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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...

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...

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

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...

RNA Stability

RNA Stability

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...

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...

Types of RNA

Types of RNA

Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...

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Related Experiment Video

Updated: Nov 23, 2025

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

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

Published on: December 9, 2022

R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.

Holly McCann¹, Caeden D Meade¹, Loren Dean Williams¹

¹NASA Center for Integration of the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

Biorxiv : the Preprint Server for Biology

|January 13, 2025

Summary

This summary is machine-generated.

R2DT 2.0 enhances RNA secondary structure visualization with new features like position-specific data display and template-free folding. This software provides reproducible RNA 2D structure layouts for functional analysis.

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Last Updated: Nov 23, 2025

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Area of Science:

Molecular Biology
Bioinformatics
Structural Biology

Background:

RNA secondary (2D) structure visualization is crucial for understanding RNA function.
R2DT is a software package for consistent and reproducible RNA 2D structure visualization.

Purpose of the Study:

To introduce the latest release of R2DT, version 2.0, highlighting its new features and improvements.
To present R2DT as a comprehensive platform for RNA 2D structure visualization and analysis.

Main Methods:

R2DT 2.0 incorporates position-specific information display (e.g., SNPs, SHAPE reactivities).
Introduces a template-free mode for visualizing RNAs without pre-existing templates.
Supports constrained folding, animated visualizations, and interactive diagram modification via manual input or natural language prompts.

Main Results:

R2DT 2.0 offers enhanced visualization capabilities, including template-free and constrained folding modes.
Improved performance, an expanded template library, and integration with biological databases.
Enables interactive editing and generation of publication-quality RNA 2D structure images.

Conclusions:

R2DT 2.0 represents a significant advancement in RNA 2D structure visualization tools.
The software is a versatile and accessible platform for researchers, integrated into major biological databases.
Accessible at https://r2dt.bio, R2DT facilitates deeper understanding of RNA function through improved visualization.