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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Revisiting the effects of sequence and structure on the hydrogen bonding and π-stacking interactions in nucleic acids
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Revisiting the effects of sequence and structure on the hydrogen bonding and π-stacking interactions in nucleic acids

机译：回顾序列和结构对核酸中氢键和π堆积相互作用的影响

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摘要

Calculated electron densities from PBE0/6-31+G(d,p) were analyzed with respect to the hydrogen bonding within a nucleic acid base pair and the π-stacking between sets of base pairs. From published X-ray crystallographic data, base pairs were isolated from a total of 11 DNA and RNA duplexes, and their experimental geometry was maintained throughout the analyses. Focusing solely on Watson-Crick base pairs, from the values of the electron density between interacting nuclei (at the bond critical points), we provide quantitative data on individual weak interactions. For hydrogen bonding, in addition to quantifying the scissoring effect in GC base pairs, the origin of the controversy around the relative stability of AT and AU base pairs is identified and resolved. Thus, it is illustrated how the conclusion as to their relative stability rests on the specific choice of oligonucleotides compared. For π-stacking, sequence effects for tandem AT base pairs are captured, quantified, and explained, and the greater sensitivity of GC, over AT, sequences to the rise parameter is established. The results presented here show that, from experimental geometries and their electron densities, previously determined effects of the sequence and structure of a duplex on the stabilizing interactions can be captured, quantified, and traced back to the geometry of the base pairs.
机译：关于核酸碱基对内的氢键键合和碱基对组之间的π堆积，分析了从PBE0 / 6-31 + G（d，p）计算出的电子密度。从公开的X射线晶体学数据中，从总共11个DNA和RNA双链体中分离出碱基对，并在整个分析过程中保持其实验几何形状。我们仅关注Watson-Crick碱基对，从相互作用核之间（键的临界点）的电子密度值，我们提供了有关单个弱相互作用的定量数据。对于氢键作用，除了量化GC碱基对中的剪除作用外，围绕AT和AU碱基对的相对稳定性的争论的起源也得到了确定和解决。因此，说明了关于它们的相对稳定性的结论如何取决于所比较的寡核苷酸的特定选择。对于π叠加，捕获，量化和解释了串联AT碱基对的序列效应，并且建立了相对于AT而言，GC对AT参数更高的敏感性。此处给出的结果表明，根据实验几何形状及其电子密度，可以确定，定量并追溯到先前确定的双链体序列和结构对稳定相互作用的影响，并可以追溯到碱基对的几何形状。

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