1.19.5 Primer Pairs

  • It is possible to pair an existing primer in a project with another new or existing primer in the project on the opposite strand.

Pairing Primers via the Primer Dialog

  • Open the Create or Edit Primer dialog and under the "Primer actions" section at the bottom of the dialog, click "Pair." You choose to pair your primer with an existing primer or a new primer (Figure

    Figure "Pair" in the Primer Design dialog.

  • In order to pair with an existing primer, you must have a primer on the opposite strand to pair with. Only primers on the opposite strand will appear as options to pair with your current primer (Figure
  • Or you can choose to pair the primer with a new primer.

    Figure Pairing a primer with an existing primer.

  • Pairing with existing or new primers, will open a second primer tab within the primer dialog with all the same primer options and with the opposite strand selected. In this dialog you also have the option to unpair the primers at any time using the "Detach Pair" button under the "Primer Actions". (Figure

    Figure Pairing a primer with a newly created primer.

  • You can also view the pair properties along the top of the Primer dialog; namely the Tm difference between the primers and the Product Length. Clicking on the "eye" icon to highlight the PCR product in the corresponding project sequence. (Figure

    Figure Pairing a primer with a newly created primer.

Pairing Primers via the Primer Summary Table

  • Primers can also be paired through the Primer Summary Table (Figure by selecting two primers on opposite strands and then pressing "Create Pair".

    Figure Pairing a primer through the Primer Summary Table.

  • Primers pairs can also be detached via the Primer Summary table. Click "Show Paired Primers" and this will take you to a summary table of just the paired primers. Select the pair you wish to detach and click the "Detach Pair" icon (see Figure
  • You can also detach primer pairs through the edit icon in the appropriate primer row and the primer editing dialog will reappear with the option to click the "Detach Pair" button .

    Figure Detaching a primer pair through the Primer Pairs Summary Table.