Department of Organic Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.
Sci Rep. 2021 Jan 11;11(1):435. doi: 10.1038/s41598-020-80161-z.
The characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.
生物分子和纳米结构配合物的特性描述具有重要意义，有助于合理开发和设计纳米生物技术中的纳米材料和纳米器件。在这项工作中，我们使用了经分散修正的密度泛函理论（DFT-D）以及基于密度泛函理论的分子动力学模拟，从原子水平上理解了 DNA 碱基和 Au13 纳米团簇的相互作用特性。考虑到相对取向和距离，我们探索了相互作用分子的各种活性位点。我们的目标是激发两个实体之间的结合特性，并通过相互作用能、电荷转移、电子结构以及碱基-Au13 体系的分子性质来评估这种结合特性。这项综合研究的主要结果表明，核酸碱基与 Au 团簇具有很强的结合亲和力，属于化学吸附类型，遵循以下趋势：腺嘌呤>胞嘧啶>鸟嘌呤>胸腺嘧啶。AIM 分析表明，相互作用物质的结合性质主要是部分共价和高极性的。我们讨论了我们的发现对基因-纳米载体、生物传感应用以及 DNA 测序纳米器件的意义。
