Gibson, or Golden Gate Assembly Wizard.

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