ssDNA适体与极光激酶A蛋白结合的硅片法。

Q4 Biochemistry, Genetics and Molecular Biology Methods in molecular biology Pub Date : 2025-01-09 DOI:10.1007/7651_2024_596

Haregewoin Bezu Woldekidan, Adugna Abdi Woldesemayat

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引用次数: 0

摘要

虽然传统的检测方法在检测特定蛋白质方面面临挑战，但适体以其高特异性和亲和力而闻名，正在成为一种有价值的生物标志物检测工具。极光激酶A （Aurora kinase A， AURKA）在细胞分裂和影响干细胞重编程中起作用。在本研究中，采用计算机方法对随机选择的ssDNA适配体序列及其与AURKA的结合进行了分析。根据AURKA的结构和从PDB RCSB中获得的核酸序列设计适配体。利用RNAfold和RNA composer对适体的二级和三级结构进行了预测。通过HDOCK和HADDOCK分析蛋白质与适体的结合，并在LIGPLOT+ v1.4中可视化二维相互作用。使用Autodock 4和NAMD 2.3工具进行对接和MD仿真研究。

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In Silico Method for ssDNA Aptamer Binding with Aurora Kinase A Protein.

While traditional assay methods face challenges in detecting specific proteins, aptamers, known for their high specificity and affinity, are emerging as a valuable biomarker detection tool. Aurora kinase A (AURKA) plays a role in cell division and influences stem cell reprogramming. In this study, an in silico approach method was conducted for a random ssDNA aptamer sequence selection and its binding with AURKA. The aptamer was designed based on AURKA's structure and nucleic acid sequence, obtained from PDB RCSB. Using RNAfold and RNA composer, we predicted the aptamer's secondary and tertiary structures. Protein-aptamer binding was analyzed via HDOCK and HADDOCK, with 2D interactions visualized in LIGPLOT+ v1.4. Autodock 4 and NAMD 2.3 tools were used to conduct docking and MD simulation studies.

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来源期刊

Methods in molecular biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

2.00

自引率

0.00%

发文量

3536

期刊介绍： For over 20 years, biological scientists have come to rely on the research protocols and methodologies in the critically acclaimed Methods in Molecular Biology series. The series was the first to introduce the step-by-step protocols approach that has become the standard in all biomedical protocol publishing. Each protocol is provided in readily-reproducible step-by-step fashion, opening with an introductory overview, a list of the materials and reagents needed to complete the experiment, and followed by a detailed procedure that is supported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice.