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Related Concept Videos

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...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: May 10, 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-Seq: High-Throughput RNA Structure Analysis.

Stefanie A Mortimer1, Cole Trapnell, Sharon Aviran

  • 1Department of Molecular and Cell Biology, University of California, Berkeley, California.

Current Protocols in Chemical Biology
|June 22, 2013
PubMed
Summary
This summary is machine-generated.

This study presents a protocol for RNA structure analysis using selective 2'-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq). This method rapidly characterizes RNA structures in high-throughput experiments.

Keywords:
RNA structurechemical probinghigh throughputnext‐generation sequencing

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Last Updated: May 10, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
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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

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Understanding RNA structure is crucial for its biological functions and for engineering RNA-based systems.
  • Current methods for RNA structure determination can be time-consuming and limited in throughput.

Purpose of the Study:

  • To present a protocol for high-throughput RNA structure characterization.
  • To enable the study of RNA structure and interactions in various conditions.

Main Methods:

  • The protocol utilizes selective 2 -hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq).
  • This method combines structure-dependent chemical probing with next-generation sequencing.
  • It includes RNA mixture design, synthesis, and analysis of structure-dependent sequencing libraries.

Main Results:

  • SHAPE-Seq allows for the structural characterization of hundreds of RNAs in a single experiment.
  • The protocol is applicable in a variety of experimental conditions.
  • It provides rapid, high-throughput RNA structure analysis.

Conclusions:

  • SHAPE-Seq is a powerful tool for understanding RNA biology and engineering RNA systems.
  • The protocol facilitates the rapid characterization of RNA structures in vitro.
  • This method advances the study of RNA structure and interactions.