Rna Protein Interactions
Rna Protein Interactions - Related Videos
06:30
SELEX-Based In Vitro Binding Assay to Identify RNA-Protein Interactions
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2025
In this video, we describe the systematic evolution of ligands by the exponential enrichment (SELEX) method to identify specific RNA-binding sequences for a target protein of interest. The protein is incubated with a large pool of randomized RNA sequences, and the protein-binding RNA sequences are isolated, PCR-amplified, and sequenced to identify their protein-binding sites.
12:26
Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
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Cited by 5 •
2022
This protocol presents a complete experimental workflow for studying RNA-protein interactions using optical tweezers. Several possible experimental setups are outlined including the combination of optical tweezers with confocal microscopy.
10:45
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Cited by 203 •
2011
The spatial arrangement of RNA-binding proteins on a transcript is a key determinant of post-transcriptional regulation. Therefore, we developed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) that allows precise genome-wide mapping of the binding sites of an RNA-binding protein.
11:32
Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Cited by 20 •
2017
Here, we detail the method of Sequencing of Psoralen crosslinked, Ligated, and Selected Hybrids (SPLASH), which enables genome-wide mapping of intramolecular and intermolecular RNA-RNA interactions in vivo. SPLASH can be applied to study RNA interactomes of organisms including yeast, bacteria and humans.
05:07
RNA-Protein Pull-Down Assay to Isolate RNA-Binding Proteins via Affinity Extraction
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2025
This video demonstrates an in vitro RNA pull-down assay to identify RNA-binding proteins (RBPs), which interact with the adenylate-uridylate-rich element (ARE) sequences in mRNA. The target RBPs from a cell lysate are mixed with an RNA probe to form RNA-protein complexes. The complexes are isolated via affinity purification utilizing the affinity of the desthiobiotin label of the RNA probe to a streptavidin-labeled magnetic bead.
FAQs
Several complementary contacts can stabilize an RNA-protein complex. Electrostatic attraction links positively charged protein surfaces with the negatively charged RNA phosphate backbone, while hydrogen bonding can distinguish particular RNA features. Recognition may depend on nucleotide sequence or on three-dimensional RNA structure, so both chemical complementarity and molecular shape influence which partners associate.
RNA recognition motifs are protein domains that participate in identifying RNA targets. Their contribution is understood alongside contacts made by other protein surfaces and with RNA sequences or three-dimensional features. This combination allows an interaction to reflect more than general attraction to the phosphate backbone, helping connect a protein with a particular RNA substrate or structure.
RNA-protein recognition can depend on three-dimensional RNA features as well as sequence information. A protein may therefore respond to the way an RNA folds or presents chemical groups, rather than to nucleotide order alone. This structural dimension helps explain how complexes achieve specificity and organize RNA into functional ribonucleoprotein assemblies.
Measurements of binding affinity indicate how strongly the partners associate, whereas specificity studies examine whether a protein favors particular RNA sequences or structural features. Analyses of complex formation show whether the components assemble together. Taken together, these observations help characterize ribonucleoprotein assemblies and connect molecular binding behavior with RNA organization and function.
Their effects extend across transcription, RNA processing, translation, transport, and degradation. In each pathway, association with proteins can influence how an RNA is organized, where it is localized, how stable it remains, or how it functions. Examining these interactions therefore provides a biochemical framework for linking molecular complexes with the progression of cellular RNA pathways.
Studying these associations can clarify how ribonucleoprotein assemblies operate in normal cells and how altered interactions may relate to infectious disease. The same biochemical knowledge supports therapeutic RNA design by revealing the binding properties, structural features, and assembly behavior that determine how an RNA engages protein partners. These insights connect molecular analysis with disease-focused and applied research.