BINDING OF NUCLEIC-ACIDS TO ESCHERICHIA-COLI RNASE HI OBSERVED BY NMRAND CD SPECTROSCOPY

To clarify the mechanism by which the RNA portion of a DNA/RNA hybrid is specifically hydrolyzed by ribonuclease H (RNase H), the binding of a DNA/RNA hybrid, a DNA/DNA duplex, or an RNA/RNA duplex to RNase HI from Escherichia coli was investigated by H-1-N-15 heteronuclear NMR. Chemical shift changes of backbone amide resonances were monitored whi le the substrate, a hybrid 9-mer duplex, a DNA/DNA 12-mer duplex, or a n RNA/RNA 12-mer duplex was titrated. The amino acid residues affected by the addition of each 12-mer duplex were almost identical to those affected by the substrate hybrid binding, and resided close to the act ive site of the enzyme. The results reveal that all the duplexes, hybr id-, DNA-, and RNA-duplex, bind to the enzyme. From the linewidth anal ysis of the resonance peaks, it was found that the exchange rates for the binding were different between the hybrid and the other duplexes. The NMR and CD data suggest that conformational changes occur in the e nzyme and the hybrid duplex upon binding.