How do I simulate PCR amplification?

Open the Template Sequence

Open the sequence that will be the template for PCR.

In Map view or Sequence view, select the region for amplification.

Start the PCR Tool

To open the PCR dialog, click Actions → PCR....  

Specify the Primers

When the region for amplification is selected prior to running the tool, the tool will automatically open the "Choose Primers" dialog.

If no sequence was open or selected prior to running the PCR tool, then select the "Template" via the dropdown, select the region for amplification, then click Choose PCR Primers....

Type the desired Tm for the primers and click Choose Primers.

Choose PCR Primers

In the PCR dialog, review the primer names and phosphorylation state.

Manually add primer extensions if required.

Choose the Polymerase

Use the Polymerase: menu to choose the type of ends for the amplified fragment.

Name the Product

When you are ready to simulate PCR, type an appropriate name for the product, then click PCR.

View and Save the Product

The product will be shown in a new window. For information on using SnapGene to clone an amplified fragment into a vector, see the Insert Fragment lesson.

Click File → Save to save the product sequence to an appopriate location on your computer.

PCR with Preexisting Primers

To perform PCR using preexisting primers on a sequence, open sequence file, click to select the forward primer, then Shift-click to select the reverse primer plus the intervening sequence, then click Actions → PCR....  

Review the PCR History

To view the product history, switch to History view.

A list of PCR primers and their sequences can be obtained by clicking the primer names. The primer sequences can then be copied and pasted into a text file.