The monoalkylation and cross-linking reactivities of a group of four structurally related DNA-DNA interstrand cross-linkers have been determined on restriction enzyme fragments and select oligomers. These highly potent cytotoxic DNA-DNA cross-linkers consist of two cyclopropa[c]pyrrolo[3,4-3]indol-4(5H)-one indoles [(+)-CPI-I] joined by a urea (Bizelesin) or a bisamido furan, bisamido pyrrole, or bisamido N-methylpyrrole linker. Using a thermal cleavage assay in combination with radio-labeled restriction enzyme fragments, we have shown that these compounds cross-link duplex DNA six or seven base pairs apart on opposite strands, but they differ among themselves for both alkylation reactivity and DNA sequence selectivity. Bizelesin and the [(+)-CPI-I](2) bisamido furan and [(+)-CPI-I](2) bisamido N-methyl pyrrole compounds prefer purely AT-rich sequences (e.g., 5’-(T) under bar(A/T)(4) or (5)A*-3’, where (T) under bar represents the cross-strand adenine alkylation and A* represents an adenine alkylation), while the [(+)-CPI-I](2) bisamido pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., 5’-(T) under bar(A/T)(2)G(A/T)(2)A*-3’). By comparison of the cross-linking reactivity of the four compounds in 21-mer duplex oligomers containing strategically placed GC or IC base pairs, the sequence and linker requirements for high reactivity of the six- and seven-base-pair cross-linkers in 5’-(T) under bar(N)(4) or (5)A*-3’ sequences were determined. In the duplex, to attain highest reactivity, a centrally placed GC base pair and the exocyclic 2-amino group were required, while for the linker in the bisamido pyrrole compound, an unsubstituted amine in the pyrrole ring was necessary. On the basis of the known requirements for monoalkylation of duplex DNA by (+)-CPI-derived compounds and the structural consequences of monoalkylation, together with the information gleaned from this study, we are able to provide a rationale for the structural requirements for the specific sequence cross-linked with high reactivity by the pyrrole compound. We propose that, because monoalkylation of the duplex produced a bent DNA duplex that is unsuitable for cross-linking, the duplex has to first undergo a ligand-induced rearrangement involving two hydrogen-bonding donor-acceptor pairs, which reinstates the requirements necessary for the second alkylation reaction.