[论文解读] Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"

Ryan M. Harrison, Flavio Romano+3 more|arXiv (Cornell University)|Jun 30, 2015

Bacteriophages and microbial interactions参考文献 38被引用 8

一句话总结

本研究采用oxDNA粗粒化模型研究DNA强弯曲行为，发现高度弯曲的DNA构型更倾向于形成局部扭结（即碱基配对和堆积作用被破坏），而非均匀弯曲。扭结态通过最小化弯曲能，解释了实验中观察到的增强柔韧性，包括分子卡钳实验的结果，并与实验数据在末端间距和扭结概率方面表现出高度一致。

ABSTRACT

DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of these studies, however, remain controversial. We use a coarse-grained model, previously fitted to DNA's basic thermodynamic and mechanical properties, to explore strongly bent systems. We find that as the end-to-end distance is decreased sufficiently short duplexes undergo a transition to a state in which the bending strain is localized at a flexible kink that involves disruption of base-pairing and stacking. This kinked state, which is not well-described by the worm-like chain model, allows the duplex to more easily be sharply bent. It is not completely flexible, however, due to constraints arising from the connectivity of both DNA backbones. We also perform a detailed comparison to recent experiments on a "molecular vice" that probes highly bent DNA. Close agreement between simulations and experiments strengthens the hypothesis that localised bending via kinking occurs in the molecular vice and causes enhanced flexibility of duplex DNA. Our calculations therefore suggests that the cost of kinking implied by this experiment is consistent with the known thermodynamic and mechanical properties of DNA.

研究动机与目标

• 理解超出蠕虫状链（WLC）模型限制的强弯曲DNA构型的热力学行为。
• 探究局部扭结（表现为碱基配对和堆积作用破坏）是否可解释实验中观测到的DNA超WLC柔韧性。
• 通过将模拟结果与Fields等人近期在分子卡钳系统中获得的实验数据对比，验证扭结假说。
• 量化短DNA双链中扭结形成相关的自由能成本及结构转变。
• 确定在不同长度和序列下，扭结相对于连续弯曲占主导地位的条件。

提出的方法

• 采用oxDNA粗粒化模型，该模型能够捕捉DNA的热力学性质、力学性能及序列依赖性。
• 使用伞样法和自由能计算，以末端间距为变量，计算弯曲自由能。
• 应用能量探测器，基于50%构型中存在碱基对和堆积作用破坏，识别扭结态。
• 模拟分子卡钳装置，通过调节环长和双链长度，探测扭结、解链和开链转变。
• 开展温度依赖性模拟，评估碱基配对减弱对扭结倾向的影响。
• 对模拟得到的结构性质（如末端间距、扭结概率）与Fields等人提供的实验数据进行对比分析。

实验结果

研究问题

• RQ1 DNA中的局部扭结是否可解释如分子卡钳实验中观测到的增强柔韧性？
• RQ2 短DNA双链中扭结形成的热力学成本是多少？与WLC预测相比如何？
• RQ3 扭结形成如何依赖于DNA长度、序列以及结构缺陷（如错配或缺口）？
• RQ4 在DNA双链中，从连续弯曲到扭结态的转变发生在何种末端间距？
• RQ5 温度和碱基对稳定性如何调节高度弯曲DNA中扭结发生的可能性？

主要发现

• 涉及碱基配对和堆积作用局部破坏的扭结态在末端间距较短时变得能量上有利，从而支持高度弯曲的DNA构型。
• 对于平均碱基序列，扭结转变的中点出现在末端间距约18.0 Å处，弯曲自由能为18.0 kcal/mol。
• 对于28聚体双链，扭结在poly(AT)序列中最有利（ΔG_trans = 14.8 kcal/mol），在poly(GC)序列中最不利（ΔG_trans = 21.1 kcal/mol）。
• 在分子卡钳中，扭结态在中等环长（N_loop ≈ 30）时占主导，而较短环长下则以解链和开链为主。
• 当N_dup = 88 bp时，扭结概率降至2%以下，表明在更长长度下发生向连续弯曲的转变。
• 在45 °C时，分子卡钳中扭结可忽略不计，与碱基配对减弱促进解链而非扭结的实验现象一致。