STRAND-SPECIFIC CLEAVAGE OF MISMATCH-CONTAINING DNA BY DEOXYINOSINE 3'-ENDONUCLEASE FROM ESCHERICHIA-COLI

A deoxyinosine-specific endonuclease, deoxyinosine 3'-endonuclease (Ya o, M., Hatahet, Z., Melamede, R. J., and Bow, Y. W. (1994) J. Biol. Ch em. 269, 16260-16268), from Escherichia coli was found to recognize mi smatches 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 S' endonuclease on mismatch-containing DNA was affected by the nature of the mismatches, The cleavage activity was also affected by the sequence context surrou nding 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, o ne 5' and the other 3' to the mismatch, abolishes the ability of the e nzyme to recognize the mismatch, Interestingly, deoxyinosine 3'-endonu clease showed strong strand specificity on DNA containing mismatches, and only one strand of the mismatch-containing DNA was nicked by the e nzyme, This strand specificity of mismatch cleveage was not affected b y the nature of the mismatch, Preliminary data suggest that the strand specificity is terminus de pendent; the enzyme cleaves the strand wit h the mismatch closer to its 5' terminus, However, when DNA duplexes c ontaining deoxyinosine were used as substrates, deoxyinosine 3'-endonu clease cleaved exclusively the strand containing deoxyinosine. Deoxyin osine 3'-endonuclease also cleaved single-stranded DNA containing deox yinosine, but not DNA containing normal deoxynucleotides or deoxynebul arine, suggesting the enzyme uses different mechanisms of recognition for deoxyinosine and mismatches in DNA.