Antisense phosphorothioate oligonucleotides direct both site-specific and nonspecific RNAse H cleavage of in vitro synthesized p120 mRNA

To determine the sequence specificity with which various antisense phosphorothioate oligonucleotides to the p120 gene could direct RNAse H-dependent cleavage of p120 mRNA, an in vitro RNAse H assay was done on in vitro synthesized p120 mRNA. Three oligonucleotides tested (ISIS 3462, coding region; ISIS 3466, 3' untranslated region; and ISIS 3782, 3' untranslated region) directed cleavage of p120 mRNA at the target sites. In addition, several additional cleavage products from nontarget sites were detected. A computer sequence homology search revealed that these additional bands probably result from cleavage at regions of complementarity of eight or nine contiguous bases of the oligonucleotide and the p120 mRNA. These findings suggest that such nontarget specific cleavages may account for multiple effects of phosphorothioate oligonucleotides.