Direct Rna Interaction
Direct Rna Interaction - 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.
07:04
Site-Directed Mutagenesis for In Vitro and In Vivo Experiments Exemplified with RNA Interactions in Escherichia Coli
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Cited by 2 •
2019
Site-directed mutagenesis is a technique used to introduce specific mutations in deoxyribonucleic acid (DNA). This protocol describes how to do site-directed mutagenesis with a 2-step and 3-step polymerase chain reaction (PCR) based approach, which is applicable to any DNA fragment of interest.
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.
07:27
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
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Cited by 11 •
2010
The fate of the replisome following a collision with a head-on RNA polymerase (RNAP) is unknown. We find that the replisome stalls upon collision with a head-on RNAP, but resumes elongation after displacing the RNAP from DNA. Mfd promotes replication restart by facilitating displacement of the RNAP after the collision.
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
Complementary base pairing allows one RNA sequence to recognize and associate with another through matching bases. This sequence-dependent contact can help form regulatory relationships between RNA molecules, including interactions involving noncoding RNAs. Because the pairing depends on molecular complementarity, changes in RNA sequence can alter whether an interaction forms and thereby influence downstream genetic regulation.
RNA secondary structure creates folded shapes that can expose, conceal, or position interaction sites. Some associations depend less on an exact sequence match than on recognition of these structural features. Structural changes can therefore modify RNA accessibility and affect folding, stability, localization, or translation, linking the physical shape of an RNA molecule to how genetic information is used.
RNA-binding proteins provide protein-mediated contacts that connect with RNA molecules or recognize particular RNA features. Their involvement can influence how an RNA folds, how long it remains stable, where it is localized, and whether it is translated. In genetic regulation, these proteins add a layer of control beyond sequence complementarity and help connect RNA interactions with cellular responses.
RNA interactions regulate how genetic instructions are handled after information has been encoded in DNA. Associations among messenger RNAs, noncoding RNAs, and RNA-binding proteins can alter RNA production and use by affecting stability, localization, folding, or translation. This provides regulatory flexibility without requiring a change to the underlying DNA sequence, helping cells adjust gene activity to changing conditions.
An investigation should consider whether the association depends on complementary bases, RNA secondary structure, or protein-mediated contact. Researchers can then relate the interaction to changes in RNA folding, stability, localization, or translation. Examining these connected features helps distinguish the physical basis of an interaction from its consequences for genetic information and cellular regulation.
These studies can clarify regulatory networks involving noncoding RNAs, explain how messenger RNA production and use are controlled, and examine how cells respond to changing conditions. They also provide context for investigating RNA-based mechanisms of disease. In applied research, the resulting understanding can support the development of diagnostic and therapeutic strategies centered on RNA regulation.