13.1 Design New Primers

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.


Figure 13.1: The primer design dialog

Two options are available for primer design: Design New or Design with Existing. 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.

If any documents were selected which either are primer sequences or contain primer annotations then these will be made available for selection as primers in a drop-down box. Selected sequences are treated as primer or probe sequences if they are 150bp in length or less.

For each of these options, Generic or Cloning primers can be designed.

   13.1.1 Generic primers
   13.1.2 Cloning primers
   13.1.3 Tm calculation
    Tm estimates generated by Primer3
    Rough Tm
   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