School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, United States.
Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, U.K.
J Chem Theory Comput. 2020 Dec 8;16(12):7764-7775. doi: 10.1021/acs.jctc.0c00286. Epub 2020 Nov 4.
We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on individual nucleotides are explored and related to model potentials, and using our framework, internal forces are calculated for two simple DNA systems and for a recently published nanoscopic force clamp. Our results highlight some pitfalls associated with conventional methods for estimating internal forces, which are based on elastic polymer models, and emphasize the importance of carefully considering secondary structure and ionic conditions when modeling the elastic behavior of single-stranded DNA. Beyond its relevance to the DNA nanotechnological community, we expect our approach to be broadly applicable to calculations of internal force in a variety of structures-from DNA to protein-and across other coarse-grained simulation models.
我们提出了一种新的方法，用于使用粗粒模型计算 DNA 结构中的内力，并通过 oxDNA 模型展示了其效用。我们探讨了单个核苷酸上的瞬时力，并将其与模型势能相关联，并且使用我们的框架，我们计算了两个简单的 DNA 系统和最近发表的纳米级力钳的内力。我们的结果强调了基于弹性聚合物模型的传统内力估算方法存在的一些缺陷，并强调了在模拟单链 DNA 的弹性行为时仔细考虑二级结构和离子条件的重要性。除了与 DNA 纳米技术社区相关之外，我们预计我们的方法将广泛适用于各种结构（从 DNA 到蛋白质）和其他粗粒模拟模型中的内力计算。
