The pyrrole–imidazole (Py–Im) triamide–cyclopropa pyrroloindole (CPI) conjugates ImPyImLDu86 ( 7 ) and ImImPyLDu86 ( 14 ) were synthesized and their alkylating activities and inhibitory effects on DNA hydrolysis by restriction endonucleases were examined. Sequencing gel analysis demonstrated that conjugates 7 and 14 specifically alkylated DNA at 5′‐CGCGC G ‐3′ and 5′‐PyGGCC Pu ‐3′, respectively. Agarose gel electrophoresis indicated that incubation of a supercoiled plasmid, pSPORT I (4109 bp), with conjugate 7 effectively inhibited its hydrolysis by Bss HII (5′‐G_CGCGC‐3′), whereas conjugate 14 had no effect on this hydrolysis. These results suggest that conjugate 7 sequence‐specifically inhibits the hydrolysis of DNA by Bss HII. Sequence‐specific alkylation by the Py–Im triamide–CPI conjugates was further confirmed by inhibition of the Eco 52I (5′‐C_GGCCG‐3′) hydrolysis of conjugate 14 ‐treated pQBI PGK (5387 bp). In clear contrast, hydrolysis of pQB1 PGK by Dra I (3′‐TTT_AAA‐3′) was not inhibited by 5 µM conjugate 14 . That ImImPy did not inhibit the hydrolysis of pQB1 PGK indicates that covalent bond formation is necessary for inhibition. A similar experiment, using linear pQBI PGK, achieved the same extent of protection of the DNA with approximately half the concentration of conjugate 14 as was required to protect supercoiled DNA from hydrolysis.