PDF(Pubmed)
Abstract：
Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules.
摘要：
由DNA结合配体驱动的结构化DNA组件的化学机械变形为生物和治疗应用提供了有希望的途径。然而,如何有效地建模和预测它们对DNA结构的变形和机械性能的影响仍然难以捉摸。这里,我们提出了一个计算框架，用于模拟结构化DNA组件的化学机械变化。我们通过分子动力学模拟特别量化了溴化乙锭（EtBr）嵌入对DNA碱基对的几何形状和机械性能的影响，并将其集成到基于有限元的结构分析中，以预测DNA对象的形状和属性。所提出的模型捕获了由EtBr结合引起的各种结构变化，例如形状变化，灵活性调制，和超卷不稳定性。通过结合分子，它可以合理设计具有可调形状和机械性能的结构化DNA组件。
