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分子动态的评估结果的三维RNA的aptamer结构预测结构的分子动力学结果

Bejo Ropii¹, Maulidwina Bethasari², Isa Anshori^1,3

¹School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung, West Java, Indonesia.

|July 27, 2023

概括

本研究介绍了一种计算方法,用于生成3DRNA吸收体模型,改进低效的SELEX方法. 结合使用mFold,RNAComposer和分子动力学模拟,可以为潜在的治疗和生物感知应用提供准确的aptamer结构.

科学领域:

生物化学生物化学
计算生物学计算生物学
分子生物学分子生物学

背景情况:

单链DNA或RNA的aptamers通过结合特定点来模仿抗体.
对抗体而言,阿普塔默具有优势,包括更低的合成成本,没有批量变化和更容易的化学修饰.
目前通过SELEX进行体外RNA胺体鉴定是低效和复杂的.

研究的目的:

开发和评估一种计算方法,用于生成准确的三维 (3D) RNA 吸收体模型.
评估将mFold,RNAComposer和分子动力学 (MD) 模拟用于aptamer建模的实用性.
为了比较计算生成的aptamer模型与实验确定结构.

主要方法:

用mFold和RNAComposer生成五个RNA吸收体的3D模型,使用它们的序列.
采用分子动力学 (MD) 模拟来完善和改进生成的体模型.
评估并将计算模型与实验确定结构进行比较.

主要成果:

综合方法 (mFold,RNAComposer,MD) 成功生成了不同长度 (14-29个核酸) 的3DRNA吸收体模型.
计算模型表现出与实验确定结构相似的几何和拓.
模拟MD使得在aptamer循环中形成非正规的基对,从而提高了模型的准确性.

结论:

结合mFold,RNAComposer和MD模拟是一种可行的策略,用于生成精确的3DRNA吸收体模型.
这种计算方法可以克服传统SELEX方法的局限性.
建议进行聚类分析,以便从模拟中选择最具代表性的aptamer模型.

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Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
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RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...