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Molecules 2019, 24(1), 150; https://doi.org/10.3390/molecules24010150

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

1
Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
2
Laboratory for Molecular Modeling, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
*
Author to whom correspondence should be addressed.
Received: 5 December 2018 / Revised: 21 December 2018 / Accepted: 26 December 2018 / Published: 2 January 2019
(This article belongs to the Special Issue Receptor-Dependent QSAR Methods)
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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. View Full-Text
Keywords: adduct; aflatoxin B1; DNA; formamidopyrimidine; linear interaction energy; linear response approximation; free energy; molecular dynamics simulation; molecular structure; thermal stability adduct; aflatoxin B1; DNA; formamidopyrimidine; linear interaction energy; linear response approximation; free energy; molecular dynamics simulation; molecular structure; thermal stability
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Klvana, M.; Bren, U. Aflatoxin B1–Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures. Molecules 2019, 24, 150.

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