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Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA

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Peptide Nucleic Acids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2105))

Abstract

Because of the important roles noncoding RNAs play in gene expression, their sequence-specific recognition is important for both fundamental science and the pharmaceutical industry. However, most noncoding RNAs fold in complex helical structures that are challenging problems for molecular recognition. Herein, we describe a method for sequence-specific recognition of double-stranded RNA using peptide nucleic acids (PNAs) that form triple helices in the major grove of RNA under physiologically relevant conditions. We also outline methods for solid-phase conjugation of PNA with cell-penetrating peptides and fluorescent dyes. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.

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Acknowledgments

This work was supported by NIH grant GM071461 (to E.R.) and NSF grants CHE-1406433 and CHE-1708761 (to E.R.) and CHE-1708699 (to J.A.M.).

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Authors and Affiliations

  1. Department of Chemistry, Binghamton University, Binghamton, NY, USA

    Nikita Brodyagin, Dziyana Hnedzko & Eriks Rozners

  2. Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA, USA

    James A. MacKay

Authors
  1. Nikita Brodyagin
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  2. Dziyana Hnedzko
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  3. James A. MacKay
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  4. Eriks Rozners
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Corresponding author

Correspondence to Eriks Rozners .

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Editors and Affiliations

  1. Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Peter E. Nielsen

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Brodyagin, N., Hnedzko, D., MacKay, J.A., Rozners, E. (2020). Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA. In: Nielsen, P. (eds) Peptide Nucleic Acids. Methods in Molecular Biology, vol 2105. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0243-0_9

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  • DOI: https://doi.org/10.1007/978-1-0716-0243-0_9

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  • Online ISBN: 978-1-0716-0243-0

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