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从DMS反应性来描述3DRNA结构特征

D H Sanduni Deenalattha¹, Chris P Jurich¹, Bret Lange¹

¹Department of Chemistry, University of Nebraska, 639 North 12 St, Lincoln, NE 68588, USA.

bioRxiv : the preprint server for biology

|November 28, 2024

概括

硫酸二甲基 (DMS) 的化学测绘揭示了RNA结构细微差别. 在DMS反应性中,偏离标准的沃森-克里克基配对规则,可以让我们深入了解复杂的RNA3D构造和动态.

科学领域:

分子生物学分子生物学
生物化学生物化学
结构生物学结构生物学

背景情况:

硫酸二甲基 (DMS) 是一种用于研究RNA结构的化学探针.
DMS反应性通常表明核酸可访问性:低反应性表明沃森-克里克 (WC) 基对,而高反应性意味着未配对的核酸.
之前的研究发现了这一规则的例外,但这些异常值的频率和结构基础尚未完全理解.

研究的目的:

在大量RNA结构数据集中系统地分析DMS反应模式.
识别与非正规DMS反应相关的反复出现的3D结构特征.
探索DMS反应的潜力,用于详细的RNA结构和动态建模.

主要方法:

从7500个已知3D结构的RNA结构中对DMS反应性数据进行系统分析.
DMS反应性值与基配对状态 (WC与非WC),溶剂可访问性,结,堆叠和结交动态的相关性.
针对原子距离和基数对几何学的非正规对的DMS反应性的研究.

主要成果:

DMS的反应性跨越四个数量级,WC和非WC核酸之间~10%的重叠.
具有受保护的DMS反应性的非WC基体显示出增加的键和减少溶剂可访问性.
具有更高DMS反应性的WC对通常位于结点,与较弱的基层堆叠和更高的动力学有关.
非正规对中的DMS反应性与几何参数相关,允许对3D形状进行区分.

结论:

DMS化学映射提供了 RNA 3D 结构的原子级分辨率,超出了简单的基配对状态.
DMS反应率的偏差与特定的结构特征有关,例如结,溶剂可访问性和连接动力学.
可以利用DMS反应模式来构建更准确的RNA结构和动态模型.

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