Abstract
The diverse roles of RNAs depend on their ability to fold so as to form biologically functional structures. Thus, understanding the function of a given RNA molecule often requires experimental analysis of its secondary structure by in vitro RNA probing, which is more accurate than using prediction programs only. This chapter presents in vitro RNA probing protocols that we routinely use, from RNA transcript production and purification to RNA structure determination using enzymatic (RNases T1, T2, and V1) and chemical (DMS, CMCT, kethoxal, and Pb2+) probing performed on both unlabeled and end-labeled RNAs.
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Acknowledgments
J.V.P. was supported by a graduate fellowship from the french Ministère Délégué à la Recherche et aux Technologies. This work was supported by grants from the Agence Nationale pour la Recherche contre le Sida (ANRS), the European Alternative Splicing Network of Excellence (EURASNET, FP6 life sciences, genomics and biotechnology for health) and the European Associated Laboratory (LEA) on pre-mRNA splicing created by CNRS, UL, UM1, UM2 and Max Planck Institut. V. Vautrot is acknowledged for providing materials for illustration of the enzymatic probing experiment.
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Philippe, JV., Ayadi, L., Branlant, C., Behm-Ansmant, I. (2015). Probing Small Non-Coding RNAs Structures. In: Rederstorff, M. (eds) Small Non-Coding RNAs. Methods in Molecular Biology, vol 1296. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2547-6_12
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DOI: https://doi.org/10.1007/978-1-4939-2547-6_12
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