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

80.2K
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...
80.2K
RNA Structure01:19

RNA Structure

8.2K
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...
8.2K
RNA Structure01:23

RNA Structure

29.7K
29.7K
Nucleic Acid Structure01:25

Nucleic Acid Structure

10.0K
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...
10.0K
RNA Stability01:53

RNA Stability

36.2K
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...
36.2K
RNA Stability01:53

RNA Stability

12.1K
12.1K

You might also read

Related Articles

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

Sort by
Same author

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026
Same author

LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits.

Bioinformatics (Oxford, England)·2026
Same author

Continuation of anti-tuberculosis therapy after Clostridioides difficile infection: a retrospective cohort study.

Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy·2026
Same author

Age-related decline in nuclear envelope LINC complex drives neuronal aging via axon initial segment dysfunction.

EMBO reports·2026
Same author

Haemoptysis Caused by Right Intercostal Artery-To-Pulmonary Artery Fistulas Mimicking Cryptogenic Haemoptysis.

Respirology case reports·2026
Same author

A poorly reactogenic lipid nanoparticle-mRNA vaccine unveils an innate immune pathway for adverse reactions.

NPJ vaccines·2026

Related Experiment Video

Updated: Mar 21, 2026

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

5.4K

Rtools: a web server for various secondary structural analyses on single RNA sequences.

Michiaki Hamada1, Yukiteru Ono2, Hisanori Kiryu3

  • 1Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, 135-0064 Tokyo, Japan.

Nucleic Acids Research
|May 1, 2016
PubMed
Summary

This study presents a web server for predicting RNA secondary structures and calculating structural features. It offers diverse solutions and detailed analyses, improving RNA bioinformatics accessibility.

More Related Videos

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.5K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

7.1K

Related Experiment Videos

Last Updated: Mar 21, 2026

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

5.4K
RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

32.5K
An Assay for Quantifying Protein-RNA Binding in Bacteria
07:02

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

7.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA secondary structures and nucleotide sequences are crucial for RNA function.
  • Thermodynamic models show low probability for any single secondary structure, limiting prediction accuracy.
  • Existing tools offer limited compensation for imperfect RNA secondary structure predictions.

Purpose of the Study:

  • To develop a user-friendly web server integrating tools for RNA secondary structure prediction and analysis.
  • To provide rich structural information, including multiple structure predictions and detailed feature calculations.

Main Methods:

  • Implementation of a web server integrating CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange, and RintD.
  • Utilizing thermodynamic energy models for secondary structure prediction and feature calculation.
  • Providing an interface for users to input RNA sequences and obtain various structural insights.

Main Results:

  • The web server provides multiple secondary structure solutions for a given RNA sequence.
  • It calculates marginal probabilities (base-pairing, loop) and local base accessibilities.
  • Users can assess energy changes from mutations and obtain validation measures for predictions.

Conclusions:

  • The developed web server enhances the accessibility and utility of RNA secondary structure prediction and analysis tools.
  • It offers comprehensive insights into RNA structural features, aiding functional characterization.
  • The integrated platform facilitates a deeper understanding of RNA molecules through user-friendly access to complex computational tools.