{"title":"In Silico Method for ssDNA Aptamer Binding with Aurora Kinase A Protein.","authors":"Haregewoin Bezu Woldekidan, Adugna Abdi Woldesemayat","doi":"10.1007/7651_2024_596","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Methods in molecular biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1007/7651_2024_596","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 0
Abstract
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.
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.
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