Backbones & Assembly

Choose a plasmid backbone for your design, export complete plasmid maps, and generate junction primers for cloning.

Selecting a backbone

Click the Backbone button in the editor toolbar to open the backbone picker. You can filter by organism, cloning method, and resistance marker. Backbones with full sequences show their length in base pairs; those marked “metadata only” have curated annotations but no sequence data yet.

What a backbone affects

• GenBank export — When a backbone is selected, the exported file contains the full plasmid: backbone sequence with your circuit insert spliced in at the insertion site. All backbone features (origin, resistance marker, etc.) are annotated with correct offsets.
• Primer design — The Backbone Assembly method appears in the Primer dialog when a backbone is set. It generates junction primers that bridge your circuit fragments to the backbone flanking regions, ready for Gibson or Golden Gate assembly.

Synthesis ordering and the sequence viewer operate on the circuit insert only and are not affected by backbone selection.

Available backbones

The database includes common lab vectors such as pUC19, pET-28a(+), pSB1C3, pBAD33, pACYC184, pBR322, pRS series (yeast), and more. Three backbones (pUC19, pBR322, pACYC184) have verified NCBI GenBank sequences; the rest have curated metadata.

Removing a backbone

To remove a backbone from your design, open the backbone picker and click Remove on the green indicator bar. Your circuit elements are unaffected — only the backbone association is cleared.