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Related Concept Videos

RNA Structure01:23

RNA Structure

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...
RNA Structure01:23

RNA Structure

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...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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...
RNA Structure01:19

RNA Structure

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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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 has a double-helix structure. The...

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Related Experiment Video

Updated: May 8, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

ShapeRNA: an integrated web server for RNA secondary structure, ensemble, and functional analysis.

Jialu Liang1, Minghao Zhou1, Mingyi Xie2,3,4

  • 1Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL 32611, United States.

Nucleic Acids Research
|April 23, 2026
PubMed
Summary
This summary is machine-generated.

ShapeRNA is a new web server that integrates RNA secondary structure prediction, modeling, and functional annotation. It offers a user-friendly platform for analyzing RNA structures and their regulatory roles, aiding gene regulation research.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Related Experiment Videos

Last Updated: May 8, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA secondary structure is crucial for gene regulation.
  • Current tools for RNA structure analysis are fragmented.
  • Integrated approaches are needed for comprehensive RNA structure studies.

Purpose of the Study:

  • To present ShapeRNA, a web server for integrated RNA secondary structure analysis.
  • To provide a user-friendly platform for prediction, ensemble modeling, and functional annotation.
  • To facilitate the investigation of RNA structural heterogeneity and regulatory mechanisms.

Main Methods:

  • Developed ShapeRNA, a web server integrating multiple prediction algorithms.
  • Implemented sequence-based prediction, reactivity-guided modeling (SHAPE/DMS), and sequencing-guided ensemble inference.
  • Integrated tools for data processing, ensemble clustering, visualization, and mapping of regulatory elements.

Main Results:

  • ShapeRNA supports diverse RNA structure analysis workflows.
  • The platform enables mapping of modification sites, miRNA targets, and RBP motifs.
  • Demonstrated utility in analyzing mutation effects, conformational heterogeneity, and lncRNA regulation.

Conclusions:

  • ShapeRNA offers an accessible and extensible platform for RNA structure research.
  • The tool aids in understanding RNA structural heterogeneity and its regulatory impact.
  • ShapeRNA is freely available to all users without login requirements.