Nuclease enzymes use a ‘cup’ shaped active site to interact with the DNA, allowing 16-18 nucleotides to be bound. Using specific residues in the nuclease, the restriction site can be identified in the nucleic acid, allowing targeted cleavage.
Conserved motifs are used to identify DNA sequences for cleavage, enabling interaction with specific nucleotides.
EcoRI and EcoRV are two nucleases found in E. coli and now commonly used in research, and both are homodimers.