DNA
计算生物学
分子
生物物理学
化学
纳米技术
材料科学
生物
生物化学
有机化学
作者
Jae Young Lee,Yang‐Gyun Kim,Do‐Nyun Kim
标识
DOI:10.1038/s41467-024-50871-3
摘要
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.
科研通智能强力驱动
Strongly Powered by AbleSci AI