How can I create a primer?
SnapGene version 7.0 and later allow you to visualize primer insertions such as enzymes, codon or short peptide sequences added to your primers.
Option 1: Add a Known Primer Sequence
To create a primer, first open a target sequence, then click menu Primers → Add Primer... to open the "Add Primer" dialog.
Paste or type a sequence into the Primer field. The binding location of the primer (provided it matches the target sequence) will be displayed in the lower panel.
Option 2: Create a Primer Based on the Target Sequence
Switch to Sequence view, then select the desired primer binding site on your sequence. When you click the mouse and drag to select, the length and predicted melting temperature of the selected region will be shown.
To add a primer based on the selected region click menu Primers → Add Primer.
Specify the Selected Strand
Specify whether the primer should be based on the Top Strand (5'-3') or Bottom Strand (5'-3') of the selection.
Name the New Primer
Give the primer a name and if required add a description.
Modify a Primer (optional)
Click at the appropriate location within the primer sequence to make modifications to the primer sequence.
"Insertion tools" will appear to assist with addition of Codons, Enzyme sites or short features to the primer sequence .
Manually edit the primer sequence, or use the insertion tools to add sequence to the primer.
Example: Add an Enzyme Site to the Primer 5' end
Place the cursor at the 5' end of the primer.
Choose a restriction site from the Enzyme site drop down.
Choose whether to add upstream bases to ensure proper digestion.
Click Insert to add the site to the primer.
1). Any addition will be shown in red.
2). The new restriction site will be annotated with a green line. Hover over the site to see the enzyme name.
3). Information about the primer, including length, number of detected binding sites, number of annealed bases, and recalculated Tm are shown.
4). The new primer extension and it's predicted interaction with the target (if any) will be shown in the lower panel.
Click Add Primer to template to add the primer to your target sequence.
View the Primer
The new primer will be displayed on the target sequence.
Hover over the primer to see a tooltip showing details about the primer.
Click Save to save the target sequence and new primer.
