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Molecules. 2019 Jan 2;24(1). pii: E150. doi: 10.3390/molecules24010150.

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

Author information

1
Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia. contact@martinklvana.com.
2
Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia. urban.bren@um.si.
3
Laboratory for Molecular Modeling, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia. urban.bren@um.si.

Abstract

Thermal stabilities of DNA duplexes containing Gua (g), α- (a) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B₁ (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.

KEYWORDS:

DNA; adduct; aflatoxin B1; formamidopyrimidine; free energy; linear interaction energy; linear response approximation; molecular dynamics simulation; molecular structure; thermal stability

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