Study of Docking-based In silico Post-SELEX Minimization for H1N1 Influenza DNA Aptamers

• Main Authors: Hui-Yu Chiang, 江蕙妤
• Other Authors: Chien-Yu Chen
• Format: Others
• Language: en_US
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/65866236458835659409

碩士 === 國立臺灣大學 === 生物產業機電工程學研究所 === 102 === Aptamers screened out from SELEX (systematic evolution of ligands by exponential enrichment) are generally 60 to 120 bases in length, and only a fragment, called mini-aptamer, containing 15 to 40 bases contributes to the specific binding activity. In this study, structures of the aptamer-protein complexes were predicted, and mini-aptamers were identified from the predicted structures of complexes. The accuracy of prediction was as high as 0.92 when applying the pipeline to five verified aptamers. The result suggests that this pipeline is a potential tool for minimization of aptamers. The same pipeline was used to predict mini-aptamers from H1N1 aptamers obtained by viral SELEX. Compared to the full-length aptamers, mini-aptamers showed 2.1-fold improvement in viral neutralization test in average. Among these aptamers, viral neutralization test using truncated BR92 resulted in 98% of cell viability, which is 3.4-fold higher than full-length BR92. Furthermore, the docking results provided evidences that aptamers screened out by sialyllactose competitive selection tended to bind to the HA1 domain on hemagglutinin, and enzyme-linked aptamer assay (ELAA) also proved that these aptamers do specifically bind to hemagglutinin recombinant protein. In silico aptamer minimization pipeline proposed in this thesis provides a novel method to predict possible mini-aptamer sequences. Optimization of the pipeline can be done to enhance the prediction performer by introducing more aptamer database in the future.