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Food safety is one of the primary demands of modern society. Mycotoxins are toxic metabolites of food-contaminating fungi. Fungi enter the food chain by infecting crops and irreversibly contaminate them due to the structural stability of mycotoxins. Mycotoxins are stable even at extremely high temperatures; they do not lose their activity during food processing, thus posing a threat to human health. Therefore, it is crucial to detect mycotoxins in food crops during the planting process and at the beginning of the harvest, which requires a rapid and simple detection method. One of the current solutions for this problem is aptamer-based sensors. Here, we deciphered the structure of the binding site in the developed DNA aptamer against deoxynivalenol. The binding site is formed by short single-stranded sequences at the 5′- and 3′-ends of the hairpin, with the Cyanine 3 label at 3′-end. The shortest aptamer with the affinity for deoxynivalenol was used as a recognition element in the surface-enhanced Raman spectroscopy-based sensor to detect mycotoxins in wheat crops. [ABSTRACT FROM AUTHOR]

Surface-enhanced Raman scattering (SERS) is a powerful technique for decoding of 2-5-component mixes of analytes. Low concentrations of analytes and complex biological media are usually non-decodable with SERS. Recognition molecules, such as antibodies and aptamers, provide an opportunity for a specific binding of ultra-low contents of analyte dissolved in complex biological media. Different approaches have been proposed to provide changes in SERS intensity of an external label upon binding of ultra-low contents of the analytes. In this paper, we propose a SERS-based sensor for the rapid and sensitive detection of botulinum toxin type A. The silver nanoisland SERS substrate was functionalized using an aptamer conjugated with a Raman label. The binding of the target affects the orientation of the label, providing changes in an analytical signal. This trick allowed detecting botulinum toxin type A in a one-stage manner without additional staining with a monotonous dose dependence and a limit of detection of 2.4 ng/mL. The proposed sensor architecture is consistent with the multiarray detection systems for multiplex analyses. [ABSTRACT FROM AUTHOR]

A quantitative technique for estimation of the oligomeric state of G-quadruplexes has been developed for the first time. The simplest 15-mer G-quadruplex antithrombin aptamer HD1 and its analogues, namely RA36 as a covalent dimer of HD1 as well as GL2–HD1 as a non-covalent dimer with G-quadruplex lock, were used as model objects. HD1 and RA36 have been shown to be single-stranded G-quadruplexes, whereas GL2–HD1 forms non-covalent dimers (GL2–HD1) 2 in a concentration-dependent manner, affording ∼50% of the dimers at 1 mmol dm−3 concentration. [ABSTRACT FROM AUTHOR]

Nucleic acid aptamers are prospective molecular recognizing elements. Similar to antibodies, aptamers are capable of providing specific recognition due to their spatial structure. However, the apparent simplicity of oligonucleotide folding is often elusive, as there is a balance between several conformations and, in some cases, oligomeric structures. This research is focused on establishing a thermodynamic background and the conformational heterogeneity of aptamers taking a series of thrombin DNA aptamers having G-quadruplex and duplex modules as an example. A series of aptamers with similar modular structures was characterized with spectroscopic and chromatographic techniques, providing examples of the conformational homogeneity of aptamers with high inhibitory activity, as well as a mixture of monomeric and oligomeric species for aptamers with low inhibitory activity. Thermodynamic parameters for aptamer unfolding were calculated, and their correlation with aptamer functional activity was found. Detailed analysis of thrombin complexes with G-quadruplex aptamers bound to exosite I revealed the similarity of the interfaces of aptamers with drastically different affinities to thrombin. It could be suggested that there are some events during complex formation that have a larger impact on the affinity than the states of initial and final macromolecules. Possible mechanisms of the complex formation and a role of the duplex module in the association process are discussed. [ABSTRACT FROM AUTHOR]