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Biophysical Analysis of Small Molecule Binding to Viral RNA Structures

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Nucleic Acid Aptamers

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2570))

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Abstract

RNA molecules are essential for carrying genetic information and regulating gene expression in most organisms including human pathogenic RNA and relate retro viruses. Targeting viral RNA (vRNA) structures provide broad opportunities to develop chemical tools to probe molecular virology and to discover novel targets for therapeutic intervention. An increasing number of RNA binding small molecules are being identified, stimulating increased interests in small molecule drug discovery for RNA targets. In this chapter, we describe protocols to characterize and robustly validate vRNA-small molecule (vRNA-sm) interactions starting from vRNA sample preparation, followed by small molecule screening against vRNA targets and finally to validating the vRNA-sm interactions via NMR spectroscopy and calorimetric titrations.

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Acknowledgments

This work was funded by National Institutes of Health grants GM126833 and AI150830.

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Authors and Affiliations

  1. Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA

    Liang-Yuan Chiu, Jesse Davila-Calderon & Blanton S. Tolbert

  2. Department of Chemistry, Duke University, Durham, NC, USA

    Zhengguo Cai

Authors
  1. Liang-Yuan Chiu
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  2. Jesse Davila-Calderon
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  3. Zhengguo Cai
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  4. Blanton S. Tolbert
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Corresponding author

Correspondence to Blanton S. Tolbert .

Editor information

Editors and Affiliations

  1. Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany

    Günter Mayer

  2. Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Potsdam, Germany

    Marcus M. Menger

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Chiu, LY., Davila-Calderon, J., Cai, Z., Tolbert, B.S. (2023). Biophysical Analysis of Small Molecule Binding to Viral RNA Structures. In: Mayer, G., Menger, M.M. (eds) Nucleic Acid Aptamers. Methods in Molecular Biology, vol 2570. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2695-5_16

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  • DOI: https://doi.org/10.1007/978-1-0716-2695-5_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2694-8

  • Online ISBN: 978-1-0716-2695-5

  • eBook Packages: Springer Protocols

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