Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA Structure01:23

RNA Structure

76.1K
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...
76.1K
RNA Structure01:19

RNA Structure

5.8K
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...
5.8K
RNA-seq03:21

RNA-seq

10.8K
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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.8K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

4.5K
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...
4.5K
Nucleic Acid Structure01:25

Nucleic Acid Structure

7.7K
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...
7.7K
Ribosome Profiling02:24

Ribosome Profiling

3.8K
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...
3.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

How can biological databases support the new UN mechanism for benefit-sharing from digital sequence information?

Scientific data·2026
Same author

OTTR-seq profiling reveals dynamic tRNA modification landscapes across diverse archaeal species.

Genome biology·2026
Same author

From "synthetic" to defined microbial communities for clearer terminology.

Nature communications·2026
Same author

Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT.

bioRxiv : the preprint server for biology·2026
Same author

HMMER web server: 2026 update.

Nucleic acids research·2026
Same author

The regulation, function and disease relevance of cytoplasmic tRNAs.

Nature reviews. Molecular cell biology·2026

Related Experiment Video

Updated: Nov 2, 2025

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.8K

R2DT is a framework for predicting and visualising RNA secondary structure using templates.

Blake A Sweeney1, David Hoksza2, Eric P Nawrocki3

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.

Nature Communications
|June 10, 2021
PubMed
Summary

Researchers developed R2DT, a novel method for visualizing non-coding RNA (ncRNA) structures. This tool generates standardized 2D layouts, aiding in RNA structure analysis and comparison.

More Related Videos

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.7K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.8K

Related Experiment Videos

Last Updated: Nov 2, 2025

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

31.8K
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.7K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.8K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Non-coding RNAs (ncRNAs) are crucial for cellular functions, with their activity heavily influenced by their 3D and 2D structures.
  • Existing visualization tools for ncRNAs often lack automated, consistent 2D layout generation, hindering comparative analysis.
  • Standardized visualization is essential for understanding RNA structure-function relationships.

Purpose of the Study:

  • To introduce R2DT, a new method for predicting and visualizing diverse RNA structures using standardized 2D layouts.
  • To address the limitations of current visualization software in generating consistent and recognizable RNA structures.
  • To facilitate easier construction, comparison, and analysis of RNA secondary structures.

Main Methods:

  • R2DT utilizes a comprehensive library of 3,647 templates derived from known structured RNAs.
  • The method applies these templates to predict and generate 2D structural diagrams for a wide range of ncRNA sequences.
  • Integration with the RNAcentral database for large-scale application.

Main Results:

  • R2DT successfully generated over 13 million 2D RNA structure diagrams, establishing the largest dataset of its kind.
  • The software produces standardized and recognizable 2D layouts, improving consistency in visualization.
  • The method is adaptable for community contributions and expansion.

Conclusions:

  • R2DT provides a robust solution for standardized RNA 2D structure visualization.
  • The generated large-scale dataset will significantly advance RNA research and analysis.
  • R2DT is freely available, promoting wider accessibility and collaborative development in the field.