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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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RNA Structure01:19

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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.
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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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.
DNA Structure
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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.
Applications of ribosome profiling
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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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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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Jan 1, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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MultiSETTER: web server for multiple RNA structure comparison.

Petr Čech1, David Hoksza2,3, Daniel Svozil4

  • 1Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic.

BMC Bioinformatics
|August 13, 2015
PubMed
Summary
This summary is machine-generated.

The MultiSETTER web server provides the first multiple RNA structure alignment tool. It enables visualization of 3D structures to reveal evolutionary relationships missed by other methods.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Analyzing RNA tertiary and quaternary structures is crucial for understanding molecular function.
  • While pairwise RNA structure superposition is feasible, aligning large structures remains challenging.
  • Existing methods for RNA alignment often rely on sequence or secondary structure, potentially missing key evolutionary insights.

Purpose of the Study:

  • To develop and present an updated web server implementing the MultiSETTER algorithm for multiple RNA structure alignment.
  • To provide a user-friendly interface for analyzing complex RNA structural relationships.

Main Methods:

  • Extension of the SETTER algorithm for pairwise RNA structure superposition to handle multiple RNA structures (MultiSETTER).
  • Implementation of the MultiSETTER algorithm within a web server interface.
  • Acceptance of RNA structures via PDB IDs or uploaded PDB files.

Main Results:

  • The updated SETTER web server now features a user-friendly interface for the MultiSETTER algorithm.
  • The server computes RNA structure superposition, generates 3D visualizations, and provides detailed reports and statistics.
  • The MultiSETTER algorithm enables the alignment of multiple RNA structures.

Conclusions:

  • The MultiSETTER web server is the first publicly accessible tool for multiple RNA structure alignment.
  • 3D visualization of multiple RNA alignments can uncover structural and functional relationships missed by sequence-based or secondary structure-based methods.