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Aflatoxin B??Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures.

ABSTRACT: Thermal stabilities of DNA duplexes containing Gua (g), ?- (a) or ?-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B? (b) differ markedly (Tm: 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.

SUBMITTER: Klvana M 

PROVIDER: S-EPMC6337653 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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

Klvana Martin M   Bren Urban U  

Molecules (Basel, Switzerland) 20190102 1

Thermal stabilities of DNA duplexes containing Gua (<i>g</i>), α- (<i>a</i>) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B₁ (<i>b</i>) differ markedly (T<sub>m</sub>: 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,  ...[more]

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