Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State

DNA缩合 化学 DNA 冷凝 核小体 纳米颗粒 化学物理 乙醇 生物物理学 静电 纳米技术 结晶学 热力学 有机化学 生物化学 染色质 材料科学 物理 基因 生物 量子力学 转染
作者
Qinsi Xiong,One‐Sun Lee,Chad A. Mirkin,George C. Schatz
出处
期刊:Journal of the American Chemical Society [American Chemical Society]
卷期号:145 (1): 706-716 被引量:5
标识
DOI:10.1021/jacs.2c11834
摘要

Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.
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