Oligodeoxyribonucleotides (ODNs) with conjugated reactive groups are potential sequence-specific gene inactivating agents. The antitumor antibiotic CC-1065 binds preferably in the minor groove of A-T-rich sites of double-stranded DNA, and the cyclopropapyrroloindole (CPI) subunit of the drug alleviates adenines at their N3 position. Pure enantiomeric (+)- and (-)-CPI and its N5-methyl homologue (MCPI) were synthesized and conjugated to an ODN. These conjugates were evaluated for their ability to alkylate a target containing a duplex region immediately adjacent to a single-stranded complementary binding region for the ODN conjugate. The conjugates demonstrated excellent stability in physiologic conditions and stereospecific, hybridization-triggered alkylation of the synthetic ODN targets. The dependence of the reaction rates on sequence of the duplex target region was in accord with the predicted minor groove binding of the conjugated CPI. The reactivity was highly dependent on the structure of the cross-linking group. Natural (+)-enantiomers alkylate 10-20 times faster than the corresponding (-)-enantiomers. Regiospecificity of the alkylation reaction is conferred by the length of the spacer arm. N5-Methylation of the CPI moiety suppresses the reactivity by a factor of 3-5. Addition of a 1,2-dihydro-3H-pyrrolo[3,2-e]indole-7-carboxylate (DPI) binding subunit of CC-1065 between CPI or MCPI residues and an ODN results in a significant enhancement of the reactivity which is especially pronounced for (-)-enantiomers, The main products of sequence-specific alkylation were determined for complexes with the most efficient reactions.