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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...
RNA Stability01:53

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 Stability01:53

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...
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...

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Related Experiment Video

Updated: May 11, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

RNAstructure: Web servers for RNA secondary structure prediction and analysis.

Stanislav Bellaousov1, Jessica S Reuter, Matthew G Seetin

  • 1Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA.

Nucleic Acids Research
|April 27, 2013
PubMed
Summary

RNAstructure software now offers advanced RNA secondary structure prediction and analysis via a new web server. This tool provides free energy minimization, pseudoknot, and conserved structure predictions for researchers.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA secondary structure plays a crucial role in gene regulation and protein binding.
  • Accurate prediction and analysis of RNA structures are essential for understanding RNA function.
  • Existing tools may lack comprehensive features or user-friendly interfaces for RNA structure analysis.

Purpose of the Study:

  • To introduce a new web server providing the full functionality of the RNAstructure software package.
  • To offer advanced RNA secondary structure prediction and analysis tools through an accessible web interface.
  • To facilitate research in RNA biology by providing robust computational resources.

Main Methods:

  • Web server implementation of RNAstructure software.
  • Algorithms for RNA secondary structure prediction including free energy minimization and maximum expected accuracy.
  • Methods for pseudoknot prediction and analysis of conserved secondary structures in homologous RNA sequences.
  • Calculation of folding free energy changes using nearest neighbor rules.
  • Tools for secondary structure comparison and visualization.

Main Results:

  • A comprehensive web server for RNA secondary structure prediction and analysis is now available.
  • The server supports various prediction methods, including pseudoknot and conserved structure prediction.
  • Users can analyze folding free energy, compare structures, and visualize results in multiple formats (SVG, PDF, etc.).

Conclusions:

  • The new RNAstructure web server provides a powerful and accessible platform for RNA secondary structure research.
  • Its diverse functionalities enhance the ability to predict, analyze, and compare RNA structures.
  • This resource is freely available to the public, supporting advancements in the field of RNA biology.