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Related Concept Videos

RNA Structure01:23

RNA Structure

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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.
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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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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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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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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Analysis Using RNAstructure.

David H Mathews1

  • 1Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York.

Current Protocols in Bioinformatics
|June 19, 2014
PubMed
Summary
This summary is machine-generated.

RNAstructure software predicts RNA secondary structures and identifies oligonucleotide binding sites. This user-friendly tool is accessible via web, GUI, or command-line for multiple operating systems.

Keywords:
RNA secondary structure predictionfree energy minimizationthermodynamics

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Area of Science:

  • * Computational Biology
  • * Bioinformatics
  • * Molecular Biology

Background:

  • * RNA secondary structure prediction is crucial for understanding RNA function.
  • * Existing tools may lack user-friendliness or comprehensive features.
  • * Accurate prediction aids in drug discovery and molecular diagnostics.

Purpose of the Study:

  • * To introduce RNAstructure, a versatile software for RNA secondary structure analysis.
  • * To provide protocols for predicting RNA secondary structures.
  • * To detail methods for identifying high-affinity oligonucleotide binding sites on structured RNA targets.

Main Methods:

  • * RNAstructure software suite: available as a web server, graphical user interface (GUI), and command-line tools.
  • * Cross-platform compatibility: runs on Microsoft Windows, Macintosh OS X, and Linux.
  • * Protocols cover secondary structure prediction and oligonucleotide binding site identification using GUI and web server.

Main Results:

  • * RNAstructure offers a user-friendly platform for complex RNA structure analysis.
  • * Successful prediction of RNA secondary structures is demonstrated.
  • * High-affinity binding sites for oligonucleotides on RNA targets can be accurately identified.

Conclusions:

  • * RNAstructure provides a robust and accessible solution for RNA structure prediction and analysis.
  • * The software facilitates research in RNA biology, drug design, and diagnostics.
  • * Its availability in multiple formats enhances its utility for diverse research needs.