DNA和金纳米粒子自组装的分子动力学模拟

发布时间：2018-04-30 03:31

  本文选题：分子动力学模拟 + DNA-AuNPs　； 参考：《电子科技大学》2015年硕士论文

【摘要】：在DNA纳米技术中,利用DNA良好的编码性,结合纳米粒子进行生物纳米制造具有很大前景,同时也具有巨大挑战。在科学实验中,利用DNA和金纳米粒子(Au NPs)得到了完美晶体,制造出了纳米器械,这给DNA-Au NPs自组装研究带来了更多积极的启示。近期在DNA-Au NPs自组装的实验研究中,发现无化学官能团修饰的DNA和Au NPs具有吸附现象,能自组装成DNA-Au NPs结构单元,打破了传统的DNA和Au NPs的连接。随着计算机技术的高速发展,先进的计算机技术被广泛应用到DNA-Au NPs自组装的研究中,特别是分子动力学模拟技术的发展,加快了DNA-Au NPs自组装研究的脚步。本文基于分子动力学原理,应用Materials Studio分子模拟软件,对无化学官能团修饰的DNA和金纳米粒子(Au NPs)进行自组装模拟分析。体系建模采用全原子建模方式,能清楚的观察到模型的化学元素组成及其结构变化。目标体系由生物分子DNA、Au NPs和溶剂分子组成,其中DNA模型是从3D-DART模型生成器中得到的B-DNA骨架结构,包含10个腺嘌呤脱氧核苷酸,然后根据DNA的化学结构,利用Materials Studio软件补全DNA骨架结构中缺失的原子和化学键,得到完善的DNA全原子结构;Au NPs是金的晶体结构模型,由Materials Studio软件建模得到,由201个金原子组成;溶剂是由水分子组成。整个体系用分子力场中的COMPASS全原子模型力场进行描述。本文首先用分子动力学模拟的方法模拟实现了无化学官能团修饰的DNA和Au NPs自组装吸附的过程,分析了体系的能量变化,并发现静电相互作用力是DNA和Au NPs发生自主装吸附现象的主导因素。为了分析对DNA和Au Nps自组装吸附情况的影响因素,本文从平衡时间、均方根偏差(RMSD)、吸附能等方面研究水溶液和温度对吸附的影响。我们发现,水溶液对DNA-Au NPs自组装体系具有“奴役”作用,相对于真空体系,水溶液中的DNA的动力学特征和吸附作用更弱。另外,在DNA的活性范围内,温度对DNA-Au NPs自组装体系影响较大,在280K到360K的模拟温度下,我们发现,当体系温度为340K时,DNA和Au NPs的吸附作用最强,稳定性最好。
[Abstract]:In DNA nanotechnology, it has great prospect and great challenge to use DNA to code well and combine nanoparticles to fabricate biological nanocrystals. In scientific experiments, the perfect crystal was obtained by using DNA and gold nanoparticles au NPs, and the nanoscale instruments were manufactured, which brought more positive enlightenment to the study of DNA-Au NPs self-assembly. Recently, in the experimental study of DNA-Au NPs self-assembly, it was found that DNA and au NPs without chemical functional group were adsorbed and could self-assemble into DNA-Au NPs structure unit, which broke the connection between DNA and au NPs. With the rapid development of computer technology, advanced computer technology is widely used in the research of DNA-Au NPs self-assembly, especially the development of molecular dynamics simulation technology, which speeds up the research of DNA-Au NPs self-assembly. Based on the principle of molecular dynamics, Materials Studio molecular simulation software was used to simulate the self-assembly of DNA and au nanoparticles modified with no chemical functional groups. The chemical element composition and structure change of the model can be clearly observed by using the whole atomic modeling method. The target system is composed of NPs and solvent molecules, in which the DNA model is a B-DNA skeleton structure obtained from the 3D-DART model generator, containing 10 adenine deoxynucleotides, and then according to the chemical structure of DNA. By using Materials Studio software to complement the missing atoms and chemical bonds in the DNA skeleton structure, a perfect DNA all-atomic structure au NPs is obtained, which is a crystal structure model of gold, which is modeled by Materials Studio software and composed of 201 gold atoms, and the solvent is composed of water molecules. The whole system is described by the force field of the COMPASS model in the molecular force field. In this paper, the adsorption process of DNA and au NPs without chemical functional group modification was simulated by molecular dynamics simulation, and the energy change of the system was analyzed. It is also found that electrostatic interaction force is the dominant factor of DNA and au NPs self-loading adsorption phenomenon. In order to analyze the factors affecting the adsorption of DNA and au Nps, the effects of aqueous solution and temperature on adsorption were studied from the aspects of equilibrium time, RMSD deviation and adsorption energy. We found that aqueous solution has "enslavement" effect on DNA-Au NPs self-assembly system, and the kinetic characteristics and adsorption of DNA in aqueous solution are weaker than that in vacuum system. In addition, in the range of DNA activity, the temperature has a great influence on the DNA-Au NPs self-assembly system. At the simulated temperature of 280K to 360K, we find that the adsorption of DNA-Au NPs and au NPs is the strongest and the best when the system temperature is 340 K.
【学位授予单位】：电子科技大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：Q523;TB383.1
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本文编号：1822895