13.9 Primer Extensions

You can add an extension to a primer annotation using the “Edit Annotation” button in the sequence view or by double-clicking the annotation. You can also add a primer extension to an existing oligonucleotide PIC sequence by selecting Primers Add 5’ Extension. You can add an arbitrary sequence, a restriction site, and/or Gateway cloning site. Multiple components can be added to an extension, and the preview window in the 5’ extension dialog (figure 13.9 ) shows how the extension components will be arranged on the primer. The components can be rearranged by dragging and dropping them in this window. Primer extensions can also be added at the time the primer is designed from within the “Design New Primers” options.

The 5’ extension sequence and annotations are visible on primer annotations in the sequence view. The extension sequence is also shown in the list of the annotation’s properties in the Annotation Table.


Figure 13.9: Primer extension editing dialog


Figure 13.10: Primer with 5’ extension, shown as an extracted primer above, and mapped onto a sequence below

If a primer annotation is extracted to a separate document, the extension will be included. It is not covered by the binding region annotation, but may have its own annotations, as shown in figure 13.10 . If a PCR product is extracted using this annotation, the result will include the extension. Extensions have no effect on how Geneious Prime calculates binding characteristics of the primer and will be ignored when primer testing is conducted against potential target sequences.