Strand-specific cleavage of mismatch-containing DNA by deoxyinosine 3'-endonuclease from Escherichia coli.

A deoxyinosine-specific endonuclease, deoxyinosine 3'-endonuclease (Yao, M., Hatahet, Z., Melamede, R. J., and Kow, Y. W. (1994) J. Biol. Chem. 269, 16260-16268), from Escherichia coli was found to recognize mismatches in DNA. Using DNA duplexes containing a unique mismatch, the enzyme was found to hydrolyze the second phosphodiester bond 3' to the mismatch. The cleavage efficiency of deoxyinosine 3'-endonuclease on mismatch-containing DNA was affected by the nature of the mismatches. The cleavage activity was also affected by the sequence context surrounding the mismatches. The presence of a G/C or C/G pair immediately 3' or 5' to the mismatch substantially reduced the ability of the enzyme to nick the mismatch-containing DNA. The presence of two G/C pairs, one 5' and the other 3' to the mismatch, abolishes the ability of the enzyme to recognize the mismatch. Interestingly, deoxyinosine 3'endonuclease showed strong strand specificity on DNA containing mismatches, and only one strand of the mismatch-containing DNA was nicked by the enzyme. This strand specificity of mismatch cleavage was not affected by the nature of the mismatch. Preliminary data suggest that the strand specificity is terminus dependent; the enzyme cleaves the strand with the mismatch closer to its 5' terminus. However, when DNA duplexes containing deoxyinosine were used as substrates, deoxyinosine 3'-endonuclease cleaved exclusively the strand containing deoxyinosine. Deoxyinosine 3'-endonuclease also cleaved single-stranded DNA containing deoxyinosine, but not DNA containing normal deoxynucleotides or deoxynebularine, suggesting the enzyme uses different mechanisms of recognition for deoxyinosine and mismatches in DNA.