Figure 13.1:
The primer design dialog
Geneious Prime uses Primer3 to design PCR primers. The Primer Design dialog allows you to set options for where your PCR primers should sit, what size product to return and characteristics such as primer length and melting temperature.
Three options are available for primer design: Design New, Design with Existing, or Design for Sequencing.
Design New designs a pair of forward and reverse primers. You can specify if you wish to design with or without a matching probe. Design with Existing can design a partner primer to match an existing one, for example a reverse primer for a forward or vice versa. It also allows you to design a probe to match a pair of primers. For both of these options, Generic (section 13.1.1 ) or Cloning (section 13.1.2 ) primers can be designed. Design for Sequencing (section 13.1.10 ) allows you to tile primers across a sequence in one or both directions to facilitate Sanger sequencing of the selected molecule or region.