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Related Concept Videos

RNA Structure01:23

RNA Structure

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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.
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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...
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Translational Regulation01:29

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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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...
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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.
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Ribosome Profiling02:24

Ribosome Profiling

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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.
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Related Experiment Video

Updated: Aug 11, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.

Hong Wang1,2,3, Xiaoyan Lu1, Hewei Zheng4

  • 1National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China.

Computational and Structural Biotechnology Journal
|February 3, 2023
PubMed
Summary

This study introduces RNAsmc, a novel tool for analyzing RNA secondary structures. RNAsmc identifies structural motifs and quantifies their functions, aiding in RNA research and classification.

Keywords:
Allosteric effectFamily classificationRNA secondary structureRiboSNitchesStructure comparing

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genetics

Background:

  • RNA secondary structures (RSS) are fundamental to gene regulation, stability, and biological processes.
  • Identifying and analyzing structural motifs is key to understanding RNA functions.
  • Existing methods may lack robustness or comprehensive analysis capabilities for diverse RNA structures.

Purpose of the Study:

  • To present RNAsmc, a strategy for dynamic alignment of RNA secondary structural motifs.
  • To enable quantitative evaluation of molecular functions underlying these motifs.
  • To provide a robust and versatile tool for RNA structure analysis.

Main Methods:

  • Developed a structural motif-based dynamic alignment strategy named RNAsmc.
  • Tested RNAsmc's robustness against variations in sequence length, folding protocols, and chemical probing data.
  • Applied RNAsmc to quantify structural variations in RNA editing events like SNVs/SNPs and indels.

Main Results:

  • RNAsmc effectively identifies structural motifs and evaluates their molecular functions.
  • Demonstrated robustness across different sequence lengths, folding protocols, and RNA structural profiles.
  • Successfully quantified structural variations in RNA editing events.
  • RNAsmc uncovered RNA secondary structure heterogeneity and scored component similarities, facilitating RNA family clustering and allosteric effect evaluation.
  • Achieved remarkable detection efficiency for experimentally-derived RiboSNitches.

Conclusions:

  • RNAsmc is a powerful, robust, and versatile tool for RNA secondary structure motif analysis.
  • The R software package provides an automated toolkit for exploring, aligning, and clustering RSS.
  • RNAsmc advances the understanding of RNA structure-function relationships and facilitates RNA research.