Apurinic/apyrimidinic (AP) sites constitute the most frequent form of DNA damage. They have proven to produce oxidative interstrand cross-links, but the structural mechanism of cross-link formation within a DNA duplex is poorly understood. In this work, we study three AP-containing d[GCGCGCXCGCGCG]*d[CGCGCGKGCGCGC] duplexes, where X = C, A, or G and K denotes an α,β-unsaturated ketoaldehyde derived from elimination of a C4′-oxidized AP site featuring a 3′ single-strand break. We use explicit solvent molecular dynamics simulations, complemented by quantum chemical density functional theory calculations on isolated X:K pairs. When X = C, the K moiety in the duplex flips around its glycosidic bond to form a stable C:K pair in a near-optimal geometry with two hydrogen bonds. The X = A duplex shows no stable interaction between K and A, which contrasts with AP sites lacking a strand scission that present a preferential affinity for adenine. Only one, transient G:K hydrogen bond is formed in the X = G duplex, although the isolated G:K pair is the most stable one. In the duplex, the stable C:K pair induces unwinding and sharp bending into the major groove at the lesion site, while the internal structure of the flanking DNA remains unperturbed. Our simulations also unravel transient hydrogen bonding between K and the cytosine 5′ to the orphan base X = A. Taken together, our results provide a mechanistic explanation for the experimentally proven high affinity of C:K sites in forming cross-links in DNA duplexes and support experimental hints that interstrand cross-links can be formed with a strand offset