Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein-nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. In this review, we describe recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. We highlight the use of diverse computational methods to address specific problems of the fields and discuss unexplored possibilities that lie ahead for the computational approaches in these areas.

中文翻译：

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DNA 复制和修复机制的分子机制：来自微观模拟的见解。

繁殖是生物活动的标志，需要精确复制遗传物质，以使后代继承父母的特征。在所有活细胞中，DNA 复制过程是通过多种蛋白质的协同作用来进行的，形成松散的蛋白质-核酸复合物，即复制体。校对和纠错通常伴随着复制，但也独立发生，在细胞周期的所有阶段保护遗传信息。细胞内过程的生化表征、蛋白质组学和单分子生物物理学的出现带来了丰富的信息宝库，等待着将其组装成 DNA 复制过程的精确机械模型。在这篇综述中，我们描述了最近使用计算机模拟对 DNA 复制和修复过程的元素进行建模的努力，这种方法在分子生物物理学的许多领域获得了广泛的欢迎，但尚未成为 DNA 代谢界的主流。我们强调使用不同的计算方法来解决该领域的特定问题，并讨论这些领域的计算方法面临的尚未探索的可能性。