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Development of HGF‐binding aptamers with the combination of G4 promoter‐derived aptamer selection and in silico maturation
Author(s) -
Yokoyama Tomomi,
Tsukakoshi Kaori,
Yoshida Wataru,
Saito Taiki,
Teramoto Kentaro,
Savory Nasa,
Abe Koichi,
Ikebukuro Kazunori
Publication year - 2017
Publication title -
biotechnology and bioengineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.136
H-Index - 189
eISSN - 1097-0290
pISSN - 0006-3592
DOI - 10.1002/bit.26354
Subject(s) - aptamer , systematic evolution of ligands by exponential enrichment , in silico , computational biology , selection (genetic algorithm) , selex aptamer technique , biology , microbiology and biotechnology , genetics , rna , computer science , gene , machine learning
We describe the selection of aptamers based on bioinformatics‐based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR‐amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer‐screening method, G4 promoter‐derived aptamer selection (G4PAS), and an aptamer‐improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively. In this study, we succeeded in identifying new aptamers against hepatocyte growth factor (HGF) by G4PAS as well as improving the specificity of the HGF aptamers by ISM. Using ISM improved the specificity of the aptamer for HGF by up to 45‐fold in comparison with the original aptamer. These methods enable easy and efficient identification of good aptamers, and the combination of G4PAS with ISM can thus serve as a potent approach for aptamer identification. Biotechnol. Bioeng. 2017;114: 2196–2203. © 2017 Wiley Periodicals, Inc.