Altun Ahmet, Garcia-Ratés Miquel, Neese Frank, Bistoni Giovanni
Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
Chem Sci. 2021 Sep 2;12(38):12785-12793. doi: 10.1039/d1sc03868k. eCollection 2021 Oct 6.
Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.
在此，我们运用先进的量子力学方法，对构成大部分人类B-DNA双链结构固有稳定性的分子间相互作用有了新的认识。我们的结果表明：（i）非相邻碱基对链间相互作用的影响小到可以忽略不计；（ii）伦敦色散效应对于双链结构的稳定性至关重要；（iii）对双链结构稳定性贡献最大的是沃森-克里克碱基对，这与之前的计算研究一致；（iv）相邻碱基间的堆积作用影响相对较小，但对双链结构稳定性仍然至关重要；（v）链内堆积与链间碱基配对相互作用之间不存在协同效应。这些结果与原子力显微镜测量结果一致，并首次为预测任意DNA序列热力学数据的最近邻方法提供了理论验证。
