How do I switch a sequence between circular or linear topology?
The "Circularize" command described below simulates circularization of a phosphorylated linear fragment by ligation using DNA ligase. This command will create a new circular product file, and record a "Circularization" step in the product file History.
In SnapGene 8.0 or later, if you want to correct a sequence wrongly imported as linear or circular, then use menu Edit → Change Sequence Properties → Topology. This command will update the existing file and record the step as "Change Topology" in the file History. To "bulk change" the topology of multiple files in one step see Bulk Actions in SnapGene 8.0.
Open a Linear DNA Sequence
Create, import or open a linear sequence.
Circularize the Linear Sequence
Click Actions → Circularize.
Choose to phosphorylate at least one 5' end (if requested) and click Phosphorylate.
When circularizing a linear sequence SnapGene simulates ligation by DNA ligase, hence the requirement for at least one phosphorylated 5' strand
A new file will be created. Enter a name for the new file, set the "Bacterial Transformation Strain" if required, then click Circularize.
Save the New Circular Sequence
Click Save, or click menu File → Save, to save the new circular sequence to an appropriate location.
Linearize a Circular DNA Sequence
Open a circular sequence and in Sequence view, click to the left of the position to set the precise "break" position for linearization. Alternatively, click menu Edit → Go To to set the coordinate to "Place insertion point cursor".
Click Actions → Linearize.
A new file will be created. Enter a name for the new file, then click Linearize.
Click Save, or click menu File → Save, to save the new linear sequence to an appropriate location.
Linearize a Circular Sequence at a Restriction Site
This linearization method simulates linearization by digestion with a restriction enzyme
Open a circular sequence, turn on display of restriction enzyme sites. In Map view or Sequence view, select the site for linearization (digestion).
Click Actions → Linearize.
Confirm the linearization (cut) position is correct, name the new sequence that will be created, then click Linearize.
By default the new sequence will be shown as an "interrupted" circle.
Click the "Show as interrupted circle" button in the side toolbar if you wish to view as a linear sequence.
View the linearized sequence in Sequence view. Linearization at a restriction site simulates digestion so will create phosphorylated single stranded overhangs for any enzyme that is not a "blunt"-cutter.