A model for the dynemicin-DNA complex has been constructed by using energy minimization (EM) and molecular dynamics (MD) techniques. The model is consistent with the available experimental data. This has allowed us to gain insights into (1) how dynemicin A is activated into a DNA cleaver, (2) its mode of binding to DNA, (3) the absolute stereochemistry of dynemicin A, and (4) its DNA cleavage patterns and specificity.