Significance of the DNA bond strength in programmable nanoparticle thermodynamics and dynamics
Significance of the DNA bond strength in programmable nanoparticle thermodynamics and dynamics
复制标题
DNA 键强度在可编程纳米粒子热力学和动力学中的意义
DOI：
10.1039/c7sm02456h
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发表时间：
2018
期刊：
影响因子：
3.4
通讯作者：
Wang Rong
中科院分区：
文献类型：
--
作者：
Yu Qiuyan;Hu Jinglei;Hu Yi;Wang Rong
包覆互补DNA链的纳米粒子（NPs）组装产生具有纳米级基本单位的新型晶体，而不是传统的原子、离子或分子。组装过程是通过特定碱基配对相互作用介导的DNA杂交，并与DNA双链的解离动力学相关。dna水平的物理化学量，包括热力学和动力学，是理解这一过程的关键，也是设计DNA-NP晶体的必要条件。熔融转变性质有助于判断相关DNA探针的热稳定性和灵敏度或其他应用。用分子动力学方法研究了三种不同的情况，通过改变连接剂的长度和间隔剂的长度来影响熔炼性能。熔点温度的确定采用基于杂化百分数随温度变化的s型熔点曲线和Lindemann熔点规律。我们提供了一种基于粗粒度模型的计算策略，从实验中容易获得的杂化百分比中估计杂化焓、熵和自由能。重要的是，还计算了基于温度的DNA键去杂化的寿命和依赖于DNA键强度的活化能。仿真结果与理论分析和现有实验数据吻合较好。我们的研究提供了一个很好的策略来预测DNA定向纳米颗粒系统的熔化温度，并通过定量估计DNA键杂交的平衡常数来连接DNA定向纳米颗粒系统的动力学和热力学。
Assembly of nanoparticles (NPs) coated with complementary DNA strands leads to novel crystals with nanosized basic units rather than classic atoms, ions or molecules. The assembly process is mediated by hybridization of DNA via specific base pairing interaction, and is kinetically linked to the disassociation of DNA duplexes. DNA-level physiochemical quantities, both thermodynamic and kinetic, are key to understanding this process and essential for the design of DNA-NP crystals. The melting transition properties are helpful to judge the thermostability and sensitivity of relative DNA probes or other applications. Three different cases are investigated by changing the linker length and the spacer length on which the melting properties depend using the molecular dynamics method. Melting temperature is determined by sigmoidal melting curves based on hybridization percentage versus temperature and the Lindemann melting rule simultaneously. We provide a computational strategy based on a coarse-grained model to estimate the hybridization enthalpy, entropy and free energy from percentages of hybridizations which are readily accessible in experiments. Importantly, the lifetime of DNA bond dehybridization based on temperature and the activation energy depending on DNA bond strength are also calculated. The simulation results are in good agreement with the theoretical analysis and the present experimental data. Our study provides a good strategy to predict the melting temperature which is important for the DNA-directed nanoparticle system, and bridges the dynamics and thermodynamics of DNA-directed nanoparticle systems by estimating the equilibrium constant from the hybridization of DNA bonds quantitatively.