Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes
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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Date
2022-12-08
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en
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17577–17586
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Analytical Chemistry, Volume 94
Abstract
Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (KD) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.Description
Funding Information: This work was supported by the Academy of Finland (Grants 308992 and 324352) and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement 713645. J.R. was partially funded by the Academy of Finland Flagship Programme, Photonics Research, and Innovation (PREIN), Decision Number 320167. Publisher Copyright: © 2022 American Chemical Society. All rights reserved.
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Huang, Y, Ryssy, J, Nguyen, M K, Loo, J, Hällsten, S & Kuzyk, A 2022, ' Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes ', Analytical Chemistry, vol. 94, no. 50, pp. 17577–17586 . https://doi.org/10.1021/acs.analchem.2c04034