Target Rna Interactions
Target Rna Interactions - Related Videos
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.
02:30
Isolation of Small Regulatory RNA–Bound Bacterial Target RNA Using Affinity Purification
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2025
Source: Mercier, N., et. al., MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria. J. Vis. Exp. (2021)This video demonstrates the isolation of MS2-tagged small regulatory RNA (sRNA) bound to its bacterial target RNA using affinity purification with a maltose-binding protein (MBP)–MS2 coat protein fusion immobilized on amylose resin.
04:10
Helicase Activity Measurement of a Target Protein Using Biotin-Labeled RNA Duplexes
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2025
In this video, we demonstrate the procedure to determine the helicase activity of a target protein to unwind the biotin-labeled dsRNA substrate. The activity of the enzyme was identified by analyzing the electrophoretic mobility shift, followed by a chemiluminescence assay using chemiluminescent enzyme-conjugated streptavidin.
09:36
RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
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Cited by 59 •
2018
This RNA pull-down method allows identifying the RNA targets of a long non-coding RNA (lncRNA). Based on the hybridization of home-made, designed anti-sense DNA oligonucleotide probes specific to this lncRNA in an appropriately fixed tissue or cell line, it efficiently allows the capture of all RNA targets of the lncRNA.
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.
FAQs
Sequence complementarity provides a recognition basis through Watson–Crick base pairing, allowing an RNA molecule to associate with a matching region of a target transcript. Specificity can also depend on structural features rather than sequence alone. Together, these recognition signals help determine which RNA is contacted and whether its stability, processing, localization, or translation is affected.
A target is recognized through both its nucleotide sequence and the way that sequence is arranged within an RNA structure. Structural features can influence whether a complementary region or protein-recognition site is accessible. This adds a regulatory layer beyond simple sequence matching and helps explain why particular RNA contacts produce different effects on cellular function.
Recognition can be followed by recruitment of regulatory proteins or enzymes that alter the target RNA. These factors may influence RNA stability, processing, localization, or translation, converting a molecular contact into a measurable change in gene expression. The recruited components therefore help determine the outcome rather than serving only as passive binding partners.
MicroRNAs, small interfering RNAs, and antisense oligonucleotides all use target recognition to modulate transcript activity, but they represent distinct RNA-based regulatory approaches. Their shared principle is selective interaction with target transcripts, while the biological outcome depends on the recognized sequence or structure and the regulatory factors or enzymes recruited after binding.
A focused analysis should consider the recognized RNA sequence, relevant structural features, associated proteins, and downstream effects on the transcript. Researchers can then relate the interaction to changes in RNA stability, processing, localization, or translation. Examining these linked features connects molecular recognition with its consequence for post-transcriptional gene regulation.
Studying these interactions clarifies how cells regulate gene expression after transcription has occurred. It can show how target transcripts are controlled through changes in stability, processing, localization, or translation, and how RNA-associated regulatory components contribute. This perspective helps connect specific molecular contacts with broader changes in cellular function.
These interactions are relevant because they provide a molecular basis for regulating target transcripts. Research applications include investigating disease-associated changes, supporting biomarker development, and informing RNA-based therapeutic strategies. Their value comes from linking selective transcript recognition to controllable effects on RNA activity and, consequently, post-transcriptional gene expression.