Figure 14.2: Characteristics of restriction site of Type II restriction enzymes.

Sticky Ends: The type II restriction enzymes cut the both DNA strand together to generates DNA with hanging DNA stretch with 4-6 nucleotide. These DNA stretch containing fragments are cohesive to each other as the sequence present on complex 1 will be complementary to the sequence present on complex 2.

Mechanism of Restriction-Methylation system: The mechanism of type-II restriction-methylation system to recognize foreign DNA to cut into small fragments and protect the methylated self DNA is given in Figure 14.3. it involves descrete steps as follows:

1. Recognition of clevage site: Type II restriction enzymes have specific recognition DNA sequences. To rapidly identify the site, enzyme scan the strecth of DNA through a non-specific interaction and diffusion along the length of DNA. To expedite the recognition process, enzyme does not makes interaction with the bases, instead, it makes contact with DNA back bone.

2. Binding to the recognition site: Once the recognition site is located, enzymes makes specific interaction with the nucleotides present at the recognition site via entry through the major groove. Hydrogen bonding and van der waals interactions play crucial role in this step. Enzyme: DNA closed complex formation induces major conformational changes in restriction enzyme.