How can I simulate destruction of a restriction site in a circular plasmid by digestion and blunting (polishing)?
Specify the Restriction Site
To select the restriction site, click the enzyme name.
Open the Destroy Restriction Site Dialog
To open the Destroy Restriction Site dialog, click Actions → Restriction Cloning → Destroy Restriction Site..., or simply press the Delete key.
Preview the Product
The Destroy Restriction Site dialog will show the product preview. If the sticky ends were incompatible, they will be blunted automatically as shown in the overview at the bottom.
Blunting (or polishing) simulates enzymatic backfilling or removal of single-stranded overhangs - see Blunting.
In this example, the enzyme T4 DNA polymerase could be used to remove the 3' overhangs generated by KpnI.
Specify the Transformation Strain and Name the Product
To specify the bacterial transformation strain, click the Product tab, then click the Bacterial Transformation Strain dropdown menu to change the chosen strain or to edit the strains list.
Enter a name for the product, then click Clone to create a new "Product" file.
View the Product History Colors
To turn on the product history colors in Map and Sequence views, click the "Show colors" button in the side toolbar and choose History Colors. The red and blue colors represent where the restriction site was destroyed.
In Sequence view, the history colors illustrate more precisely where the restriction site was destroyed.
To illustrate in History view where the restriction site was destroyed, click the "Destroy Restriction Site" operation name.
