Frequently, a PCR product must be further manipulated by cleavage with restriction enzymes. For convenience, restriction enzyme digestion can be performed directly in the PCR mix without any purification of the DNA. This table summarizes the percent activity of restriction enzymes on the DNA in the Taq PCR mixes described below.

In these reactions, 5 units of restriction enzyme were incubated at the appropriate reaction temperature for 1 hour in a PCR mix containing 1 µg of DNA and 1 unit of Taq DNA Polymerase in a 50 µl reaction volume of 1X ThermoPol Buffer or 1X Standard Taq DNA Polymerase Buffer supplemented with dNTPs (200 µM final concentration). Enzyme activity was analyzed by gel electrophoresis.

Notes: The polymerase is still active and can alter the ends of DNA fragments after they have been cleaved, affecting subsequent ligation. Primers containing the recognition site of the restriction enzyme can act as competitive inhibitors in the cleavage reaction. The use of restriction enzymes under non-optimal conditions does increase the likelihood of star activity. If any problems are encountered, the DNA should be purified using a commercial spin column or by phenol/chloroform followed by alcohol precipitation.

Please also check these additional information about:
Activity of Restriction Enzymes in a Vent PCR Mix

Chart Legend: Cleavage in extension mix with 5 units of enzyme: 
+++ complete cleavage;   ++ ~50% cleavage;   + ~25% cleavage; – no activity