The recognition site for Xho1 enzyme is 5CTCGAG and for Sal1

The recognition site for Xho1 enzyme is 5\'CTCGAG, and for Sal1 enzyme is 5\'GTCGAC. Both enzymes make staggered cuts (arrow heads). Design a strategy to join two pieces of DNA one cut with Xho1 and another one cut with Sal1. SHOW ALL STEPS INVOLVED.

Solution

Xho1 and Sal1 produce compatible ends. It is notoriously difficult to work with this combination. Another important fact is once ends produced by Xho1 and Sal1 ligates among them. It cannot be cleaved by either of the enzyme later. Compatible Cohesive Ends are produced when you have two separate enzymes that recognize very similar sequences, and cut so that the overhang produced by one can hydrogen-bond with the overhang produced by the other.

Cutting using Xho1 and Sal1 enzymes produces the following Cohesive ends.

    --G                                       TCGAG--

    --CAGCT                                       C--

The resulting cohesive ends can then be ligated together and it produces following sequence.

            --GTCGAG--

            --CAGCTC--

In this particular case, the resulting site cannot be cut by either Xho1 or Sal1 again. However, there are cases where the site is still recognized by one of the enzymes.