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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...
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-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 Acids02:43

Nucleic Acids

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.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

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Related Experiment Video

Updated: Jun 26, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Accurate SHAPE-directed RNA structure determination.

Katherine E Deigan1, Tian W Li, David H Mathews

  • 1Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.

Proceedings of the National Academy of Sciences of the United States of America
|December 26, 2008
PubMed
Summary
This summary is machine-generated.

Predicting RNA secondary structures is crucial for understanding gene expression. New methods using SHAPE (selective 2-hydroxyl acylation analyzed by primer extension) experiments improve RNA structure prediction accuracy for large RNAs.

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

Related Experiment Videos

Last Updated: Jun 26, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
11:58

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Biophysics

Background:

  • RNA secondary structures are essential for gene expression regulation.
  • Accurate prediction of RNA secondary structures is vital for understanding structure-function relationships.
  • Predicting secondary structures for large RNAs remains a significant challenge.

Purpose of the Study:

  • To develop a highly accurate method for RNA secondary structure prediction.
  • To integrate experimental data into computational structure prediction models.
  • To improve the prediction accuracy for large RNA molecules.

Main Methods:

  • Utilizing quantitative, nucleotide-resolution data from SHAPE experiments.
  • Interpreting SHAPE data as a pseudo-free energy term.
  • Employing free energy minimization with SHAPE pseudo-free energies and nearest neighbor parameters.

Main Results:

  • Achieved high accuracy in predicting RNA secondary structures.
  • Demonstrated accurate prediction for deproteinized Escherichia coli 16S rRNA (>1,300 nt).
  • Obtained prediction accuracies of up to 96-100% for various RNA sizes.

Conclusions:

  • SHAPE experimental data can significantly enhance RNA secondary structure prediction accuracy.
  • The developed method provides accurate predictions comparable to comparative sequence analysis.
  • This approach offers a reliable way to determine RNA secondary structures for large molecules.