Tetrodotoxin (TTX) is a lethal neurotoxin produced by the endosymbiotic bacteria in the gut of puffer fish. Currently, there is no effective and economical method to detect TTX, so it is very interesting to develop low-cost and high-sensitivity detection methods by using nucleic-acid aptamers as the recognition molecules. However, traditional SELEX screening of aptamers for targeting small molecules such as TTX is labor-intensive, and usually the success rate is low. Here, we employed a strategy of "repurposing old aptamers for new uses" to develop high-affinity aptamers for TTX. To this end, we first collected thermally stable DNA aptamers and predicted their affinities for TTX by molecular docking; then, we identified high-affinity candidates and verified them by microscale thermophoresis (MST) experiments. In this way, two thermally stable aptamers (Tv-51 and AI-57) were found to possess nanomolar affinities for TTX. Moreover, we performed spontaneous binding simulations to reveal their binding mechanisms to TTX and thereby identified the key bases for the binding. Guided by these, two variants (Tv-46 and AI-52) with higher affinities and specificities were subsequently engineered and confirmed by the MST experiments. So, this study not only provides potential recognition molecules for the technology developments of TTX detection, but also demonstrates an effective repurposing approach to the discovery of high-affinity aptamers for new target molecules.
Keywords: Drug repurposing; Molecular docking; Nucleic-acid aptamer; Spontaneous binding simulation; Tetrodotoxin.
© 2022 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.