Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia.
Laboratory for Molecular Modeling, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
Molecules. 2019 Jan 2;24(1):150. doi: 10.3390/molecules24010150.
Thermal stabilities of DNA duplexes containing Gua (), α- () or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B₁ () differ markedly (T: 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.
含有 Gua()、α-()或β-()异构形式的酰胺嘧啶-N7-9-羟基黄曲霉毒素 B₁()的 DNA 双链的热稳定性差异显著（T：a < g < b），但这种实验观察到的现象的潜在分子起源尚未确定和确定。在这里，我们通过使用显式溶剂分子动力学模拟结合使用组合线性相互作用能/线性响应近似方法的自由能计算，根据三个结构特征（体积、有序性和紧凑性）和三个能量贡献（非极性、静电和预组织静电）来解释 T m 的定量差异，从而推进了我们对 DNA 双螺旋结构、自由能和热稳定性之间关系的理解。
