The sensitivity of the model DNA containing dA .cntdot. dG and dG .cntdot. dG heteroduplex regions of defined length to S1 and mung bean single-strand specific nucleases was tested by polyacrylamide gel electrophoretic analysis of the distribution of product oligonucleotides. Single-base mismatch heteroduplexes were extremely resistant to these nucleases, although low levels of cleavage at the heteroduplex nucleotide were observed at high nuclease concentrations. The nuclease sensitivity of dA .cntdot. dG heteroduplex regions increased gradually as the length of the heteroduplex region increased from 1 to 6 nucleotides. The sensitivity of dG .cntdot. dG heteroduplexes 3-5 nucleotides long was considerably greater than that of the single dG .cntdot. dG mismatch.