Each restriction enzyme recognizes and cuts at a specific palindromic sequence. For example, the commonly used restriction enzyme EcoRI binds to and cleaves the palindromic sequence 5'-GAATTC-3'. The two strands of DNA will have the following complementary sequences at the EcoRI site:
Top strand: 5'-...G AATTC... = ...CTTAA G...-3'
Bottom strand: 3'-...C TTAA G... = ...GAATTC...-5'
The palindrome is evident in the complementary sequences. When the DNA is cleaved by EcoRI, the two resulting sticky ends will also be palindromic, allowing for easy ligation to other restriction fragments with compatible overhangs.
Furthermore, some restriction enzymes cleave the DNA strand within the recognition sequence, while others cut a few nucleotides away from the site. This property leads to either blunt ends or cohesive ends (also known as "sticky ends") upon digestion, respectively. Understanding the palindrome recognition and cleavage pattern of restriction enzymes is crucial for manipulating and analyzing DNA in genetic engineering and biotechnological applications.