Navigate to Bulk Assembly

To access the Bulk Assembly tool, navigate to the blue navigation tool bar on the left-hand side of the workspace. Click on the Global create (+ icon), hover over "DNA Sequence" and select "Bulk Assemble DNA." 


The Bulk Assembly tool can be used to generate plasmids from various backbones and insert fragments, in bulk. Output plasmids are created in a combinatorial fashion; where 1 backbones and 2 inserts are matched together to create 2 unique, output plasmids (picture below). 

Assembling plasmids in bulk involves 4 steps:

  1. Selecting files to work with: Backbone and inserts
  2. Selecting fragment ends: Enzyme, Homology, Concatenation
  3. Select fragment size: Larger or smaller
  4. Select the direction: Forward or reverse

1. Select files to work with

For step 1, make sure that your backbone and insert fragments are saved in a folder(s) that you can easily recognize and navigate to. Once you've located your folder, you can designate each fragment(s) as your backbone and/or inserts. 

To highlight all of the fragments at once, click on the folder icon on the left hand side of the folder name. To select a specific set of fragments, click on the individual fragments or shift-click for bulk selection of sequences/folders. 

2. Select fragment ends by assembly method

Restriction enzymes

Scientists can choose a restriction enzyme that occurs exactly once in the sequence. The neighboring fragment must use a compatible enzyme on one of its ends.

Choose from a dropdown list of restriction enzymes. When selecting fragment ends for your insert, Benchling will automatically remember which restriction enzymes that were selected for the backbone and present them as options under the "Enzyme" list.


Scientists can search for a homologous region of the sequence, and use that to combine it with a neighboring fragment. Overlaps are used to orient the assembly of the fragments and not are duplicated. Select >7 base pairs as your homology region to assure that a non-specific region of your sequence is not selected.

Benchling will automatically remember the homology regions that were selected for the backbone and present them as options under the "Homology" text box.

If the homologous regions of two neighboring slots do not match exactly, you will see this error:


Users define the regions of the sequence entered in each slot, and concatenate those sequences together. Users define a region by either:  

  • searching for bases
  • selecting the start/end of the sequence.

3. Select fragment size 

Select the fragment piece that you'd like to assemble by choosing between the larger or smaller fragments. 

4. Select fragment orientation

Select the fragment orientation that you'd like. 

Use the display feature listed under the Fragment summary window to confirm that you’ve selected the correct fragment size and orientation

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