In order to investigate the hydrogen-bonding interactions between Escherichia coli ribonuclease HI and the 2′-hydroxyl functions of the substrate, oligonucleotide duplexes containing 2′-amino-2′-deoxyuridine or 2′-fluoro-2′-deoxyuridine at a specific site were used, and their affinities for the enzyme were determined by kinetic analyses. The results indicate that the hydroxyl groups of the nucleoside 3′-adjacent to the cleaved phosphodiester linkage and the second nucleoside 5′ to the cleaved phosphodiester act as both a proton donor and an acceptor and as a proton acceptor, respectively, in the enzyme-substrate complex. A molecular model was constructed using the interactions derived from the results.
