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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.
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RNA Structure

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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
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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.
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Related Experiment Video

Updated: Jul 6, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.

Hugo M Martinez¹, Jacob V Maizel, Bruce A Shapiro

¹Center for Cancer Research Nanobiology Program National Cancer Institute, Building 469, Room 150, Frederick, MD 21702, USA.

Journal of Biomolecular Structure & Dynamics

|April 11, 2008

Summary

RNA2D3D rapidly generates 3D RNA structures from 2D information, allowing interactive editing and refinement for complex RNA folding. This tool aids in exploring conformations for applications in ribozymes and nanobiology.

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Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

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Published on: November 12, 2014

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

RNA molecules play crucial roles in various biological processes.
Accurate 3D structure prediction is essential for understanding RNA function.
Existing methods may struggle with complex RNA architectures and pseudoknots.

Purpose of the Study:

To develop an automated program, RNA2D3D, for rapid generation of 3D RNA conformations.
To provide interactive tools for refining and manipulating RNA structures.
To facilitate the exploration of diverse RNA folding possibilities.

Main Methods:

Utilizes primary and secondary RNA structure information.
Employs interactive graphical editing for overlap removal and conformational adjustments.
Incorporates base-pair manipulation, coaxial stacking, strand shaping, and rigid body transformations.
Features a compaction algorithm to optimize base stacking and reveal folding motifs.
Supports refinement using energy-based techniques and incorporation of existing coordinates.

Main Results:

RNA2D3D generates a first-order approximation of 3D RNA structure rapidly.
The program handles arbitrary branching complexity and pseudoknots.
Interactive editing allows for efficient modification and refinement of conformations.
Applications demonstrated in ribozymes, viral kissing loops, IRES, and nanobiology.

Conclusions:

RNA2D3D offers an efficient approach for generating and refining 3D RNA models.
The tool is versatile, applicable to various RNA structures and complexities.
Facilitates structural analysis and hypothesis testing in RNA research.