The DNA groove interactions of the pluramycins determine the base-pair specificity to the 5'-side of the covalently modified guanine. The DNA reactivity of these drugs at defined sites can be further increased by structural and dynamic DNA distortion induced by TATA binding protein (TBP) binding to the TATA box. This enhanced drug reactivity has led to the proposal that protein-induced DNA conformational dynamics might be responsible for the more selective biological consequences of the pluramycins. To identify the structural and/or dynamic determinants that account for the enhanced drug reactivity, DNA heteroduplexes that contain base mismatches were examined for enhanced alkylation by altromycin B. The results demonstrate that base mismatches located at the 5'-side of the target guanine enhance drug reactivity. An analysis of the structural and dynamic properties of the base mismatches demonstrates that the pluramycin reactivities are not only determined by dynamic conformation of the base mismatch, which improves the accessibility of the drug to the DNA helix, but also by the specific groove interactions between the DNA and the drug, which results in stabilization of the precovalent drug-DNA complex. Having established that the highest pluramycin reactivity with heteroduplex DNA is produced by a thymine:thymine (T:T) mismatch, we next addressed how the same mismatch affects pluramycin reactivity in the flanking region to the TBP-TATA box complex. When this mismatch is introduced into the downstream flanking sequence of the TATA box, TBP binding cooperatively enhances the drug alkylation on a downstream guanine adjacent to the inserted mismatch. While an obvious structural similarity between the T:T mismatch and the TBP-induced effects at a downstream site of the TATA box does not exist, we propose that the base pair destabilizing effects of the T:T mismatch may resemble the dynamically accessible intercalation site on the downstream side of the TATA box induced by binding of TBP to the TATA box.