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Related Concept Videos

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 Structure01:19

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-seq03:21

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 microarray-based...
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...
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...

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Related Experiment Video

Updated: Jun 15, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

RNAstructure: software for RNA secondary structure prediction and analysis.

Jessica S Reuter1, David H Mathews

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

BMC Bioinformatics
|March 17, 2010
PubMed
Summary
This summary is machine-generated.

RNAstructure software predicts RNA secondary structures using thermodynamics. New extensions enhance user-friendliness for RNA structure analysis and design applications.

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Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding RNA structure is crucial for determining its function.
  • RNA secondary structure is vital for designing RNA interference (RNAi) and antisense oligonucleotide therapies.
  • Thermodynamic modeling aids in predicting RNA secondary structures and forming hypotheses.

Purpose of the Study:

  • To introduce new extensions to the RNAstructure software package.
  • To improve the user-friendliness of RNA secondary structure prediction and analysis.
  • To provide a versatile tool for researchers in RNA biology and drug design.

Main Methods:

  • Utilizes thermodynamic principles and the latest nearest neighbor parameters from the Turner group.
  • Incorporates algorithms for secondary structure prediction, base pair probability calculation, and bimolecular structure prediction.
  • Introduces a C++ library for integration into other programs, a Java-based graphical user interface (GUI), and Unix-style text interfaces.

Main Results:

  • RNAstructure offers comprehensive RNA secondary structure prediction and analysis capabilities.
  • New extensions include a C++ library, a Java GUI, and text interfaces, enhancing usability.
  • The software supports various prediction methods, including those for bimolecular structures and common structures between sequences.

Conclusions:

  • The extended RNAstructure package significantly improves the user-friendliness of RNA secondary structure prediction.
  • The software is readily available for download, supporting research in RNA structure and function.
  • RNAstructure provides a valuable resource for RNA-related research and therapeutic design.