Mycotoxins are fungal secondary metabolites that contaminate a wide range of agricultural commodities worldwide. Ochratoxin A (OTA) is of particular interest as it is one of the most abundant mycotoxins. Aptamers are single-stranded oligonucleotides, typically DNA or RNA, that are capable of specifically interacting with high affinity to a desired target. We have aimed to understand the secondary structures of OTA aptamers using a DNase I assay. The affinity of each aptamer to OTA has also been tested using a DNase I assay, and a magnetic bead affinity assay. We found that using Kd affinity
methods to compare aptamers was unreliable and instead developed several direct competitive affinity tests. Initial results appear promising, however further testing is required. Once the optimal conditions are found, the chosen aptamer can be used in existing antibody technology. This can be done to develop useful, cost efficient, sensors and detection methods for OTA.