In order to investigate the hydrogen-bonding interactions between Esch
erichia coli ribonuclease HI and the 2'-hydroxyl functions of the subs
trate, oligonucleotide duplexes containing 2'-amino-2'-deoxyuridine or
2'-fluoro-2'-deoxyuridine at a specific site were used, and their aff
inities for the enzyme were determined by kinetic analyses. The result
s indicate that the hydroxyl groups of the nucleoside 3'-adjacent to t
he 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 t
he results.