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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...
Protein Organization01:13

Protein Organization

Overview

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Related Experiment Video

Updated: Jun 12, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

SHAPE-directed RNA secondary structure prediction.

Justin T Low1, Kevin M Weeks

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

Methods (San Diego, Calif.)
|June 18, 2010
PubMed
Summary
This summary is machine-generated.

This study presents an efficient strategy for determining RNA secondary structures, even for large molecules. Combining SHAPE chemistry with computational prediction achieves over 95% accuracy, aiding RNA biology and biotechnology.

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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 12, 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

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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
  • Biotechnology
  • Bioinformatics

Background:

  • RNA's functional roles are dictated by its structure.
  • Accurate RNA structure knowledge is crucial for understanding RNA biology and its applications.
  • Current methods struggle with large RNA structures (>500 nucleotides).

Purpose of the Study:

  • To outline an efficient strategy for accurate RNA secondary structure modeling.
  • To develop models for RNAs of arbitrary length.
  • To facilitate new model development and refinement of existing RNA structure models.

Main Methods:

  • Melding structural information from SHAPE chemistry.
  • Utilizing structure prediction with nearest-neighbor rules.
  • Employing the dynamic programming algorithm in RNAstructure software.

Main Results:

  • Achieved prediction accuracies of >=95% for kilobase-scale RNAs.
  • Successfully illustrated the approach using the HIV-1 Gag-Pol frameshift element.
  • Demonstrated efficient development and refinement of RNA secondary structure models.

Conclusions:

  • Integrated experimental and computational approaches enable accurate RNA secondary structure determination.
  • This strategy is applicable to RNAs of arbitrary length.
  • Advances bring the goal of efficient and accurate RNA structure establishment closer.