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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

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 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...

RNA Editing

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...

RNA-seq

RNA-seq

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...

Protein Folding Quality Check in the RER

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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...

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Related Experiment Video

Updated: Jan 13, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Exornata: A Web-based Tool for the Visualization and Editing of RNA Secondary Structures.

Caeden Meade¹, Biswajit Banerjee¹, Yuzheng Yang¹

¹NASA Center for Integration of the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA; School of Chemistry and Biochemistry Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, USA.

Journal of Molecular Biology

|January 8, 2026

Summary

Exornata is a new web-based tool for creating and editing RNA secondary structures. This RNA visualization software offers detailed modeling and supports interoperability with other bioinformatics resources.

Keywords:

RNA base pairing RNA editor RNA secondary structure RNA viewer

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Last Updated: Jan 13, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

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Published on: May 31, 2013

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

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

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Published on: December 9, 2022

Area of Science:

Computational Biology
Molecular Biology
Bioinformatics

Background:

RNA secondary structures are crucial for understanding RNA function and organization.
Existing tools may lack modern features for efficient RNA structure visualization and editing.

Purpose of the Study:

To introduce Exornata, a web-based RNA secondary structure editor.
To provide a flexible and interactive platform for detailed RNA structure modeling.

Main Methods:

Exornata is built using React and JavaScript/TypeScript for enhanced interactivity and rendering.
It supports loading, editing, and exporting RNA structures in various formats, including a custom JSON schema.
Constraint-based editing modes allow precise manipulation of RNA elements.

Main Results:

Exornata facilitates the generation of detailed and standardized RNA secondary structure models.
The software enables interactive visualization of canonical and non-canonical base pairs.
It supports integration into bioinformatics pipelines through interoperable data formats.

Conclusions:

Exornata is a powerful, open-source tool for RNA secondary structure modeling and visualization.
Its features enhance RNA research by providing flexible editing and data interoperability.