User GuidesSnapGene User Guide Gibson Assembly®Circularize a Fragment by Gibson Assembly®

Circularize a Fragment by Gibson Assembly®

How do I simulate circularization of a DNA fragment by Gibson Assembly?

You can circularize a single fragment by Gibson assembly in SnapGene 6.0 and later.

Open a Sequence

Open the sequence for recircularization by Gibson Assembly.

The source sequence can be a linear sequence, or a circular sequence.

In Map view or Sequence view, select the region of the sequence to be recircularized.

Alternatively, right click on the sequence and from the contextual menu click Select Range to specify a precise nucleotide range.

Alternatively, you can select the region to be removed, then click Edit → Invert Selection to select the region of the sequence to be recircularized.

Start the Gibson Assembly Tool

Click Actions → Gibson Assembly → Assemble Multiple Fragments....

By default the "Gibson Assembly:Assemble Multiple Fragments" tool expects two input fragments.

The open document is set as "Fragment 1".

Click the "Number of Fragments" dropdown and choose "Fragment 2".

With "Fragment 2" selected, click the minus (-) button to delete the second fragment.

The select region of the single input sequence is now ready for primer design to create overlapping ends.

If your input sequence is a linear fragment that already has appropriate overlapping ends for Gibson Assembly, then:

  1. Choose the option "Use directly as the fragment".
  2. Give the Product an appropriate name.
  3. Skip the following "Design PCR primers step" and click Assemble.

Design PCR Primers

Switch to the Product tab and click Choose Overlapping PCR Primers....

Set the desired Tm and overlap for assembly.

Check the option to "Generate a circular product".

Click Choose Primers to design appropriate primers for amplification of the fragment.

Name the Primers

Switch to the Fragment tab and enter appropriate names for the newly designed primers (Optional).

Create the Product Sequence

The length of the overlap created by PCR using the newly designed primers, and the overlap Tm, is marked in the bottom panel.

Enter an appropriate name for the product sequence and click Assemble to generate a new product sequence file.

View Product Sequence History

The product sequence History records the above procedure as PCR and Gibson Assembly steps.