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Investigation of RNA structure-switching aptamers in tunable sol–gel-derived materials

  • Original Paper: Sol-gel and hybrid materials for biological and health (medical) applications
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Abstract

In recent years RNA aptamers have emerged as potential recognition elements for solid phase assays, including assays that utilize sol–gel based biohybrid materials. However, there is still very little knowledge regarding the behavior of RNA aptamers when entrapped in sol–gel-derived materials. In this work, we evaluated the performance of an adenosine triphosphate (ATP)-binding structure-switching RNA aptamer in a series of sol–gel derived materials and compared the results to those previously reported for an ATP-binding DNA aptamer. It was observed that the nature of the entrapping material is the key parameter affecting the functionality of the entrapped ATP-binding RNA aptamer, which mainly impacts its ability to remain fully hybridized to signaling DNA strands upon entrapment. We observed that those materials with a high organic content provided the best performance for entrapped RNA aptamers at early times after entrapment. However, upon aging, materials derived from sodium silicate provided the best performance. Overall, the results suggest that polar materials that do not produce alcohol are optimal for entrapment of both DNA and RNA aptamers that bind ATP.

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Acknowledgements

We thank the Natural Sciences and Engineering Research Council of Canada (NSERC) and Pro-Lab Diagnostics Inc. for funding this work. We also thank the Canada Foundation for Innovation and the Ministry of Research and Innovation (Ontario Research Fund) for support of this work. YL holds the Canada Research Chair in Directed Evolution of Nucleic Acids. JDB holds the Canada Research Chair in Bioanalytical Chemistry and Biointerfaces.

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Authors and Affiliations

  1. Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada

    Christy Y. Hui, Yingfu Li & John D. Brennan

  2. Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada

    Pui Sai Lau & Yingfu Li

Authors
  1. Christy Y. Hui
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  2. Pui Sai Lau
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  3. Yingfu Li
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  4. John D. Brennan
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Correspondence to John D. Brennan.

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The authors declare that they have no conflict of interest.

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Highlights:

  • We show that RNA aptamers perform best when entrapped in polar silica-based materials

  • Entrapped RNA aptamers show better detection limits that RNA aptamers in solution

  • Entrapped RNA aptamers remain stable over at least a month of storage

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Hui, C.Y., Lau, P.S., Li, Y. et al. Investigation of RNA structure-switching aptamers in tunable sol–gel-derived materials. J Sol-Gel Sci Technol 89, 234–243 (2019). https://doi.org/10.1007/s10971-018-4588-z

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  • DOI: https://doi.org/10.1007/s10971-018-4588-z

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