AbstractOne popular recombinant DNA tool is the EcoRI endonuclease, which cleaves DNA at GAATTC sites and serves as a paradigm for sequence specific DNA‐enzyme interactions. The recently revised X‐ray crystal structure of an EcoRI‐DNA complex reveals EcoRI employs novel DNA recognition motifs, a four α‐helix bundle and two extended chains, which project into the major groove to contact substrate purines and pyrimidines. Interestingly, pyrimidine contacts had been predicted based on genetic and biochemical studies. Current work focuses on the EcoRI active site structure, enzyme and substrate conformational changes during catalysis, and host‐restriction system interactions.