Effect of COF Presence on DNA Molecular Interactions: A QM/MM and MD Simulations Study,ChemistrySelect

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Effect of COF Presence on DNA Molecular Interactions: A QM/MM and MD Simulations Study
ChemistrySelect ( IF 1.9 ) Pub Date : 2021-09-22 , DOI: 10.1002/slct.202102157
Rahim Ghadari ₁ , Enayat Mohsenzadeh ₁

Affiliation

Four models of DNA including A-DNA, B-DNA, Triple helix-DNA (T-DNA), and Z-DNA along with a COF molecule were prepared. Molecular dynamics simulations were performed on all DNAs and their complex with COF (embedded DNAs in the central hole of COF). Comprehensive analyses such as Base pair distance, hydrogen bonding, Van der Waals, and electrostatic interaction numbers were carried out to investigate the effect of COF molecule on DNA intermolecular interactions. Furthermore, quantum-mechanics studies were performed to explore the accuracy of intermolecular and intramolecular interactions. The results obtained based on promolecular density in two selected base pairs. Noncovalent interaction (NCI) analysis to investigate the strength of hydrogen bonds, Van der Waals interactions, and steric effect was done. Density Overlap Regions Indicator (DORI) analysis was accomplished to study the accuracy of π-π stacking interactions between adjacent bases. δg functions were evaluated to analyze the strength of chemical bonds, hydrogen bonds and also the steric effect. The average distance between O^…H, N^…H, and H_…O that are contributing in H-bonding are ∼1.88, 1.97, and 1.95 Å in A-DNA, respectively. Also, the average number of H-bonding numbers in A-DNA calculated to be 14.43 and 13.04 in pure and complex form. All the achieved results showed that designed COF did not make any changes in DNA structures, but in some cases, had some effects on the interactions of DNAs.

中文翻译：

COF 存在对 DNA 分子相互作用的影响：QM/MM 和 MD 模拟研究

制备了四种 DNA 模型，包括 A-DNA、B-DNA、三重螺旋-DNA (T-DNA) 和 Z-DNA，以及一个 COF 分子。对所有 DNA 及其与 COF（嵌入在 COF 中心孔中的 DNA）的复合物进行了分子动力学模拟。进行碱基对距离、氢键、范德华力和静电相互作用数等综合分析，研究COF分子对DNA分子间相互作用的影响。此外，还进行了量子力学研究以探索分子间和分子内相互作用的准确性。基于两个选定碱基对中的前分子密度获得的结果。进行了非共价相互作用 (NCI) 分析以研究氢键的强度、范德华相互作用和空间效应。完成密度重叠区域指标 (DORI) 分析以研究相邻碱基之间 π-π 堆积相互作用的准确性。评估 δg 函数以分析化学键、氢键的强度以及空间效应。O之间的平均距离^... H、N ^... H 和 H _... O 对 H 键有贡献，在 A-DNA 中分别为~1.88、1.97 和 1.95 Å。此外，A-DNA 中氢键数的平均数计算为纯和复杂形式的 14.43 和 13.04。所有取得的结果表明，设计的 COF 没有对 DNA 结构产生任何改变，但在某些情况下，对 DNA 的相互作用有一些影响。

更新日期：2021-09-22

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