Nucleic acid bulges have been implicated in a number of biological pro
cesses and are specific cleavage targets for the enediyne antitumor an
tibiotic neocarzinostatin chromophore in a base-catalyzed, radical-med
iated reaction. The solution structure of the complex between an analo
g of the bulge-specific cleaving species and an oligodeoxynucleotide c
ontaining a two-base bulge was elucidated by nuclear magnetic resonanc
e. An unusual binding mode involves major groove recognition by the dr
ug carbohydrate unit and tight fitting of the wedge-shaped drug in the
triangular prism pocket formed by the two looped-out bulge bases and
the neighboring base pairs. The two drug rings mimic helical DNA bases
, complementing the bent DNA structure. The putative abstracting drug
radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulg
e nucleotide. This structure clarifies the mechanism of bulge recognit
ion and cleavage by a drug and provides insight into the design of bul
ge-specific nucleic acid binding molecules.