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.