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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...
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...
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...

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Related Experiment Video

Updated: Jun 16, 2026

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

IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.

Pierre Hardouin1, Nan Pan2, Francois-Xavier Lyonnet du Moutier1

  • 1CNRS UMR 8038, CiTCoM Cibles Thérapeutiques et Conception de Médicaments, Université Paris Cité, 4 avenue de l'Observatoire, 75270 Paris, France.

NAR Genomics and Bioinformatics
|March 26, 2025
PubMed
Summary
This summary is machine-generated.

IPANEMAP Suite simplifies RNA structure analysis from chemical probing data to secondary structure models. This platform integrates experimental datasets for accurate RNA structure modeling and comparative analysis.

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RNA Secondary Structure Prediction Using High-throughput SHAPE

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Related Experiment Videos

Last Updated: Jun 16, 2026

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

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • RNA structure is crucial for function but challenging to determine experimentally.
  • Computational RNA structure modeling benefits from integrating experimental data like chemical probing.
  • Current analysis of RNA structure probing data is often complex and requires manual intervention.

Purpose of the Study:

  • To introduce IPANEMAP Suite, a platform for streamlined RNA secondary structure modeling.
  • To facilitate the integration of diverse chemical probing datasets for enhanced accuracy.
  • To enable comparative RNA structure analysis under various conditions and interactions.

Main Methods:

  • Development of the IPANEMAP Suite platform.
  • Integration of low-resolution experimental data (chemical probing) with computational modeling.
  • Utilizing integrative modeling with multiple chemical probing datasets and phylogenetic data.

Main Results:

  • IPANEMAP Suite successfully guides users from raw chemical probing data to informative secondary structure models.
  • The platform enables seamless integration of various experimental datasets for comparative analysis.
  • Integrative modeling within IPANEMAP Suite significantly improves RNA secondary structure model accuracy.

Conclusions:

  • IPANEMAP Suite offers a comprehensive and user-friendly solution for RNA structure analysis.
  • The platform enhances the accuracy and traceability of RNA secondary structure modeling.
  • IPANEMAP Suite simplifies the study of RNA structure, including interactions with proteins and small molecules.