Aflatoxin B1-Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures

Thermal stabilities of DNA duplexes containing Gua (g), alpha- (a) or beta-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B-1 (b) differ markedly (T-m: a < g < b), but the underlying molecular origin of this experimentally observed phenomenon is yet to be identified and determined. Here, by employing explicit-solvent molecular dynamics simulations coupled with free-energy calculations using a combined linear-interaction-energy/linear-response-approximation approach, we explain the quantitative differences in T-m in terms of three structural features (bulkiness, order, and compactness) and three energetical contributions (non-polar, electrostatic, and preorganized-electrostatic), and thus advance the current understanding of the relationships between structures, free energies, and thermal stabilities of DNA double helices.