论文标题
测量单链DNA中的内力：应用于DNA力夹
Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
论文作者
论文摘要
我们提出了一种使用粗粒模型来计算DNA结构内部力的新方法，并使用OxDNA模型证明了其效用。探索了单个核苷酸上的瞬时力并与模型电势相关，并使用我们的框架计算了两个简单的DNA系统和最近发布的纳米镜夹。我们的结果突出了一些与估计内部力的常规方法相关的陷阱，这些方法基于弹性聚合物模型，并强调在建模单链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纳米技术界相关之外，我们还希望我们的方法广泛适用于从DNA到蛋白质的各种结构中的内力计算以及其他粗粒型模拟模型。
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 emphasise the importance of carefully considering secondary structure and ionic conditions when modelling the elastic behaviour 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.
