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GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity

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Abstract

GOLD SELEX, a novel SELEX approach has been developed that obviates the need for target immobilization for aptamer development. The approach purely relies on the affinity of the aptamers towards its target, to get detached from the gold nanoparticle (GNP) surface (weak attraction) after binding with its target. Thus, only the completely detached aptamers are selected for the next round of SELEX. This, in-process, also addresses the issue of residual binding and thus improves the sensitivity of the developed aptamers. As a proof of concept for establishing the utility of the approach for small molecules, we have developed aptamers against dichlorvos (DV), a pesticide in just 8 rounds. Using these aptamer candidates, we have developed an aptamer-NanoZyme (GNP having peroxidase mimic activity) based colorimetric assay. The developed aptamer displayed high affinity (Kd in sub micromolar range) and selectivity for DV. The developed assay could detect as low as 15 μM DV. The best-performing aptamer was also able to work in real samples like river water and commercial apple juice. The GOLD SELEX approach developed in this study, we believe, can act as a template for future SELEX strategy development and can replace the conventional SELEX strategy.

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Acknowledgments

The aptamer sequences mentioned in the manuscript is deposited to Indian Patent Office (Patent No. 202011004692).

Funding

This work was supported through the THSTI Core Grant and Innovative Young Biotechnologist Award (IYBA), grant number (BT/010/IYBA/2016/10) to TKS. BC and AA were supported by the Biotechnology Industrial Research Assistance Council (BIRAC), Govt. of India in the form of post-doctoral and Technical Assistant position respectively through BIRAC-PACE grant to TKS. NK was recipient of Department of Science and Technology (DST) National Post-Doctoral Fellowship (NPDF). The excellent technical assistance of Mr. Rajkumar Dwivedi is duly acknowledged.

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  1. Neeti Kalyani and Anjali Anand contributed equally to this work.

Authors and Affiliations

  1. Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India

    Bandhan Chatterjee, Neeti Kalyani, Anjali Anand, Soonjyoti Das & Tarun Kumar Sharma

  2. Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India

    Eshan Khan & Amit Kumar

  3. Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Lab (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia

    Vipul Bansal

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Supplementary material includes chemical structures of the pesticides, percentage base composition of sequences, multiple sequence alignment of the sequences, phylogenetic dendrogram, Sequences and length of the selected aptamers, TEM images of the GNPs, UV-Vis spectra, peroxidase activity graph, LOD and LOQ calculation. It is available in the online version of this article at https://doi.org/10.1007/s12274-***-****-* (automatically inserted by the publisher). (DOCX 4.18 mb)

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Chatterjee, B., Kalyani, N., Anand, A. et al. GOLD SELEX: a novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity. Microchim Acta 187, 618 (2020). https://doi.org/10.1007/s00604-020-04577-0

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