Create a Primer

How can I create a primer?

To see a video about creating primers and PCR , see our "Getting Started" lesson, Primers & PCR.

Paste a Primer Sequence

To create a primer, click Primers → Add Primer... , then copy and paste a sequence.

Select the Binding Site (optional)

Alternatively, you can begin by selecting the desired binding site on your sequence. If you click the mouse and drag to select, the melting temperature of a corresponding primer will be shown.  To add the primer at the selected location, go to Primers → Add Primer.

Specify the Selected Strand (optional)

If the primer will be made from a selected binding site, specify whether the Top Strand or Bottom Strand of the selection should be used.

Name the Primer

If desired, type the primer name.

Edit the Description

If desired, type a description. The Description tab is open by default.

Modify the Primer (optional)

If desired, modify the primer to add a 5’ extension or introduce a mutation. There are two options.

One option is to manually edit the primer sequence in the text box.

The other option is to click in the primer sequence at the location of the change, and then click the Insertions tab. Use the dialog controls to add a desired codon, restriction site, or peptide coding sequence.

View the Binding Sites and Melting Temperature

The number of binding sites and the calculated melting temperature is shown at the bottom of the window. To see a summary of the melting temperature calculation methods, click the blue text at the lower right corner of the dialog.

View the Primer

Click Add Primer to Template to see the new primer.