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sRNA Structural Modeling Based on NMR Data

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Bacterial Regulatory RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2741))

Abstract

Small non-coding RNAs (sRNAs) play vital roles in gene expression regulation and RNA interference. To comprehend their molecular mechanisms and develop therapeutic approaches, determining the accurate three-dimensional structure of sRNAs is crucial. Although nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for structural biology, obtaining high-resolution structures of sRNAs using NMR data alone can be challenging. In such cases, structural modeling can provide additional details about RNA structures. In this context, we present a protocol for the structural modeling of sRNA using the SimRNA method based on sparse NMR constraints. To demonstrate the efficacy of our method, we provide selected examples of NMR spectra and RNA structures, specifically for the second stem-loop of DsrA sRNA.

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Acknowledgments

This work was supported by Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China.

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Authors and Affiliations

  1. Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China

    Pengzhi Wu & Lingna Yang

  2. Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland

    Pengzhi Wu

Authors
  1. Pengzhi Wu
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  2. Lingna Yang
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Corresponding author

Correspondence to Pengzhi Wu .

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Editors and Affiliations

  1. CEA Saclay, Lab Léon Brillouin UMR12 CEA/CNRS, Gif-sur-Yvette, France

    Véronique Arluison

  2. Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo (CBMS), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes – CONICET, Bernal, Buenos Aires, Argentina

    Claudio Valverde

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Wu, P., Yang, L. (2024). sRNA Structural Modeling Based on NMR Data. In: Arluison, V., Valverde, C. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 2741. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3565-0_20

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  • DOI: https://doi.org/10.1007/978-1-0716-3565-0_20

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3564-3

  • Online ISBN: 978-1-0716-3565-0

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