Aptamer selection for the detection ofEscherichia coliK88

Abstract

In this study, the first group of single-stranded DNA aptamers that are highly specific to enterotoxigenic Escherichia coli (ETEC) K88 was obtained from an enriched oligonucleotide pool by the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure, during which the K88 fimbriae protein was used as the target and bovine serum albumin as counter targets. These aptamers were applied successfully in the detection of ETEC K88. They were then grouped under different families based on the similarity of their secondary structure and the homology of their primary sequence. Four sequences from different families were deliberately chosen for further characterization by fluorescence analysis. Having the advantage of high sensitivity, fluorescence photometry was selected as single-stranded DNA quantification method during the SELEX process. Aptamers with the highest specificity and affinity were analyzed to evaluate binding ability with E. coli. Since ETEC K88 is the only type of bacterium that expressed abundant K88 fimbriae, the selected aptamers against the K88 fimbriae protein were able to specifically identify ETEC K88 among other bacteria. This method of detecting ETEC K88 by aptamers can also be applied to bacteria other than ETEC K88.

Aptamers against pathogenic microorganisms

“…The DNA aptamer binding the fimbriae protein of enteropathogenic E. coli strain K88 was obtained by Li et al (2011). Since that strain is the only one with fimbriae, the acquired aptamer could be applied for the specific pathogen detection.…”

Aptamers—A Promising Approach for Sensing of Biothreats Using Different Bioinformatics Tools

“…Then if we calculate the energy of binding of aptamer and apatope we can easily isolate different the single stranded ss DNA/RNA sequences that were based on the difference in the energy of the target and ligand. The sequences which can be used as aptamer chosen from the fact that lowers the entropy of the system higher the stabilization of the system [18][19][20]. The sequences for ricin and abrin which had the lowest values of the MFE had shown a wide range of the binding coef-…”

“…The binding energy of the target and the ligand should be as low as possible. In this present paper we attempt to isolate some sequences of ss DNA/ RNA aptamer and predict their secondary structure based on minimum free energy [17][18][19][20].…”

High Specific DNAzyme-Aptamer Sensor for Salmonella paratyphi A Using Single-Walled Nanotubes–Based Dual Fluorescence-Spectrophotometric Methods

“…[15][16][17][18] Their application in detecting pathogens, such as Staphylococcus aureus, Salmonella typhimurium, and Escherichia coli K88, has previously been reported. [19][20][21] Catalytic nucleic acids (DNAzymes) have attracted substantial efforts for developing labels with amplified signals. One of the most extensively studied DNAzymes has been the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme, which catalyzes the oxidation of 2,2′-azinobis (3-ethylBenzthiazoline-6-sulfonic acid) ABTS 2-to the colored product ABTS -by H 2 O 2 .…”