Related Experiment Video
Updated: Jun 23, 2025
08:59
Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase
Published on: February 12, 2019
11.2K
RNA Folding, Mutation, and Detection.
Kaitlin E Klotz1, Kausik Chakrabarti2
1Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA.
Methods in Molecular Biology (Clifton, N.J.)
|June 22, 2024
Summary
Researchers use selective 2'-hydroxyl acylation-based mutational profiling to map RNA secondary structures. This high-throughput sequencing method reveals how RNA structure changes dynamically with cellular conditions.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- RNA structure is crucial for biological function.
- RNA structure is dynamic and responsive to cellular environments.
- Understanding RNA structure dynamics is key to cellular processes.
Purpose of the Study:
- To investigate RNA secondary structure prediction.
- To analyze how RNA structure changes under different cellular conditions.
- To highlight the utility of selective 2 ahydroxyl acylation-based mutational profiling.
Main Methods:
- Utilized selective 2 ahydroxyl acylation-based mutational profiling (SHAPE-MS).
- Employed high-throughput sequencing for RNA analysis.
- Compared modified and unmodified RNA samples to identify flexible bases.
Main Results:
- Identified accessible, flexible RNA bases not involved in base-pairing or protein interactions.
- Generated RNA secondary structure models based on reactivity profiles.
- Demonstrated the ability to compare structural models across various conditions.
Conclusions:
- SHAPE-MS is a powerful tool for in vivo and immunopurified RNA structure prediction.
- This method allows for the study of RNA structure dynamics in response to stimuli.
- The findings provide insights into how cellular conditions influence RNA secondary structures.
Related Concept Videos
01:29Protein Folding Quality Check in the RER
3.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.7K
03:00Molecular Chaperones and Protein Folding
17.9K
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
The...
17.9K
02:28Leaky Scanning
5.1K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.1K
03:03Amyloid Fibrils
9.5K
Amyloid fibrils are aggregates of misfolded proteins. Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils.
Amyloid deposits were observed as early as 1639 in the liver and the spleen. In 1854, Rudolph Virchow performed iodine staining,...
Amyloid deposits were observed as early as 1639 in the liver and the spleen. In 1854, Rudolph Virchow performed iodine staining,...
9.5K
02:07Improving Translational Accuracy
10.0K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
10.0K
02:24Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K