Related Experiment Video
Updated: Dec 15, 2025

07:22
Protein Extract Preparation and Co-immunoprecipitation from Caenorhabditis elegans
Published on: May 23, 2020
9.6K
mRNA structural dynamics shape Argonaute-target interactions
Suzan Ruijtenberg1,2, Stijn Sonneveld1, Tao Ju Cui3
1Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
Nature Structural & Molecular Biology
|July 15, 2020
Summary
Small interfering RNAs (siRNAs) degrade RNA, but target site accessibility is key. Ribosomes unmask target sites, overcoming RNA-RNA interactions that block Argonaute2 (AGO2) binding and cleavage.
Area of Science:
- Molecular Biology
- RNA Interference
- Biochemistry
Background:
- Small interfering RNAs (siRNAs) are crucial for RNA degradation and have clinical relevance.
- siRNAs function by guiding Argonaute2 (AGO2) to target RNA sequences for cleavage.
- Understanding in vivo control of target site accessibility for AGO2 is limited.
Purpose of the Study:
- To investigate the in vivo dynamics of the AGO2 cleavage cycle.
- To determine the rate-limiting steps in messenger RNA (mRNA) cleavage mediated by AGO2.
- To elucidate the role of mRNA structural dynamics in AGO2-target recognition.
Main Methods:
- Live-cell single-molecule imaging in human cells.
- Quantification of rate constants for the AGO2 cleavage cycle.
- Analysis of mRNA target site accessibility and unmasking dynamics.
Main Results:
- The rate-limiting step in mRNA cleavage often involves target site unmasking by translating ribosomes.
- Heterogeneous intramolecular RNA-RNA interactions can mask target sites for extended periods.
- Dynamic mRNA structural changes significantly influence AGO2-target recognition.
Conclusions:
- Ribosome activity is critical for overcoming mRNA structural barriers to AGO2 binding.
- mRNA folding and unfolding rates in vivo impact gene silencing efficiency.
- mRNA structural dynamics play a vital role in regulating mRNA-protein interactions, including siRNA-mediated silencing.
Related Concept Videos
Conservation of Protein Domains Over Different Proteins
13.8K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.8K
Nucleic Acid Structure
8.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
DNA Structure
DNA...
8.1K
RNA Structure
6.6K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
6.6K
RNA Structure
78.3K
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
78.3K
RNA Stability
35.4K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
35.4K
RNA Editing
9.6K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
9.6K

