Primer Design

Geneious Prime provides a number of tools for the importation, design and testing of oligonucleotide primers, primer-pairs and primer-pair/probe combinations.

Most of the tools described in this tutorial can be accessed via the Primers button on the Geneious Toolbar.

Some general guidelines for primer design:

• Binding region should be 17-27 bp
• Binding region Tm's in the range of 50 to 65°C
• Moderate G+C content
• Avoid repetitive poly-N regions
• Avoid secondary structure (hairpins, self dimerisation or primer dimer)
• Primer pairs should have similar Tm's (±4°C)

If you want to open the tutorial in a different window, click the new window button in the top right corner of this help window . If you prefer to view this tutorial on the web, click here.

Use the link below to jump to Exercise 1.

Exercise 1: A Primer primer
Exercise 2: Manual entry of primers
Exercise 3: Importing tables of primers
Exercise 4: Manual design of primers
Exercise 5: Design of PCR primer pairs
Exercise 6: Testing primers against a target
Exercise 7: Degenerate primer design