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Related Concept Videos

RNA Structure01:23

RNA Structure

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RNA Structure01:23

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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.
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...
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RNA Structure01:19

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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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Nucleic Acid Structure01:25

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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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RNA Stability01:53

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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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Predicting RNA-RNA Interactions Using RNAstructure.

Laura DiChiacchio1,2, David H Mathews3,4

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

Methods in Molecular Biology (Clifton, N.J.)
|September 26, 2016
PubMed
Summary
This summary is machine-generated.

Predicting RNA-RNA binding sites is complex due to competing structures. This guide uses RNAstructure software to identify hybridization sites and predict RNA-RNA structures, aiding cellular process understanding.

Keywords:
Bimolecular RNA structureRNA Duplex FormationRNA hybridization

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Bioinformatics

Background:

  • RNA-RNA binding is crucial for cellular regulation and catalysis.
  • Identifying specific RNA-RNA interaction sites is difficult due to intramolecular and intermolecular structure formation.
  • Understanding RNA binding requires knowledge of folding, accessibility, and concentration-dependent effects.

Purpose of the Study:

  • To provide guidance on using RNAstructure for predicting RNA-RNA binding sites.
  • To demonstrate the prediction of RNA-RNA structures using computational methods.
  • To aid researchers in analyzing RNA-RNA interactions within cellular contexts.

Main Methods:

  • Utilizing RNAstructure software for computational analysis.
  • Employing free energy minimization algorithms to predict stable structures.
  • Applying partition function calculations to assess binding probabilities and accessibility.

Main Results:

  • Demonstrated RNAstructure's capability in predicting RNA-RNA hybridization sites.
  • Provided a framework for analyzing concentration-dependent RNA-RNA binding.
  • Illustrated the prediction of complex RNA-RNA structures.

Conclusions:

  • RNAstructure is a valuable tool for predicting RNA-RNA binding and structures.
  • Accurate prediction requires considering folding, accessibility, and concentration.
  • This approach enhances the understanding of RNA-mediated cellular processes.