sRNA Structural Modeling Based on NMR Data
- PMID: 38217664
- DOI: 10.1007/978-1-0716-3565-0_20
sRNA Structural Modeling Based on NMR Data
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.
Keywords: Imino proton; NMR spectroscopy; RNA structure; SimRNA; Structural modeling.
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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References
-
- Storz G, Vogel J, Wassarman KM (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43(6):880–891. https://doi.org/10.1016/j.molcel.2011.08.022 - DOI - PubMed - PMC
-
- Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136(4):615–628. https://doi.org/10.1016/j.cell.2009.01.043 - DOI - PubMed - PMC
-
- Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1):15–20. https://doi.org/10.1016/j.cell.2004.12.035 - DOI - PubMed
-
- Papenfort K, Vogel J (2010) Regulatory RNA in bacterial pathogens. Cell Host Microbe 8(1):116–127. https://doi.org/10.1016/j.chom.2010.06.008 - DOI - PubMed
-
- Cech TR, Steitz JA (2014) The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157(1):77–94. https://doi.org/10.1016/j.cell.2014.03.008 - DOI - PubMed
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