Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China.
School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan 430073, China.
Molecules. 2023 Jun 17;28(12):4833. doi: 10.3390/molecules28124833.
DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.
DNA 携带着合成 RNA 和蛋白质所需的遗传信息，在许多生物发育过程中发挥着重要作用。理解 DNA 的三维（3D）结构和动态对于理解其生物学功能和指导新型材料的开发至关重要。在这篇综述中，我们讨论了用于研究 DNA 3D 结构的计算机方法的最新进展。这包括分子动力学模拟，以分析 DNA 的动力学、柔韧性和离子结合。我们还探索了用于 DNA 结构预测或折叠的各种粗粒模型，以及用于构建 DNA 3D 结构的片段组装方法。此外，我们还讨论了这些方法的优缺点，并强调了它们的差异。
