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

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.

Screening and Identification of DNA Aptamers to Tyramine Using in Vitro Selection and High-Throughput Sequencing.

Aptamers are synthetic single-stranded DNA or RNA sequences that can fold into tertiary structures allowing them to interact with and bind to targets with high affinity and specificity. This paper describes the first selection and identification of DNA aptamers able to recognize the biogenic amine tyramine. To successfully isolate aptamers to this challenging small molecule target, the SELEX methodology was adapted by combining a systematic strategy to increase the selection stringency and monitor enrichment success. As the benefits of applying high-throughput sequencing (HTS) in SELEX experiments is becoming more clear, this method was employed in combination with bioinformatics analysis to evaluate the utility of the selection strategy and to uncover new potential high affinity sequences. On the basis of the presence of consensus regions (sequence families) and family similarities (clusters), 15 putative aptamers to tyramine were identified. A recently described workflow approach to perform a primary screening and characterization of the aptamer candidates by microequilibrium dialysis and by microscale thermophoresis was next leveraged. These candidate aptamers exhibited dissociation constant (Kd) values in the range of 0.2-152 µM with aptamer Tyr_10 as the most promising one followed by aptamer Tyr_14. These aptamers could be used as promising molecular recognition tools for the development of inexpensive, robust and innovative biosensor platforms for the detection of tyramine in food and beverages.

Comprehensive analytical comparison of strategies used for small molecule aptamer evaluation.

Nucleic acid aptamers are versatile molecular recognition agents that bind to their targets with high selectivity and affinity. The past few years have seen a dramatic increase in aptamer development and interest for diagnostic and therapeutic applications. As the applications for aptamers expand, the need for a more standardized, stringent, and informative characterization and validation methodology increases. Here we performed a comprehensive analysis of a panel of conventional affinity binding assays using a suite of aptamers for the small molecule target ochratoxin A (OTA). Our results highlight inconsistency between conventional affinity assays and the need for multiple characterization strategies. To mitigate some of the challenges revealed in our head-to-head comparison of aptamer binding assays, we further developed and evaluated a set of novel strategies that facilitate efficient screening and characterization of aptamers in solution. Finally, we provide a workflow that permits rapid and robust screening, characterization, and functional verification of aptamers thus improving their development and integration into novel applications.

Comparison of slurry mixing and dry milling in laboratory sample preparation for determination of ochratoxin A and deoxynivalenol in wheat.

The significance of laboratory sample preparation for the determination of two important mycotoxins, ochratoxin A (OTA) and deoxynivalenol (DON), in wheat was investigated by comparing water-slurry mixing and dry-milling procedures. The distribution of OTA and DON in 10 kg samples of naturally contaminated wheat was established by analyzing one hundred 100 g subsamples of each sample. A normal distribution and a good repeatability of DON measurements was observed for both water-slurry mixing (mean 2290 microg/kg, CV 4.6%, median 2290 microg/kg) and dry milling (mean 2310 microg/kg, CV 6.4%, median 2290 microg/kg) procedures. For OTA determinations, reliable results could be obtained only by slurry mixing sample preparation (mean 2.62 microg/kg, CV 4.0%, median 2.62 microg/kg), whereas dry-milling comminution resulted in an inhomogeneous distribution with a high variability (mean 0.83 microg/kg, CV 75.2%, median 0.60 microg/kg) and a positive skewness (2.12). Ad hoc experiments were performed on different size portions of the same sample (10 kg) to assess accuracy and precision of the comminution/homogenization procedures (slurry mixing and dry milling). Very good results were obtained for DON determination with both procedures in terms of accuracy (>98.7% of the "weighted value") and precision (CV <3%). For OTA determination good results were only obtained by slurry mixing (99.4% of the "weighted value," CV 10%), whereas dry milling provided results with low accuracy (43.2% of the "weighted value") and high variability (CV 110%). This study clearly demonstrated that sample preparation by slurry mixing is strictly necessary to obtain reliable laboratory samples for OTA determination in wheat to minimize misclassification of acceptable/rejectable lots, mainly within official control.

A rapid fluorescence polarization immunoassay for the determination of T-2 and HT-2 toxins in wheat.

A rapid fluorescence polarization (FP) immunoassay has been developed for the simultaneous determination of T-2 and HT-2 toxins in naturally contaminated wheat samples. Syntheses of four fluorescein-labelled T-2 or HT-2 toxin tracers were carried out and their binding response with seven monoclonal antibodies was evaluated. The most sensitive antibody-tracer combination was obtained by using an HT-2-specific antibody and a fluorescein-HT-2 tracer. The developed competitive FP immunoassay in solution showed high cross-reactivity for T-2 toxin (CR% = 100%) while a very low CR% for neosolaniol (0.12%) and no cross-reactivity with other mycotoxins frequently occurring in wheat. A rapid extraction procedure using 90% methanol was applied to wheat samples prior to FP immunoassay. The average recovery from spiked wheat samples (50 to 200 µg kg(-1)) was 96% with relative standard deviation generally lower than 8%. A limit of detection of 8 µg kg(-1) for the combined toxins was determined. Comparative analyses of 45 naturally contaminated and spiked wheat samples by both the FP immunoassay and high-performance liquid chromatography/immunoaffinity clean-up showed a good correlation (r = 0.964). These results, combined with the rapidity (10 min) and simplicity of the assay, show that this method is suitable for high throughput screening as well as for quantitative determination of T-2 and HT-2 toxins in wheat.