Chapter 13
Primers

Geneious Prime provides several operations for designing and working with PCR Primers and DNA or hybridisation probes. PCR Primers and DNA or hybridisation probes can be designed for or tested on existing nucleotide sequences or alignments. A PCR product can be extracted from a sequence that has been annotated with both a forward and a reverse primer. 5’ extensions consisting of restriction enzymes or arbitrary sequence may also be added to primer documents.

In addition Geneious Prime can determine the primer characteristics for a primer sized sequence and convert it into a primer. Characteristics can also be determined for any number of primer sized selections made in the Sequence View.

To use any one of these primer operations simply select the appropriate nucleotide sequences and either select Primers from the Tools menu or right-click (Ctrl+click on Mac OS X) on the document(s) and select Primers. A popup menu will appear showing the operations valid for your current selection.

  13.1 Design New Primers
   13.1.1 Generic primers
   13.1.2 Cloning primers
   13.1.3 Tm calculation
   13.1.4 Characteristics
   13.1.5 Primer Picking Weights
   13.1.6 Degenerate Primer Design
   13.1.7 Advanced Options
   13.1.8 Batch Primer Design
   13.1.9 Output from Primer Design
   13.1.10 When no primers can be found
  13.2 Manual primer design
  13.3 Importing primers from a spreadsheet
  13.4 Primer Database
  13.5 Test with Saved Primers
  13.6 Add Primers to Sequence
  13.7 Characteristics for Selection
  13.8 Convert to Oligo
  13.9 Primer Extensions
  13.10 Extract PCR Product
  13.11 More Information