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RNA Structure

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 Structure

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 Structure

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 Structure

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 Interference

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 Interference

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...

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Updated: May 22, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method

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

Summary

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 stacking Basepair DNA 3D structure RNA 3D structure Secondary structure

Related Experiment Videos

Last Updated: May 22, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method

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.