Premium
Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development
Author(s) -
Savory Nasa,
Takahashi Yayoi,
Tsukakoshi Kaori,
Hasegawa Hijiri,
Takase Madoka,
Abe Koichi,
Yoshida Wataru,
Ferri Stefano,
Kumazawa Shizuko,
Sode Koji,
Ikebukuro Kazunori
Publication year - 2014
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.25111
Subject(s) - in silico , aptamer , streptococcus mutans , biosensor , computational biology , microbiology and biotechnology , biology , streptococcus , chemistry , biochemistry , bacteria , genetics , gene
In silico evolution with an in vitro system can facilitate the development of functional aptamers with high specificity and affinity. Although a general technique known as systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method for aptamer selection, it sometimes fails to identify aptamers with sufficient binding properties. We have previously developed in silico maturation (ISM) to improve functions of aptamers based on genetic algorithms. ISM represents an intelligent exploitation of a random search within a defined sequence space to optimize aptamer sequences and improve their function of interest. Here we demonstrated a successful application of ISM of aptamers to simultaneously improve specificity and affinity for Streptococcus mutans with discovery of a core sequence, which was required to form a polymerized guanine quadruplex structure for target binding. We applied ISM to aptamers selected by whole‐cell SELEX and identified an aptamer with up to 16‐fold improvement in affinity compared to its parent aptamers, and specificity was increased to show 12‐fold more binding to S. mutans than to Lactobacillus acidophilus . Furthermore, we demonstrated a specific flow‐through detection of S. mutans at a concentration range of 1 × 10 5 –10 8 CFU/mL using the evolved aptamer immobilized on gold colloids. Biotechnol. Bioeng. 2014;111: 454–461. © 2013 Wiley Periodicals, Inc.