How do I simulate PCR amplification?

Open the PCR Dialog

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

Specify the Primers

If not previously specified, select the region to be amplified, and click Choose PCR Primers... . If the region to be amplified was already selected, the dialog for choosing PCR primers will appear automatically.

Type the desired Tm and click Choose Primers.

Choose PCR Primers

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

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 the name of the product, then click PCR.

View 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.

Specify the Sequence for PCR Amplification

To specify the sequence for PCR amplification, click to select the forward primer, then Shift-click to select the reverse primer plus the intervening sequence. For further information on creating or editing primers, see the "Create a Primer" lesson.

Alternatively, either before or after opening the PCR dialog, select the region to be amplified. SnapGene will then choose the primers as described below.

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.