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 Structure01:19

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...
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...
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...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...

You might also read

Related Articles

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

Sort by
Same author

Identification of 3D motifs in Rfam with JAR3D.

RNA (New York, N.Y.)·2026
Same author

R2DT: a comprehensive platform for visualizing RNA secondary structure.

Nucleic acids research·2025
Same author

R2DT: a comprehensive platform for visualizing RNA secondary structure.

Nucleic acids research·2025
Same author

R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.

bioRxiv : the preprint server for biology·2025
Same author

R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.

Bioinformatics (Oxford, England)·2024
Same author

Anionic G•U pairs in bacterial ribosomal rRNAs.

RNA (New York, N.Y.)·2023
Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026
Same journal

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

RNA (New York, N.Y.)·2026
Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026
Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026
Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026
Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026
See all related articles

Related Experiment Video

Updated: May 22, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

R3DCID: circular interaction diagrams for RNA/DNA.

Patrick Nyadjo Fonga1, Syed Muhammed Abubaker1, Joey Thaman2

  • 1Bowling Green State University.

RNA (New York, N.Y.)
|May 20, 2026
PubMed
Summary
This summary is machine-generated.

R3DCID visualizes interactions in RNA and DNA 3D structures from the Protein Data Bank. This tool aids in understanding complex nucleic acid structures and their functional interactions.

Keywords:
Base stackingBasepairDNA 3D structureRNA 3D structureSecondary structure

Related Experiment Videos

Last Updated: May 22, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) contains over 21,000 3D structures of nucleic acids, featuring diverse complexities in chain numbers, nucleotide counts, and interaction types.
  • Understanding the intricate network of intra- and inter-chain interactions within large nucleic acid structures is challenging due to their scale and complexity.

Purpose of the Study:

  • To introduce R3DCID (RNA+DNA 3D structure Circular Interaction Diagram), a novel web service for visualizing pairwise interactions in nucleic acid 3D structures.
  • To provide a uniform and interpretable representation of interactions across various nucleic acid structures, regardless of size or complexity.

Main Methods:

  • Development of a web service that generates circular arc diagrams representing pairwise interactions.
  • The service processes all chains, models, assemblies, and symmetries within each PDB nucleic acid entry.
  • Output is available in PDF and SVG formats for efficient viewing and scalability.

Main Results:

  • R3DCID produces consistent circular interaction diagrams for all analyzed nucleic acid structures.
  • The generated diagrams offer a clear overview of structural organization and detailed interaction maps.
  • The tool supports understanding of both Watson-Crick and non-Watson-Crick basepairing and base-backbone interactions.

Conclusions:

  • R3DCID offers a valuable new perspective for exploring and comprehending the 3D architecture of RNA and DNA.
  • The tool serves as both a guide to overall structure and a detailed map of functionally critical interactions.
  • This visualization method enhances the study of nucleic acid structure-function relationships.