Abstract
Endoribonuclease footprinting is an important technique for probing RNA–protein interactions with single nucleotide resolution. The susceptibility of RNA residues to enzymatic digestion gives information about the RNA secondary structure, the location of protein binding sites, and the effects of protein binding on the RNA structure. Here we present a detailed protocol for using RNase T2, which cleaves single stranded RNA with a preference for A nucleotides, to footprint the protein Hfq on the rpoS mRNA leader. This protocol covers how to form the RNP complex, determine the correct dose of enzyme, footprint the protein, and analyze the cleavage pattern using primer extension.
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Acknowledgement
We would like to acknowledge Richard Lease, Subrata Panja, and Sarah Soper for providing reagents, technical advice, and useful discussions.
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Peng, Y., Soper, T.J., Woodson, S.A. (2012). RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs. In: Keiler, K. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 905. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-949-5_13
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DOI: https://doi.org/10.1007/978-1-61779-949-5_13
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Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-948-8
Online ISBN: 978-1-61779-949-5
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