Sequence-selective inhibition of restriction endonucleases by the polyintercalator bis(methidium)spermine

The design of site-specific probes of double helical nucleic acid is complicated by the fact that the critical recognition features of a defined base sequence are still not well understood. We recently reported that the nucleic acid binding affinity of the polyinterialator bis(methidium)spermine (BMSP) was substantially increased over that of the corresponding monomer, ethidium bromide (EB). In addition, from binding studies with nucleic acid homopolymers and copolymers, BMSp was found to have substantially increased sequence specificity. If this sequence- selective binding is found in heterogeneous DNA, BMSp might selectively inhibit DNA-dependent enzymes. To test for selectivity with a noncovalently binding molecule, a "kinetic sampling" assay was devised. We report that the dimer, BMSp, selectively inhibits restriction sites on the pBR322 plasmid, while the monomer, EB, shows no selective action in competition with any of the restriction enzymes utilized.