Design primers

Primer Design picks pairs with primer3 from your plasmid or a pasted sequence. Batch mode designs pairs for many targets with the same settings.

Design one primer pair

1. Open the plasmid and select the region to amplify.
2. Right-click and choose Create, then Design Primers. Or run Primer Design from the command palette (Ctrl/Cmd+K).
3. Check Target Region, or paste bases into Target Sequence.
4. Choose a Primer Type: PCR, Sequencing, Mutagenesis or Cloning.
5. Adjust Constraints if needed, then click Design Primers.
6. Tick the pairs you want. Then click Save N Pairs, Add to map, Export CSV, Plate Order CSV or Export FASTA.

Saved primers go into the plasmid's project.

Design primers for many targets

1. In Primer Design, click Batch at the top.
2. Under Global settings, set the primer type and constraints. They apply to every target.
3. Click Target (the plus button) for each target. Give each a unique name and paste its DNA.
4. Click Design batch.
5. Click Best pairs plate CSV to download an order sheet.

Plate CSV columns

Check a Tm

• Select up to 200 bases on the map. The Selection pane shows their Tm.
• For an oligo that is not on the map, run Tm Calculator. Choose Single primer or Primer pair.
• Pick a Polymerase / buffer preset: Taq, Phusion or Q5. Override Na+, Mg2+, dNTPs and primer concentration if needed.