M.S. Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran.
Department of Mechanical Engineering, Hakim Sabzevari University, 397, Sabzevar, Iran.
Mol Biotechnol. 2020 Sep;62(9):423-432. doi: 10.1007/s12033-020-00261-z. Epub 2020 Jul 4.
Since less than a decade ago, the DNA origami technique has become an important tool in nanopore fabrication. DNA origami nanopores are highly efficient because of their compatibility with biomolecules and the possibility to precisely engineer their dimensions and designs. However, accurate comprehension of their molecular behavior under various conditions is still unsatisfactory. In this study, a thin plate DNA origami nanopore is designed and investigated using molecular dynamics simulation. The thin plate is designed using caDNAno software along with the square lattice method and the molecular dynamics simulation is performed using GROMACS software. The model is simulated in a wide temperature range and its stability is investigated. The shape and dimensions of the nanopore are also compared at these temperatures. The results indicate that the designed nanopore exhibits decent stability at these temperatures and no breakdown was observed despite some distortions in the structure at high temperatures. In addition, the effect of the number of staple strands on the structure, stability, and deformation of the DNA origami plate is investigated and it is found that addition of staple strands have a significant positive effect on the stability of nanopore's shape. By the results of analyzing the shape of the nanopore, it suggests that the proposed nanopore can be used to pass a wide range of molecules, macromolecules, and drug cargoes.
自不到十年前以来，DNA 折纸技术已成为纳米孔制造的重要工具。由于 DNA 折纸纳米孔与生物分子的兼容性以及精确设计其尺寸和设计的可能性，因此其效率非常高。然而，对它们在各种条件下的分子行为的准确理解仍然不尽人意。在这项研究中，使用分子动力学模拟设计和研究了薄片状 DNA 折纸纳米孔。使用 caDNAno 软件和正方形晶格方法设计薄片，并使用 GROMACS 软件进行分子动力学模拟。在很宽的温度范围内模拟模型，并研究其稳定性。还比较了这些温度下纳米孔的形状和尺寸。结果表明，尽管在高温下结构有些变形，但设计的纳米孔在这些温度下表现出相当的稳定性，没有发生击穿。此外，还研究了订书钉数量对 DNA 折纸板的结构，稳定性和变形的影响，结果发现添加订书钉对纳米孔形状的稳定性有明显的积极影响。通过分析纳米孔的形状得出的结果表明，所提出的纳米孔可用于通过广泛的分子，大分子和药物载体。
