Make a copy of your plasmid for the assembly

Open a plasmid sequence. From the the History panel on the right (clock icon), specify your desired name/folder and select Clone Version.

Select your enzymes for the assembly

In your newly cloned sequence, click the Digests button on the right-hand toolbar (scissors icon). Select the enzymes for the assembly by using the search bar or selecting from the list on the left-hand side of the tab. If the enzyme is not listed, you can always create new lists of enzymes in Benchling by editing your restriction enzyme settings. Hovering over the enzyme will display a separate tab on the left side that includes specifics about the enzyme. Click the number listed under Jump to Cut Site to view this region on the map.


Copy the region by selecting both cut sites on the plasmid map while holding Shift. Hit cmd/ctrl + C to copy this region. 

Open your second sequence file and find the enzyme cut sites and shift-select the region between them. Paste the copied region by hitting cmd/ctrl + V.

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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