Comparison of In-Solution Biorecognition Properties of Aptamers against Ochratoxin A

Abstract

Ochratoxin A (OTA) is a mycotoxin produced as a secondary metabolite by several species of Aspergillus and Penicillium and frequently found as a natural contaminant in a wide range of food commodities. Novel and robust biorecognition agents for detecting this molecule are required. Aptamers are artificial nucleic acid ligands able to bind with high affinity and specificity to a given target molecule. In the last few years, three separate research groups have selected aptamers for ochratoxin A. While each of these three families of aptamers have been incorporated into various methods for detecting OTA, it is unclear if each aptamer candidate is better suited for a particular application. Here, we perform the first head-to-head comparison of solution-based binding parameters for these groups of aptamers. Based on our results, we provide recommendations for the appropriate choice of aptamer for incorporation into solution-based biorecognition assays and applications.

Gold Nanoparticles as a Platform for Small Molecule SELEX

“…50 Similarly, studying the binding of these aptamers to OTA through various insolution binding parameter, we are able to recommend which sequences are best suited for these solution-based assays and applications. 51 Interestingly, 1.12.2, A08, A08m H8…”

“…Similarly, the affinity of the aptamer for its target can vary depending on the binding conditions. 50,51 In a collaborative study, our research group reported that not all aptamers with affinity for a small molecule target (OTA) were capable of detecting the target through the AuNP assay. Optimization of the sensor parameters is often required when applying the sensor platform to a new aptamer sequence and target molecule.…”

Characterization and Application of Novel Structure Switching Aptamers for Aflatoxins

“…One of the potential limitations for the widespread use of aptamers is the lack of standardized characterization methods. 65 No single method is can perfectly describe the binding capabilities of an aptamer. Moreover, careful consideration must be taken for sample conditions in which aptamers are characterized when comparing Kds.…”

“…Mckeague et al reported an analytical comparison process that highlighted the inconsistencies in the many conventional aptamer affinity assays that are frequently used for characterization. 65 It has been suggested that strategies that allow the binding characterization of many aptamers in a parallel manner would help the advancement of low throughput characterization. 48 While MST is a suitable method for determining binding parameters of an aptamer that is free in solution.…”

“…MST can be performed using the intrinsic fluorescent properties of a molecule. Alternatively, aptamers can be fluorescently labelled with little restrictions since they are free in solution 65. Kd from law of mass action 114.…”