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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.
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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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...
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RNA Stability01:53

RNA Stability

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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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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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RNA-seq03:21

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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. 
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Related Experiment Video

Updated: Jul 22, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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RNA Secondary Structure Analysis Using RNAstructure.

Sara E Ali1, Abhinav Mittal1, David H Mathews1

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

Current Protocols
|July 24, 2023
PubMed
Summary
This summary is machine-generated.

RNAstructure software offers user-friendly tools for predicting RNA secondary structures and oligonucleotide binding sites. Protocols are provided for web, graphical, and command-line interfaces across multiple operating systems.

Keywords:
RNA secondary structure predictionfree energy minimizationoligonucleotide binding affinitythermodynamics

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Predicting RNA secondary structure is crucial for understanding RNA function.
  • Analyzing RNA-protein and RNA-RNA interactions requires accurate structural predictions.
  • Existing tools may lack user-friendliness or comprehensive functionality.

Purpose of the Study:

  • To provide accessible protocols for RNA secondary structure prediction using RNAstructure.
  • To detail methods for identifying high-affinity oligonucleotide binding sites on structured RNAs.
  • To offer versatile RNA structure analysis options via web, GUI, and command-line interfaces.

Main Methods:

  • Utilizing the RNAstructure web server for rapid secondary structure prediction.
  • Employing the RNAstructure graphical user interface (GUI) for detailed structure and base-pair probability analysis.
  • Using the RNAstructure command-line interface for automated secondary structure predictions.
  • Applying the OligoWalk tool within the RNAstructure GUI to predict binding affinities.

Main Results:

  • Demonstrated the utility of RNAstructure for predicting RNA secondary structures across different platforms (web, GUI, command line).
  • Successfully outlined protocols for predicting base pair probabilities, enhancing structural accuracy.
  • Provided a method for identifying potential oligonucleotide binding sites and their affinities to RNA targets.

Conclusions:

  • RNAstructure is a versatile and user-friendly software suite for comprehensive RNA secondary structure analysis.
  • The provided protocols enable researchers to predict RNA structures and binding sites efficiently.
  • The availability of multiple interfaces ensures broad accessibility for diverse research needs.