Abstract
RNA binding proteins (RBP) and small RNAs regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNAs) through their interactions with specific cis-acting elements within target RNAs. Here, we describe a novel method to detect protein–mRNA interactions, which combines FLAG-peptide modified, multiply-labeled tetravalent RNA imaging probes (FMTRIPs) with proximity ligation (PLA), and rolling circle amplification (RCA). This assay detects native RNA in a sequence specific and single RNA sensitive manner, and PLA allows for the quantification and localization of protein–mRNA interactions with single-interaction sensitivity.
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Zurla, C., Jung, J., Blanchard, E.L., Santangelo, P.J. (2017). A Novel Method to Quantify RNA–Protein Interactions In Situ Using FMTRIP and Proximity Ligation. In: Ørom, U. (eds) Enhancer RNAs. Methods in Molecular Biology, vol 1468. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-4035-6_12
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DOI: https://doi.org/10.1007/978-1-4939-4035-6_12
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