Delete Restriction Fragment

How can I delete an internal restriction fragment in a circular vector?

Specify the Restriction Fragment

To select the restriction fragment, click on the first enzyme site, then either Shift-click on the second enzyme site or drag to the second enzyme site.

Open the Delete Restriction Fragment Dialog

To open the Delete Restriction Fragment dialog, click Actions → Restriction Cloning → Delete Restriction Fragment..., or simply press the Delete key.

Preview the Product

The Delete Restriction Fragment dialog will show the product preview in the Product tab. 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 the above example, the enzyme T4 DNA polymerase could be used to remove the 3' overhangs generated by KpnI and ApaI.

To view the settings, click the Vector tab at the top of the window, then review the blunting, enzyme selection, and fragment selection.

Specify the Bacterial Transformation Strain

To specify the bacterial transformation strain, click the Product tab, then click the Bacterial Transformation Strain menu to change the chosen strain or to edit the strains list.

Name the Product

Enter a name for the product, then click Clone.

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. The red and blue colors illustrate where the restriction fragment was deleted.

In Sequence view, the history colors illustrate more precisely where the restriction fragment was deleted.

To illustrate in History view where the deletion occurred, click the Delete Restriction Fragment operation name.