SnapGene provides two different ways to Circularize/Linearize nucleic acid sequences.
Option 1: via Actions → Convert to Circular/Linear.
Option 2: via Edit → Change Sequence Properties → Topology (Circular/Linear).
These options can also be used when performing Bulk Actions - see Bulk Actions in SnapGene 8.0.
How do these two options differ, and which option should I use?
Option 1: Actions → Convert to Circular/Linear
This command simulates the equivalent of ligation (circularization) or enzymatic digestion (linearization).
Circularization requires at least one 5' phosphate on a linear fragment end. See Edit DNA Ends.
This option always creates a new "Product" file.
These operations are recorded as "Circularized" or "Linearized" steps in the History view of the new "Product" file.
Use Option 1:
- if you want to simulate circularization of a linear fragment (with compatible cohesive ends) by ligation, or
- if you select a restriction site on your sequence and chose "Linearize" to simulate digestion at that site.
Option 2: Edit → Change Sequence Properties → Topology (Circular/Linear)
This command converts sequence topology.
"Circularization" does not require a 5' phosphate on at least one of the linear fragment ends.
"Linearization" will always linearize before position 1 of the circular sequence and create blunt ends.
The existing file is updated. A new product file is not created.
These operations are recorded in the existing file History view as "Change Topology" steps.
Use Option 2 if:
- you have a file or files that has been created or imported with the incorrect topology.